Starting phenix.real_space_refine on Tue Feb 20 08:37:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o8x_0657/02_2024/6o8x_0657.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o8x_0657/02_2024/6o8x_0657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o8x_0657/02_2024/6o8x_0657.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o8x_0657/02_2024/6o8x_0657.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o8x_0657/02_2024/6o8x_0657.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o8x_0657/02_2024/6o8x_0657.pdb" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.088 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 4542 5.49 5 S 130 5.16 5 C 69018 2.51 5 N 25587 2.21 5 O 38949 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "c PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "p PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M ARG 33": "NH1" <-> "NH2" Residue "M ARG 41": "NH1" <-> "NH2" Residue "M ARG 47": "NH1" <-> "NH2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "Q PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 15": "NH1" <-> "NH2" Residue "W TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 53": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 58": "NH1" <-> "NH2" Residue "0 ARG 10": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 138230 Number of models: 1 Model: "" Number of chains: 53 Chain: "a" Number of atoms: 32746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1528, 32746 Classifications: {'RNA': 1528} Modifications used: {'rna2p_pur': 118, 'rna2p_pyr': 89, 'rna3p_pur': 739, 'rna3p_pyr': 582} Link IDs: {'rna2p': 207, 'rna3p': 1320} Chain breaks: 1 Chain: "c" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 4, 'TRANS': 199} Chain: "d" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1620 Classifications: {'peptide': 201} Link IDs: {'CIS': 2, 'PTRANS': 8, 'TRANS': 190} Chain: "e" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1204 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "f" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 795 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "g" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1229 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 7, 'TRANS': 146} Chain: "h" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 125} Chain: "i" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 990 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 120} Chain: "j" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 800 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 92} Chain: "k" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 863 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 109} Chain: "l" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1065 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 126} Chain: "m" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 884 Classifications: {'peptide': 112} Link IDs: {'CIS': 3, 'PTRANS': 3, 'TRANS': 105} Chain: "n" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "o" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 741 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "p" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 708 Classifications: {'peptide': 89} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 83} Chain: "q" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 681 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "r" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 537 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "s" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 634 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "t" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 610 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain: "A" Number of atoms: 62196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2898, 62196 Classifications: {'DNA': 1, 'RNA': 2897} Modifications used: {'rna2p_pur': 302, 'rna2p_pyr': 157, 'rna3p_pur': 1379, 'rna3p_pyr': 1055} Link IDs: {'rna2p': 459, 'rna3p': 2438} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {' G%rna3p_pur:plan2': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2478 Classifications: {'RNA': 116} Modifications used: {'p5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 55, 'rna3p_pyr': 49} Link IDs: {'rna2p': 11, 'rna3p': 104} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2114 Classifications: {'peptide': 275} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 257} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1578 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1572 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 8, 'TRANS': 197} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1391 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1344 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1129 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 7, 'TRANS': 137} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "L" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 922 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "M" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1094 Classifications: {'peptide': 146} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 140} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1117 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "O" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 978 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 898 Classifications: {'peptide': 117} Incomplete info: {'backbone_only': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 924 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "R" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 913 Classifications: {'peptide': 115} Link IDs: {'TRANS': 114} Unresolved chain links: 2 Unresolved chain link angles: 6 Unresolved chain link dihedrals: 6 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 783 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "T" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 849 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "U" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 719 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 763 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "W" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 757 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 572 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "Y" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 424 Classifications: {'peptide': 54} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "Z" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 504 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "0" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 435 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "1" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 475 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 4, 'TRANS': 55} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "3" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 419 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "4" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 373 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "5" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 522 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "6" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 304 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 4, 'TRANS': 33} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 45028 SG CYS n 24 56.704 136.689 119.838 1.00 98.96 S ATOM 45054 SG CYS n 27 60.278 137.242 119.960 1.00 98.32 S ATOM 45166 SG CYS n 40 59.622 135.754 123.181 1.00 97.98 S ATOM 45191 SG CYS n 43 59.740 139.352 122.941 1.00 96.80 S ATOM A0S3B SG CYS 2 30 251.443 137.349 88.279 1.00125.88 S ATOM A0S6J SG CYS 2 46 253.056 139.303 90.922 1.00119.01 S ATOM A0SAW SG CYS 3 9 139.260 42.946 136.572 1.00153.39 S ATOM A0SBF SG CYS 3 12 142.480 42.122 137.882 1.00156.40 S ATOM A0SHC SG CYS 3 36 141.507 41.235 134.153 1.00138.02 S ATOM A0TBR SG CYS 6 11 141.509 124.125 50.810 1.00131.10 S ATOM A0TFE SG CYS 6 27 146.021 123.972 48.759 1.00131.60 S Time building chain proxies: 51.41, per 1000 atoms: 0.37 Number of scatterers: 138230 At special positions: 0 Unit cell: (287.414, 276.444, 231.467, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 130 16.00 P 4542 15.00 O 38949 8.00 N 25587 7.00 C 69018 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 56.42 Conformation dependent library (CDL) restraints added in 7.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 2 101 " pdb="ZN ZN 2 101 " - pdb=" SG CYS 2 46 " pdb="ZN ZN 2 101 " - pdb=" SG CYS 2 30 " pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 9 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 36 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 12 " pdb=" ZN 6 101 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 27 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 11 " pdb=" ZN n 101 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 27 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 40 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 43 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 24 " Number of angles added : 6 10194 Ramachandran restraints generated. 5097 Oldfield, 0 Emsley, 5097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9540 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 72 sheets defined 27.8% alpha, 13.6% beta 1425 base pairs and 2308 stacking pairs defined. Time for finding SS restraints: 46.48 Creating SS restraints... Processing helix chain 'c' and resid 6 through 10 Processing helix chain 'c' and resid 28 through 42 removed outlier: 3.796A pdb=" N ARG c 37 " --> pdb=" O HIS c 33 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 77 removed outlier: 3.937A pdb=" N ILE c 76 " --> pdb=" O PRO c 72 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY c 77 " --> pdb=" O GLY c 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 72 through 77' Processing helix chain 'c' and resid 80 through 95 removed outlier: 3.818A pdb=" N GLU c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS c 92 " --> pdb=" O LYS c 88 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU c 93 " --> pdb=" O GLU c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 112 through 124 Processing helix chain 'c' and resid 128 through 144 removed outlier: 3.785A pdb=" N ALA c 132 " --> pdb=" O ALA c 128 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN c 133 " --> pdb=" O PHE c 129 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 15 Processing helix chain 'd' and resid 45 through 59 Processing helix chain 'd' and resid 64 through 74 removed outlier: 4.413A pdb=" N THR d 70 " --> pdb=" O ARG d 66 " (cutoff:3.500A) Processing helix chain 'd' and resid 75 through 77 No H-bonds generated for 'chain 'd' and resid 75 through 77' Processing helix chain 'd' and resid 82 through 92 Processing helix chain 'd' and resid 94 through 101 Processing helix chain 'd' and resid 108 through 116 Processing helix chain 'd' and resid 149 through 158 removed outlier: 3.561A pdb=" N GLU d 157 " --> pdb=" O LYS d 153 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA d 158 " --> pdb=" O GLU d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 192 through 199 Processing helix chain 'e' and resid 55 through 68 Processing helix chain 'e' and resid 108 through 116 removed outlier: 3.532A pdb=" N ALA e 113 " --> pdb=" O GLY e 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 132 through 147 removed outlier: 3.572A pdb=" N GLN e 146 " --> pdb=" O GLU e 142 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU e 147 " --> pdb=" O GLY e 143 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 157 removed outlier: 3.708A pdb=" N VAL e 153 " --> pdb=" O ARG e 149 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA e 154 " --> pdb=" O ALA e 150 " (cutoff:3.500A) Processing helix chain 'f' and resid 19 through 35 Processing helix chain 'f' and resid 77 through 84 removed outlier: 3.738A pdb=" N LEU f 83 " --> pdb=" O GLU f 79 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 removed outlier: 4.014A pdb=" N THR g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG g 29 " --> pdb=" O ARG g 25 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL g 30 " --> pdb=" O LEU g 26 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET g 31 " --> pdb=" O ILE g 27 " (cutoff:3.500A) Processing helix chain 'g' and resid 38 through 53 Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.785A pdb=" N MET g 70 " --> pdb=" O MET g 66 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 112 removed outlier: 3.714A pdb=" N GLY g 112 " --> pdb=" O ALA g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 117 through 128 Processing helix chain 'g' and resid 131 through 145 removed outlier: 4.181A pdb=" N VAL g 135 " --> pdb=" O THR g 131 " (cutoff:3.500A) Processing helix chain 'g' and resid 148 through 152 Processing helix chain 'h' and resid 5 through 20 removed outlier: 3.667A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL h 20 " --> pdb=" O ASN h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 42 Processing helix chain 'h' and resid 115 through 120 Processing helix chain 'i' and resid 44 through 49 Processing helix chain 'i' and resid 50 through 54 Processing helix chain 'i' and resid 76 through 91 removed outlier: 4.107A pdb=" N ARG i 80 " --> pdb=" O SER i 76 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N HIS i 81 " --> pdb=" O GLY i 77 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY i 82 " --> pdb=" O ALA i 78 " (cutoff:3.500A) Processing helix chain 'i' and resid 94 through 101 Processing helix chain 'j' and resid 15 through 33 removed outlier: 3.920A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY j 33 " --> pdb=" O ALA j 29 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 89 removed outlier: 3.535A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) Processing helix chain 'k' and resid 55 through 59 Processing helix chain 'k' and resid 60 through 77 removed outlier: 3.675A pdb=" N GLN k 64 " --> pdb=" O PRO k 60 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET k 65 " --> pdb=" O PHE k 61 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL k 73 " --> pdb=" O ALA k 69 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N HIS k 77 " --> pdb=" O VAL k 73 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 103 removed outlier: 3.650A pdb=" N ILE k 97 " --> pdb=" O ARG k 93 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 9 Processing helix chain 'm' and resid 16 through 21 Processing helix chain 'm' and resid 27 through 38 Processing helix chain 'm' and resid 49 through 63 removed outlier: 3.831A pdb=" N LEU m 63 " --> pdb=" O GLU m 59 " (cutoff:3.500A) Processing helix chain 'm' and resid 68 through 81 Processing helix chain 'm' and resid 85 through 93 removed outlier: 3.878A pdb=" N ARG m 92 " --> pdb=" O GLY m 88 " (cutoff:3.500A) Processing helix chain 'n' and resid 4 through 9 removed outlier: 3.770A pdb=" N ALA n 8 " --> pdb=" O LYS n 4 " (cutoff:3.500A) Processing helix chain 'n' and resid 16 through 20 removed outlier: 3.687A pdb=" N GLN n 19 " --> pdb=" O HIS n 16 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA n 20 " --> pdb=" O SER n 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 16 through 20' Processing helix chain 'n' and resid 40 through 50 removed outlier: 3.876A pdb=" N PHE n 44 " --> pdb=" O CYS n 40 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 12 removed outlier: 3.649A pdb=" N ILE o 12 " --> pdb=" O LYS o 8 " (cutoff:3.500A) Processing helix chain 'o' and resid 25 through 46 removed outlier: 3.788A pdb=" N ILE o 29 " --> pdb=" O PRO o 25 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 72 removed outlier: 3.935A pdb=" N ARG o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG o 71 " --> pdb=" O LEU o 67 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS o 72 " --> pdb=" O ALA o 68 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 83 Processing helix chain 'p' and resid 54 through 61 removed outlier: 4.089A pdb=" N ASP p 58 " --> pdb=" O ASP p 54 " (cutoff:3.500A) Processing helix chain 'p' and resid 67 through 76 Processing helix chain 'p' and resid 78 through 88 Processing helix chain 'r' and resid 29 through 34 removed outlier: 3.793A pdb=" N LYS r 34 " --> pdb=" O THR r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 45 through 50 removed outlier: 3.915A pdb=" N THR r 49 " --> pdb=" O PRO r 45 " (cutoff:3.500A) Processing helix chain 'r' and resid 52 through 70 removed outlier: 3.836A pdb=" N ILE r 68 " --> pdb=" O LYS r 64 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET r 69 " --> pdb=" O ARG r 65 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 21 removed outlier: 3.553A pdb=" N ALA s 21 " --> pdb=" O LYS s 17 " (cutoff:3.500A) Processing helix chain 't' and resid 7 through 42 removed outlier: 3.714A pdb=" N VAL t 11 " --> pdb=" O ALA t 7 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG t 12 " --> pdb=" O ILE t 8 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR t 13 " --> pdb=" O LYS t 9 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA t 41 " --> pdb=" O GLU t 37 " (cutoff:3.500A) Processing helix chain 't' and resid 46 through 63 removed outlier: 3.673A pdb=" N TYR t 50 " --> pdb=" O VAL t 46 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 83 removed outlier: 3.514A pdb=" N LEU t 81 " --> pdb=" O ARG t 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 15 removed outlier: 4.526A pdb=" N ASN C 15 " --> pdb=" O GLY C 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 12 through 15' Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'D' and resid 64 through 70 removed outlier: 3.708A pdb=" N VAL D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 removed outlier: 3.649A pdb=" N VAL D 101 " --> pdb=" O LYS D 98 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN D 103 " --> pdb=" O ASP D 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 25 removed outlier: 3.534A pdb=" N GLY E 25 " --> pdb=" O GLU E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 42 Processing helix chain 'E' and resid 43 through 45 No H-bonds generated for 'chain 'E' and resid 43 through 45' Processing helix chain 'E' and resid 102 through 120 removed outlier: 3.921A pdb=" N ARG E 106 " --> pdb=" O PRO E 102 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG E 107 " --> pdb=" O LYS E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 147 removed outlier: 3.588A pdb=" N PHE E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 165 Processing helix chain 'E' and resid 183 through 188 removed outlier: 3.638A pdb=" N SER E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.686A pdb=" N LEU E 199 " --> pdb=" O THR E 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 11 Processing helix chain 'F' and resid 11 through 21 removed outlier: 4.151A pdb=" N SER F 15 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU F 16 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE F 20 " --> pdb=" O LEU F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 28 Processing helix chain 'F' and resid 41 through 45 removed outlier: 3.523A pdb=" N VAL F 44 " --> pdb=" O GLY F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 61 removed outlier: 4.041A pdb=" N ALA F 53 " --> pdb=" O ASN F 49 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU F 55 " --> pdb=" O ASP F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 106 removed outlier: 4.090A pdb=" N TYR F 97 " --> pdb=" O GLY F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 111 removed outlier: 3.610A pdb=" N VAL F 111 " --> pdb=" O LEU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 174 removed outlier: 3.821A pdb=" N SER F 166 " --> pdb=" O THR F 162 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 81 removed outlier: 4.386A pdb=" N GLY G 66 " --> pdb=" O LYS G 62 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL G 79 " --> pdb=" O MET G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 150 removed outlier: 3.591A pdb=" N VAL G 141 " --> pdb=" O ASN G 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 25 through 38 removed outlier: 3.769A pdb=" N LEU K 29 " --> pdb=" O PRO K 25 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG K 38 " --> pdb=" O ALA K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 63 removed outlier: 3.793A pdb=" N VAL K 63 " --> pdb=" O ALA K 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 60 through 63' Processing helix chain 'K' and resid 90 through 95 removed outlier: 3.735A pdb=" N LEU K 93 " --> pdb=" O ALA K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 106 removed outlier: 4.027A pdb=" N LEU K 101 " --> pdb=" O ASN K 97 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE K 102 " --> pdb=" O SER K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 116 No H-bonds generated for 'chain 'K' and resid 114 through 116' Processing helix chain 'K' and resid 118 through 119 No H-bonds generated for 'chain 'K' and resid 118 through 119' Processing helix chain 'K' and resid 133 through 137 removed outlier: 3.747A pdb=" N GLN K 137 " --> pdb=" O ALA K 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 110 removed outlier: 4.025A pdb=" N LEU L 106 " --> pdb=" O ALA L 103 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU L 108 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 118 Processing helix chain 'M' and resid 2 through 6 removed outlier: 4.001A pdb=" N LEU M 6 " --> pdb=" O LEU M 3 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 26 Processing helix chain 'M' and resid 56 through 61 removed outlier: 3.990A pdb=" N LEU M 61 " --> pdb=" O PHE M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'M' and resid 129 through 139 removed outlier: 3.622A pdb=" N GLU M 134 " --> pdb=" O LYS M 130 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA M 139 " --> pdb=" O ALA M 135 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 56 removed outlier: 3.513A pdb=" N GLU N 48 " --> pdb=" O ASN N 44 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 123 Processing helix chain 'O' and resid 12 through 21 removed outlier: 3.538A pdb=" N THR O 21 " --> pdb=" O LEU O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 51 removed outlier: 4.268A pdb=" N THR O 49 " --> pdb=" O GLU O 45 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU O 50 " --> pdb=" O LYS O 46 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 3.711A pdb=" N ARG O 59 " --> pdb=" O ASP O 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 20 removed outlier: 4.319A pdb=" N THR P 10 " --> pdb=" O ASP P 6 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN P 20 " --> pdb=" O ARG P 16 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 84 removed outlier: 3.537A pdb=" N ALA P 74 " --> pdb=" O GLU P 70 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA P 80 " --> pdb=" O GLY P 76 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 114 removed outlier: 3.839A pdb=" N ASN P 114 " --> pdb=" O ALA P 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 9 Processing helix chain 'Q' and resid 97 through 101 removed outlier: 3.622A pdb=" N LEU Q 100 " --> pdb=" O LEU Q 97 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG Q 101 " --> pdb=" O TYR Q 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 97 through 101' Processing helix chain 'Q' and resid 104 through 108 Processing helix chain 'R' and resid 6 through 12 removed outlier: 4.546A pdb=" N THR R 10 " --> pdb=" O GLY R 6 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ARG R 11 " --> pdb=" O GLY R 7 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 21 Processing helix chain 'R' and resid 31 through 51 removed outlier: 3.754A pdb=" N LYS R 36 " --> pdb=" O PHE R 32 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLU R 37 " --> pdb=" O LYS R 33 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLN R 38 " --> pdb=" O SER R 34 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL R 39 " --> pdb=" O ALA R 35 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG R 51 " --> pdb=" O PHE R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 72 removed outlier: 4.061A pdb=" N ARG R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS R 59 " --> pdb=" O ARG R 55 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN R 72 " --> pdb=" O ALA R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 84 removed outlier: 3.595A pdb=" N LEU R 79 " --> pdb=" O SER R 75 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N MET R 80 " --> pdb=" O TYR R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 102 Processing helix chain 'R' and resid 102 through 117 removed outlier: 3.544A pdb=" N LEU R 117 " --> pdb=" O ALA R 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 21 through 26 removed outlier: 4.109A pdb=" N VAL T 25 " --> pdb=" O LYS T 21 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE T 26 " --> pdb=" O ALA T 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 21 through 26' Processing helix chain 'T' and resid 27 through 29 No H-bonds generated for 'chain 'T' and resid 27 through 29' Processing helix chain 'T' and resid 33 through 43 removed outlier: 3.892A pdb=" N SER T 39 " --> pdb=" O ALA T 35 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE T 43 " --> pdb=" O SER T 39 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 66 removed outlier: 3.937A pdb=" N ILE T 52 " --> pdb=" O SER T 48 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU T 53 " --> pdb=" O ALA T 49 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LYS T 54 " --> pdb=" O GLY T 50 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL T 55 " --> pdb=" O ILE T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 70 through 74 removed outlier: 3.677A pdb=" N LEU T 74 " --> pdb=" O VAL T 71 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 20 removed outlier: 3.768A pdb=" N LEU U 18 " --> pdb=" O GLU U 14 " (cutoff:3.500A) Processing helix chain 'U' and resid 34 through 44 removed outlier: 3.707A pdb=" N VAL U 38 " --> pdb=" O ASN U 34 " (cutoff:3.500A) Processing helix chain 'V' and resid 66 through 68 No H-bonds generated for 'chain 'V' and resid 66 through 68' Processing helix chain 'W' and resid 17 through 24 removed outlier: 3.582A pdb=" N HIS W 23 " --> pdb=" O ASN W 19 " (cutoff:3.500A) Processing helix chain 'W' and resid 44 through 47 removed outlier: 3.539A pdb=" N ASP W 47 " --> pdb=" O GLU W 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 44 through 47' Processing helix chain 'W' and resid 48 through 55 Processing helix chain 'Z' and resid 3 through 7 Processing helix chain 'Z' and resid 10 through 33 removed outlier: 3.840A pdb=" N LEU Z 15 " --> pdb=" O THR Z 11 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 61 removed outlier: 3.690A pdb=" N VAL Z 46 " --> pdb=" O ARG Z 42 " (cutoff:3.500A) Processing helix chain '0' and resid 16 through 24 Processing helix chain '0' and resid 41 through 48 removed outlier: 3.671A pdb=" N GLY 0 45 " --> pdb=" O GLU 0 41 " (cutoff:3.500A) Processing helix chain '2' and resid 10 through 15 Processing helix chain '2' and resid 16 through 20 removed outlier: 3.588A pdb=" N HIS 2 19 " --> pdb=" O ARG 2 16 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR 2 20 " --> pdb=" O ARG 2 17 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 16 through 20' Processing helix chain '4' and resid 26 through 36 removed outlier: 3.557A pdb=" N ARG 4 36 " --> pdb=" O ALA 4 32 " (cutoff:3.500A) Processing helix chain '5' and resid 37 through 44 removed outlier: 3.569A pdb=" N ARG 5 41 " --> pdb=" O THR 5 37 " (cutoff:3.500A) Processing helix chain '5' and resid 51 through 57 removed outlier: 3.833A pdb=" N ARG 5 57 " --> pdb=" O GLY 5 53 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'c' and resid 51 through 58 removed outlier: 6.810A pdb=" N HIS c 68 " --> pdb=" O SER c 52 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ILE c 54 " --> pdb=" O SER c 66 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER c 66 " --> pdb=" O ILE c 54 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE c 56 " --> pdb=" O ASN c 64 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ASN c 64 " --> pdb=" O ILE c 56 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ARG c 58 " --> pdb=" O ARG c 62 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ARG c 62 " --> pdb=" O ARG c 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'c' and resid 51 through 58 removed outlier: 6.810A pdb=" N HIS c 68 " --> pdb=" O SER c 52 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ILE c 54 " --> pdb=" O SER c 66 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER c 66 " --> pdb=" O ILE c 54 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE c 56 " --> pdb=" O ASN c 64 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ASN c 64 " --> pdb=" O ILE c 56 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ARG c 58 " --> pdb=" O ARG c 62 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ARG c 62 " --> pdb=" O ARG c 58 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N VAL c 103 " --> pdb=" O ILE c 65 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE c 67 " --> pdb=" O VAL c 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'c' and resid 149 through 152 removed outlier: 3.550A pdb=" N LYS c 198 " --> pdb=" O GLN c 151 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL c 197 " --> pdb=" O GLU c 186 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA c 184 " --> pdb=" O VAL c 199 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE c 201 " --> pdb=" O ASP c 182 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP c 182 " --> pdb=" O ILE c 201 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'd' and resid 125 through 126 Processing sheet with id=AA5, first strand: chain 'd' and resid 168 through 169 removed outlier: 3.532A pdb=" N GLU d 174 " --> pdb=" O ASP d 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'e' and resid 12 through 15 removed outlier: 3.689A pdb=" N VAL e 37 " --> pdb=" O GLY e 49 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY e 49 " --> pdb=" O VAL e 37 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'e' and resid 20 through 24 Processing sheet with id=AA8, first strand: chain 'e' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'f' and resid 39 through 50 removed outlier: 6.589A pdb=" N ASN f 67 " --> pdb=" O ILE f 41 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER f 43 " --> pdb=" O ILE f 65 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE f 65 " --> pdb=" O SER f 43 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASP f 45 " --> pdb=" O TYR f 63 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N TYR f 63 " --> pdb=" O ASP f 45 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLU f 47 " --> pdb=" O GLY f 61 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLY f 61 " --> pdb=" O GLU f 47 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL f 68 " --> pdb=" O TYR f 7 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL f 96 " --> pdb=" O GLU f 8 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET f 10 " --> pdb=" O MET f 94 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET f 94 " --> pdb=" O MET f 10 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'g' and resid 73 through 75 removed outlier: 3.530A pdb=" N GLU g 74 " --> pdb=" O VAL g 89 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'h' and resid 24 through 27 removed outlier: 3.647A pdb=" N ASP h 48 " --> pdb=" O PHE h 63 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'h' and resid 76 through 79 removed outlier: 3.669A pdb=" N LYS h 78 " --> pdb=" O TYR h 130 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'h' and resid 76 through 79 removed outlier: 3.669A pdb=" N LYS h 78 " --> pdb=" O TYR h 130 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE h 105 " --> pdb=" O ILE h 128 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N TYR h 130 " --> pdb=" O ILE h 103 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE h 103 " --> pdb=" O TYR h 130 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE h 106 " --> pdb=" O ILE h 113 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'i' and resid 18 through 19 removed outlier: 4.353A pdb=" N ARG i 18 " --> pdb=" O ASN i 66 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN i 66 " --> pdb=" O ARG i 18 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LYS i 27 " --> pdb=" O VAL i 63 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL i 65 " --> pdb=" O LYS i 27 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N THR i 29 " --> pdb=" O VAL i 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'j' and resid 36 through 46 removed outlier: 4.989A pdb=" N GLY j 38 " --> pdb=" O ASP j 75 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP j 75 " --> pdb=" O GLY j 38 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LYS j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR j 44 " --> pdb=" O THR j 69 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N THR j 69 " --> pdb=" O THR j 44 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN j 97 " --> pdb=" O LYS j 11 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'j' and resid 49 through 52 removed outlier: 3.606A pdb=" N PHE j 65 " --> pdb=" O TYR j 49 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL j 51 " --> pdb=" O GLU j 63 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU j 66 " --> pdb=" O LYS n 57 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS n 57 " --> pdb=" O GLU j 66 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'k' and resid 41 through 46 removed outlier: 3.840A pdb=" N ARG k 111 " --> pdb=" O VAL k 84 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'l' and resid 75 through 79 removed outlier: 3.681A pdb=" N ALA l 66 " --> pdb=" O ALA l 78 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG l 69 " --> pdb=" O CYS l 47 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N CYS l 47 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS l 43 " --> pdb=" O LEU l 95 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'p' and resid 3 through 9 removed outlier: 3.507A pdb=" N LYS p 4 " --> pdb=" O ALA p 23 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY p 38 " --> pdb=" O ILE p 20 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL p 22 " --> pdb=" O THR p 36 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N THR p 36 " --> pdb=" O VAL p 22 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL p 50 " --> pdb=" O THR p 39 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU p 48 " --> pdb=" O ASN p 41 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'q' and resid 40 through 47 removed outlier: 5.395A pdb=" N GLU q 29 " --> pdb=" O GLN q 12 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N GLN q 12 " --> pdb=" O GLU q 29 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ILE q 61 " --> pdb=" O VAL q 81 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N VAL q 81 " --> pdb=" O ILE q 61 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LYS q 63 " --> pdb=" O LEU q 79 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N ARG q 75 " --> pdb=" O THR q 67 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 's' and resid 48 through 52 removed outlier: 3.576A pdb=" N VAL s 60 " --> pdb=" O ILE s 49 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.526A pdb=" N SER C 18 " --> pdb=" O LYS C 4 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AC6, first strand: chain 'C' and resid 95 through 96 removed outlier: 4.026A pdb=" N MET C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 81 through 82 Processing sheet with id=AC8, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC9, first strand: chain 'C' and resid 172 through 175 Processing sheet with id=AD1, first strand: chain 'C' and resid 247 through 248 removed outlier: 3.557A pdb=" N GLY C 251 " --> pdb=" O SER C 248 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 4 through 5 removed outlier: 5.900A pdb=" N VAL D 108 " --> pdb=" O ASN D 173 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN D 173 " --> pdb=" O VAL D 108 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 12 through 16 removed outlier: 3.693A pdb=" N ILE D 188 " --> pdb=" O THR D 26 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL D 185 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL D 179 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU D 187 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 34 through 39 removed outlier: 4.146A pdb=" N VAL D 34 " --> pdb=" O GLY D 52 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLN D 50 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N VAL D 38 " --> pdb=" O ALA D 48 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA D 48 " --> pdb=" O VAL D 38 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 123 through 125 removed outlier: 3.862A pdb=" N ALA E 194 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU E 153 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL E 152 " --> pdb=" O SER E 174 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL E 176 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL E 154 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 31 through 35 removed outlier: 6.752A pdb=" N VAL F 157 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE F 34 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL F 155 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE F 132 " --> pdb=" O MET F 152 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE F 154 " --> pdb=" O LEU F 130 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE F 156 " --> pdb=" O TYR F 128 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR F 128 " --> pdb=" O ILE F 156 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 17 through 20 removed outlier: 3.741A pdb=" N LYS G 18 " --> pdb=" O THR G 25 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR G 25 " --> pdb=" O LYS G 18 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG G 35 " --> pdb=" O ILE G 24 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 122 through 124 removed outlier: 3.704A pdb=" N THR G 122 " --> pdb=" O LYS G 134 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL G 131 " --> pdb=" O LEU G 87 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL G 133 " --> pdb=" O LYS G 85 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU G 88 " --> pdb=" O ARG G 163 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 103 through 105 removed outlier: 3.521A pdb=" N LEU G 103 " --> pdb=" O MET G 115 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 123 through 126 removed outlier: 6.758A pdb=" N TRP K 16 " --> pdb=" O GLU K 139 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 19 through 23 removed outlier: 3.657A pdb=" N LEU L 20 " --> pdb=" O THR L 42 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL L 40 " --> pdb=" O ILE L 22 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 76 through 78 removed outlier: 4.097A pdb=" N TYR L 76 " --> pdb=" O THR Q 73 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 101 through 102 removed outlier: 3.664A pdb=" N VAL L 102 " --> pdb=" O GLU L 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'M' and resid 110 through 111 Processing sheet with id=AE6, first strand: chain 'M' and resid 122 through 125 removed outlier: 3.841A pdb=" N ALA M 125 " --> pdb=" O GLU M 144 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 32 through 33 Processing sheet with id=AE8, first strand: chain 'N' and resid 40 through 42 removed outlier: 7.089A pdb=" N SER N 76 " --> pdb=" O PRO N 90 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY N 92 " --> pdb=" O TYR N 74 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TYR N 74 " --> pdb=" O GLY N 92 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 30 through 33 removed outlier: 3.648A pdb=" N ILE O 30 " --> pdb=" O ILE O 123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'P' and resid 42 through 45 removed outlier: 7.308A pdb=" N ALA P 42 " --> pdb=" O SER P 55 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N SER P 55 " --> pdb=" O ALA P 42 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL P 44 " --> pdb=" O LEU P 53 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Q' and resid 43 through 46 Processing sheet with id=AF3, first strand: chain 'Q' and resid 32 through 34 removed outlier: 3.670A pdb=" N VAL Q 32 " --> pdb=" O ARG Q 39 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG Q 37 " --> pdb=" O GLU Q 34 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'S' and resid 4 through 7 removed outlier: 3.502A pdb=" N VAL S 12 " --> pdb=" O ILE S 5 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'S' and resid 19 through 22 Processing sheet with id=AF6, first strand: chain 'S' and resid 40 through 41 removed outlier: 3.883A pdb=" N VAL S 41 " --> pdb=" O LYS S 47 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'S' and resid 58 through 59 Processing sheet with id=AF8, first strand: chain 'T' and resid 8 through 15 removed outlier: 3.542A pdb=" N ALA T 8 " --> pdb=" O VAL T 112 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA T 10 " --> pdb=" O VAL T 110 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N SER T 106 " --> pdb=" O THR T 14 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N HIS T 107 " --> pdb=" O VAL T 81 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL T 81 " --> pdb=" O HIS T 107 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR T 109 " --> pdb=" O ALA T 79 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ALA T 79 " --> pdb=" O THR T 109 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL T 111 " --> pdb=" O SER T 77 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'T' and resid 87 through 92 Processing sheet with id=AG1, first strand: chain 'U' and resid 7 through 10 removed outlier: 3.910A pdb=" N ARG U 9 " --> pdb=" O GLU U 28 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'U' and resid 63 through 64 removed outlier: 3.509A pdb=" N GLY U 70 " --> pdb=" O LYS U 63 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'V' and resid 8 through 10 removed outlier: 6.956A pdb=" N ILE V 34 " --> pdb=" O LEU V 24 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ALA V 26 " --> pdb=" O LYS V 32 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LYS V 32 " --> pdb=" O ALA V 26 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'V' and resid 40 through 43 Processing sheet with id=AG5, first strand: chain 'V' and resid 70 through 71 removed outlier: 4.325A pdb=" N VAL V 70 " --> pdb=" O THR V 79 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR V 79 " --> pdb=" O VAL V 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'V' and resid 81 through 83 Processing sheet with id=AG7, first strand: chain 'W' and resid 38 through 43 removed outlier: 8.354A pdb=" N PHE W 91 " --> pdb=" O PRO W 28 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE W 30 " --> pdb=" O PHE W 91 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N SER W 93 " --> pdb=" O ILE W 30 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N TYR W 32 " --> pdb=" O SER W 93 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS W 76 " --> pdb=" O GLU W 90 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU W 92 " --> pdb=" O MET W 74 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N MET W 74 " --> pdb=" O LEU W 92 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE W 61 " --> pdb=" O THR W 72 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'X' and resid 31 through 32 removed outlier: 3.822A pdb=" N ARG X 48 " --> pdb=" O GLY X 31 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'X' and resid 54 through 56 removed outlier: 3.517A pdb=" N VAL X 88 " --> pdb=" O TYR X 55 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS X 85 " --> pdb=" O LYS X 81 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Y' and resid 33 through 36 removed outlier: 3.701A pdb=" N VAL Y 36 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 36 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Y' and resid 39 through 40 Processing sheet with id=AH3, first strand: chain '0' and resid 34 through 38 removed outlier: 3.570A pdb=" N GLU 0 3 " --> pdb=" O VAL 0 59 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR 0 7 " --> pdb=" O ASP 0 55 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP 0 55 " --> pdb=" O THR 0 7 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain '1' and resid 34 through 35 removed outlier: 4.005A pdb=" N THR 1 34 " --> pdb=" O THR 1 42 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR 1 42 " --> pdb=" O THR 1 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain '2' and resid 27 through 28 Processing sheet with id=AH6, first strand: chain '2' and resid 48 through 49 Processing sheet with id=AH7, first strand: chain '3' and resid 18 through 22 removed outlier: 3.893A pdb=" N LYS 3 21 " --> pdb=" O VAL 3 3 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL 3 3 " --> pdb=" O LYS 3 21 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS 3 41 " --> pdb=" O CYS 3 36 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain '5' and resid 15 through 16 removed outlier: 3.623A pdb=" N LYS 5 15 " --> pdb=" O LYS 5 23 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain '6' and resid 2 through 4 removed outlier: 5.481A pdb=" N VAL 6 23 " --> pdb=" O GLN 6 37 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE 6 17 " --> pdb=" O MET 6 24 " (cutoff:3.500A) 1128 hydrogen bonds defined for protein. 3128 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3586 hydrogen bonds 5822 hydrogen bond angles 0 basepair planarities 1425 basepair parallelities 2308 stacking parallelities Total time for adding SS restraints: 238.91 Time building geometry restraints manager: 61.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 15355 1.32 - 1.44: 65502 1.44 - 1.56: 60263 1.56 - 1.69: 9077 1.69 - 1.81: 240 Bond restraints: 150437 Sorted by residual: bond pdb=" CB ARG Q 62 " pdb=" CG ARG Q 62 " ideal model delta sigma weight residual 1.520 1.439 0.081 3.00e-02 1.11e+03 7.23e+00 bond pdb=" CA ASN P 32 " pdb=" CB ASN P 32 " ideal model delta sigma weight residual 1.533 1.490 0.044 1.72e-02 3.38e+03 6.50e+00 bond pdb=" CB ILE L 19 " pdb=" CG2 ILE L 19 " ideal model delta sigma weight residual 1.521 1.441 0.080 3.30e-02 9.18e+02 5.90e+00 bond pdb=" N9 G A 897 " pdb=" C4 G A 897 " ideal model delta sigma weight residual 1.375 1.328 0.047 2.00e-02 2.50e+03 5.56e+00 bond pdb=" CB PHE X 69 " pdb=" CG PHE X 69 " ideal model delta sigma weight residual 1.502 1.451 0.051 2.30e-02 1.89e+03 4.94e+00 ... (remaining 150432 not shown) Histogram of bond angle deviations from ideal: 95.74 - 104.09: 16094 104.09 - 112.43: 91498 112.43 - 120.77: 73039 120.77 - 129.12: 41051 129.12 - 137.46: 3905 Bond angle restraints: 225587 Sorted by residual: angle pdb=" C ILE V 71 " pdb=" N ASP V 72 " pdb=" CA ASP V 72 " ideal model delta sigma weight residual 121.80 137.46 -15.66 2.44e+00 1.68e-01 4.12e+01 angle pdb=" CA ARG O 41 " pdb=" CB ARG O 41 " pdb=" CG ARG O 41 " ideal model delta sigma weight residual 114.10 126.29 -12.19 2.00e+00 2.50e-01 3.71e+01 angle pdb=" C VAL M 15 " pdb=" N ARG M 16 " pdb=" CA ARG M 16 " ideal model delta sigma weight residual 121.54 132.83 -11.29 1.91e+00 2.74e-01 3.50e+01 angle pdb=" C ALA U 51 " pdb=" N ASN U 52 " pdb=" CA ASN U 52 " ideal model delta sigma weight residual 121.54 132.55 -11.01 1.91e+00 2.74e-01 3.32e+01 angle pdb=" CB ARG O 41 " pdb=" CG ARG O 41 " pdb=" CD ARG O 41 " ideal model delta sigma weight residual 111.30 98.23 13.07 2.30e+00 1.89e-01 3.23e+01 ... (remaining 225582 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 85265 35.95 - 71.91: 9795 71.91 - 107.86: 1108 107.86 - 143.82: 16 143.82 - 179.77: 32 Dihedral angle restraints: 96216 sinusoidal: 81391 harmonic: 14825 Sorted by residual: dihedral pdb=" CA GLY G 47 " pdb=" C GLY G 47 " pdb=" N ASN G 48 " pdb=" CA ASN G 48 " ideal model delta harmonic sigma weight residual 180.00 -105.07 -74.93 0 5.00e+00 4.00e-02 2.25e+02 dihedral pdb=" CA ILE t 66 " pdb=" C ILE t 66 " pdb=" N HIS t 67 " pdb=" CA HIS t 67 " ideal model delta harmonic sigma weight residual 180.00 110.73 69.27 0 5.00e+00 4.00e-02 1.92e+02 dihedral pdb=" CA ASP V 72 " pdb=" C ASP V 72 " pdb=" N PRO V 73 " pdb=" CA PRO V 73 " ideal model delta harmonic sigma weight residual -180.00 -118.05 -61.95 0 5.00e+00 4.00e-02 1.54e+02 ... (remaining 96213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 25560 0.078 - 0.156: 3053 0.156 - 0.234: 278 0.234 - 0.313: 30 0.313 - 0.391: 12 Chirality restraints: 28933 Sorted by residual: chirality pdb=" C3' U A 960 " pdb=" C4' U A 960 " pdb=" O3' U A 960 " pdb=" C2' U A 960 " both_signs ideal model delta sigma weight residual False -2.48 -2.09 -0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" C3' A A 890 " pdb=" C4' A A 890 " pdb=" O3' A A 890 " pdb=" C2' A A 890 " both_signs ideal model delta sigma weight residual False -2.48 -2.10 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" C1' C A 939 " pdb=" O4' C A 939 " pdb=" C2' C A 939 " pdb=" N1 C A 939 " both_signs ideal model delta sigma weight residual False 2.47 2.10 0.37 2.00e-01 2.50e+01 3.37e+00 ... (remaining 28930 not shown) Planarity restraints: 11679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP V 72 " 0.078 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO V 73 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO V 73 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO V 73 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U A2258 " 0.049 2.00e-02 2.50e+03 2.48e-02 1.39e+01 pdb=" N1 U A2258 " -0.052 2.00e-02 2.50e+03 pdb=" C2 U A2258 " -0.006 2.00e-02 2.50e+03 pdb=" O2 U A2258 " -0.004 2.00e-02 2.50e+03 pdb=" N3 U A2258 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U A2258 " 0.005 2.00e-02 2.50e+03 pdb=" O4 U A2258 " 0.016 2.00e-02 2.50e+03 pdb=" C5 U A2258 " 0.000 2.00e-02 2.50e+03 pdb=" C6 U A2258 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A2130 " -0.047 2.00e-02 2.50e+03 2.07e-02 1.28e+01 pdb=" N9 G A2130 " 0.052 2.00e-02 2.50e+03 pdb=" C8 G A2130 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G A2130 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G A2130 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G A2130 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G A2130 " -0.012 2.00e-02 2.50e+03 pdb=" N1 G A2130 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G A2130 " 0.004 2.00e-02 2.50e+03 pdb=" N2 G A2130 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G A2130 " 0.006 2.00e-02 2.50e+03 pdb=" C4 G A2130 " 0.003 2.00e-02 2.50e+03 ... (remaining 11676 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 17853 2.73 - 3.27: 115314 3.27 - 3.81: 281568 3.81 - 4.36: 328886 4.36 - 4.90: 448748 Nonbonded interactions: 1192369 Sorted by model distance: nonbonded pdb=" O2' A a 939 " pdb=" O2' A a1413 " model vdw 2.186 2.440 nonbonded pdb=" O2' G A 900 " pdb=" O6 G A 957 " model vdw 2.190 2.440 nonbonded pdb=" OD1 ASP 1 4 " pdb=" OD2 ASP 1 4 " model vdw 2.193 3.040 nonbonded pdb=" O2' C A2361 " pdb=" OH TYR 3 17 " model vdw 2.201 2.440 nonbonded pdb=" O2' A A1030 " pdb=" OP2 C A1032 " model vdw 2.207 2.440 ... (remaining 1192364 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 21.500 Check model and map are aligned: 1.370 Set scattering table: 0.860 Process input model: 507.610 Find NCS groups from input model: 2.930 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 541.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 150437 Z= 0.437 Angle : 1.013 15.661 225587 Z= 0.503 Chirality : 0.052 0.391 28933 Planarity : 0.007 0.120 11679 Dihedral : 22.789 179.774 86676 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.22 % Allowed : 14.03 % Favored : 85.76 % Rotamer: Outliers : 0.34 % Allowed : 2.39 % Favored : 97.27 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.26 % Twisted Proline : 2.07 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.55 (0.09), residues: 5097 helix: -2.96 (0.10), residues: 1284 sheet: -2.51 (0.15), residues: 904 loop : -3.33 (0.09), residues: 2909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.004 TRP R 61 HIS 0.026 0.003 HIS k 118 PHE 0.044 0.004 PHE K 45 TYR 0.039 0.004 TYR n 49 ARG 0.015 0.001 ARG M 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10194 Ramachandran restraints generated. 5097 Oldfield, 0 Emsley, 5097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10194 Ramachandran restraints generated. 5097 Oldfield, 0 Emsley, 5097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1549 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1534 time to evaluate : 5.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN F 135 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP 1 4 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 4 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: c 92 LYS cc_start: 0.8505 (mttt) cc_final: 0.8246 (ptpt) REVERT: c 133 GLN cc_start: 0.8186 (mt0) cc_final: 0.7603 (tm-30) REVERT: d 44 VAL cc_start: 0.7381 (t) cc_final: 0.6990 (t) REVERT: d 50 GLN cc_start: 0.7311 (mt0) cc_final: 0.6823 (mt0) REVERT: d 63 MET cc_start: 0.8788 (ptm) cc_final: 0.7027 (ppp) REVERT: d 65 GLU cc_start: 0.8879 (tt0) cc_final: 0.8284 (tt0) REVERT: d 68 PHE cc_start: 0.8842 (t80) cc_final: 0.8630 (t80) REVERT: d 96 ASP cc_start: 0.7466 (m-30) cc_final: 0.7260 (m-30) REVERT: d 200 ASN cc_start: 0.7740 (m-40) cc_final: 0.7305 (m110) REVERT: e 37 VAL cc_start: 0.9461 (t) cc_final: 0.9184 (p) REVERT: f 20 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8546 (pm20) REVERT: f 70 SER cc_start: 0.9131 (p) cc_final: 0.8806 (t) REVERT: f 79 GLU cc_start: 0.8769 (tp30) cc_final: 0.8519 (tp30) REVERT: f 83 LEU cc_start: 0.9445 (mt) cc_final: 0.9241 (mm) REVERT: g 21 LYS cc_start: 0.9182 (mttt) cc_final: 0.8927 (mmtp) REVERT: g 56 ASN cc_start: 0.7998 (m-40) cc_final: 0.7368 (t0) REVERT: g 70 MET cc_start: 0.6741 (ttp) cc_final: 0.6502 (tmm) REVERT: h 19 MET cc_start: 0.8974 (ttp) cc_final: 0.8727 (ttt) REVERT: h 34 ARG cc_start: 0.8733 (ttp80) cc_final: 0.8504 (ttp80) REVERT: h 35 ASP cc_start: 0.8911 (m-30) cc_final: 0.8018 (m-30) REVERT: h 61 ARG cc_start: 0.8627 (ttm170) cc_final: 0.8414 (ttm110) REVERT: j 10 LEU cc_start: 0.8399 (mp) cc_final: 0.7740 (mt) REVERT: j 68 ARG cc_start: 0.5986 (mtt180) cc_final: 0.5437 (mtt-85) REVERT: j 98 ILE cc_start: 0.7266 (pt) cc_final: 0.6793 (pt) REVERT: k 15 ASN cc_start: 0.8549 (m-40) cc_final: 0.7499 (p0) REVERT: k 36 ASP cc_start: 0.8489 (m-30) cc_final: 0.8258 (m-30) REVERT: k 56 LYS cc_start: 0.9495 (mttt) cc_final: 0.9147 (tppt) REVERT: k 65 MET cc_start: 0.9015 (ptm) cc_final: 0.8764 (ptp) REVERT: k 83 ASP cc_start: 0.8528 (m-30) cc_final: 0.8287 (m-30) REVERT: l 62 LEU cc_start: 0.7714 (mt) cc_final: 0.7502 (mt) REVERT: l 130 TYR cc_start: 0.7940 (m-80) cc_final: 0.7701 (m-80) REVERT: m 77 ILE cc_start: 0.8423 (pt) cc_final: 0.8176 (tp) REVERT: o 11 ILE cc_start: 0.9502 (pt) cc_final: 0.9041 (pt) REVERT: o 13 LYS cc_start: 0.9289 (mttt) cc_final: 0.8849 (mptt) REVERT: p 68 ASP cc_start: 0.8793 (p0) cc_final: 0.8371 (p0) REVERT: p 73 ILE cc_start: 0.9171 (pt) cc_final: 0.8706 (pt) REVERT: p 74 LEU cc_start: 0.9108 (mp) cc_final: 0.8907 (mt) REVERT: q 25 THR cc_start: 0.8175 (m) cc_final: 0.7904 (p) REVERT: q 83 GLU cc_start: 0.8590 (tt0) cc_final: 0.8381 (tm-30) REVERT: r 32 LEU cc_start: 0.9480 (tp) cc_final: 0.9265 (tp) REVERT: r 46 ARG cc_start: 0.8979 (ttp-170) cc_final: 0.8686 (ttt-90) REVERT: r 51 THR cc_start: 0.8894 (t) cc_final: 0.8140 (p) REVERT: r 64 LYS cc_start: 0.8799 (mttt) cc_final: 0.8257 (mtpt) REVERT: r 72 LEU cc_start: 0.8691 (tp) cc_final: 0.8144 (tt) REVERT: s 16 MET cc_start: 0.6077 (tpt) cc_final: 0.5792 (tpt) REVERT: s 36 ARG cc_start: 0.5810 (mmt180) cc_final: 0.4548 (tpp-160) REVERT: s 66 MET cc_start: 0.8358 (ttp) cc_final: 0.7573 (mmp) REVERT: s 67 VAL cc_start: 0.3079 (p) cc_final: 0.2763 (m) REVERT: t 20 LYS cc_start: 0.9066 (ptmm) cc_final: 0.8658 (ptmm) REVERT: t 29 ARG cc_start: 0.9010 (mtt180) cc_final: 0.8771 (ttm170) REVERT: C 20 ASP cc_start: 0.8131 (m-30) cc_final: 0.7927 (m-30) REVERT: C 104 ILE cc_start: 0.8780 (mt) cc_final: 0.8545 (mt) REVERT: D 157 ASN cc_start: 0.8882 (m-40) cc_final: 0.8645 (m110) REVERT: E 35 ASP cc_start: 0.8961 (t70) cc_final: 0.8756 (t0) REVERT: E 74 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7510 (ptt90) REVERT: E 157 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7552 (mp0) REVERT: E 158 ASN cc_start: 0.8072 (m-40) cc_final: 0.7733 (p0) REVERT: F 96 MET cc_start: 0.8690 (mmm) cc_final: 0.8026 (mmm) REVERT: F 97 TYR cc_start: 0.9178 (m-80) cc_final: 0.8900 (m-80) REVERT: F 99 PHE cc_start: 0.9487 (t80) cc_final: 0.9264 (t80) REVERT: F 152 MET cc_start: 0.8276 (mmm) cc_final: 0.8036 (mmm) REVERT: G 41 ILE cc_start: 0.7422 (mt) cc_final: 0.7118 (mt) REVERT: G 52 PHE cc_start: 0.7720 (m-10) cc_final: 0.7408 (m-80) REVERT: G 84 GLN cc_start: 0.7801 (mt0) cc_final: 0.7278 (pp30) REVERT: G 104 THR cc_start: 0.8179 (p) cc_final: 0.7244 (p) REVERT: G 115 MET cc_start: 0.7232 (mmm) cc_final: 0.6680 (mmm) REVERT: G 132 ILE cc_start: 0.9006 (mt) cc_final: 0.8804 (mp) REVERT: K 72 ASP cc_start: 0.8781 (m-30) cc_final: 0.8369 (m-30) REVERT: K 103 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8108 (mt-10) REVERT: K 117 ARG cc_start: 0.9100 (mtt180) cc_final: 0.8857 (mtm180) REVERT: K 118 LYS cc_start: 0.8939 (mttt) cc_final: 0.8416 (ttmm) REVERT: L 13 ASN cc_start: 0.9079 (m-40) cc_final: 0.8544 (m110) REVERT: L 23 LYS cc_start: 0.9102 (mtpp) cc_final: 0.8828 (mtpp) REVERT: L 80 ASP cc_start: 0.8446 (m-30) cc_final: 0.8060 (m-30) REVERT: L 88 ARG cc_start: 0.8441 (mtt180) cc_final: 0.7959 (mtt-85) REVERT: L 90 ASP cc_start: 0.7509 (m-30) cc_final: 0.6524 (m-30) REVERT: L 91 LYS cc_start: 0.8977 (mttt) cc_final: 0.8766 (mttp) REVERT: L 97 ARG cc_start: 0.8174 (mtt180) cc_final: 0.7957 (mtt180) REVERT: L 120 GLU cc_start: 0.8674 (tp30) cc_final: 0.8134 (mt-10) REVERT: M 5 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8118 (tm-30) REVERT: M 7 LYS cc_start: 0.9160 (mmmt) cc_final: 0.8823 (mmmm) REVERT: M 80 ASP cc_start: 0.8745 (m-30) cc_final: 0.7882 (m-30) REVERT: N 41 TRP cc_start: 0.8786 (m100) cc_final: 0.8276 (m100) REVERT: N 103 MET cc_start: 0.8756 (mmm) cc_final: 0.8475 (mmm) REVERT: N 129 THR cc_start: 0.8563 (p) cc_final: 0.8323 (p) REVERT: O 24 LEU cc_start: 0.8547 (mt) cc_final: 0.8028 (mp) REVERT: O 92 ASP cc_start: 0.8832 (m-30) cc_final: 0.8614 (t70) REVERT: P 13 LYS cc_start: 0.8829 (mttt) cc_final: 0.8516 (mttp) REVERT: P 14 ARG cc_start: 0.8222 (mtt180) cc_final: 0.7993 (mtm-85) REVERT: P 17 ARG cc_start: 0.8723 (mtt180) cc_final: 0.7991 (mtt90) REVERT: P 28 CYS cc_start: 0.8704 (m) cc_final: 0.8204 (p) REVERT: P 33 ILE cc_start: 0.9032 (mt) cc_final: 0.8446 (mm) REVERT: Q 40 ILE cc_start: 0.9082 (mt) cc_final: 0.8868 (mm) REVERT: Q 43 PHE cc_start: 0.7656 (m-10) cc_final: 0.7310 (m-80) REVERT: Q 65 SER cc_start: 0.9088 (p) cc_final: 0.7947 (p) REVERT: Q 85 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8344 (mt-10) REVERT: R 49 ASP cc_start: 0.8326 (m-30) cc_final: 0.8032 (m-30) REVERT: R 66 ASN cc_start: 0.7821 (m-40) cc_final: 0.7390 (m-40) REVERT: R 94 MET cc_start: 0.8526 (mmt) cc_final: 0.7941 (mmt) REVERT: S 1 MET cc_start: 0.8253 (mmm) cc_final: 0.7954 (mmm) REVERT: T 42 LYS cc_start: 0.9406 (mttt) cc_final: 0.9098 (mtmm) REVERT: U 18 LEU cc_start: 0.9419 (mt) cc_final: 0.8727 (mm) REVERT: U 30 ASP cc_start: 0.7530 (m-30) cc_final: 0.7208 (p0) REVERT: U 40 GLN cc_start: 0.8719 (mt0) cc_final: 0.8292 (mt0) REVERT: U 89 ILE cc_start: 0.8237 (mt) cc_final: 0.7993 (mt) REVERT: V 1 MET cc_start: 0.7254 (mmm) cc_final: 0.6965 (tpp) REVERT: V 40 VAL cc_start: 0.8998 (t) cc_final: 0.8554 (p) REVERT: X 53 LYS cc_start: 0.9204 (mttt) cc_final: 0.8963 (mtpp) REVERT: Y 17 ASN cc_start: 0.8598 (t160) cc_final: 0.8019 (t0) REVERT: Z 9 LEU cc_start: 0.8477 (mt) cc_final: 0.8224 (mt) REVERT: 0 46 MET cc_start: 0.8700 (mmm) cc_final: 0.8459 (mmt) REVERT: 3 30 LEU cc_start: 0.7647 (mt) cc_final: 0.7052 (mm) REVERT: 3 32 LYS cc_start: 0.7895 (mmtt) cc_final: 0.7684 (mmtp) REVERT: 3 40 ARG cc_start: 0.8759 (mtm-85) cc_final: 0.8406 (mpp80) REVERT: 3 46 ARG cc_start: 0.7604 (mtp-110) cc_final: 0.6778 (ttm-80) REVERT: 4 11 LYS cc_start: 0.8183 (mttt) cc_final: 0.7976 (mttp) REVERT: 4 36 ARG cc_start: 0.8100 (mtt180) cc_final: 0.7139 (ttm110) REVERT: 4 37 LYS cc_start: 0.8314 (mttt) cc_final: 0.8098 (mmmt) outliers start: 15 outliers final: 6 residues processed: 1540 average time/residue: 1.2825 time to fit residues: 3315.8748 Evaluate side-chains 909 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 902 time to evaluate : 5.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain D residue 119 PHE Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain U residue 48 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 803 optimal weight: 5.9990 chunk 720 optimal weight: 10.0000 chunk 399 optimal weight: 10.0000 chunk 246 optimal weight: 1.9990 chunk 486 optimal weight: 10.0000 chunk 385 optimal weight: 10.0000 chunk 745 optimal weight: 4.9990 chunk 288 optimal weight: 0.9990 chunk 453 optimal weight: 10.0000 chunk 554 optimal weight: 10.0000 chunk 863 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 6 HIS ** c 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 35 GLN ** d 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 59 HIS d 113 GLN d 200 ASN ** f 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 45 ASN i 14 ASN i 66 ASN ** j 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 24 HIS ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 HIS m 91 HIS n 10 ASN o 9 ASN o 65 ASN ** p 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 83 HIS ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 20 ASN r 56 GLN s 57 HIS C 128 ASN C 177 ASN ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 ASN E 20 ASN E 29 ASN ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN E 169 ASN E 190 ASN F 21 ASN ** F 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN K 48 HIS K 131 HIS L 13 ASN M 4 HIS N 9 HIS ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 HIS O 61 GLN ** P 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 114 ASN ** R 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 41 ASN R 81 HIS S 81 HIS S 86 GLN V 18 ASN W 20 GLN X 38 GLN X 59 ASN X 87 GLN Y 17 ASN Y 23 ASN Y 32 ASN Z 20 GLN 2 32 ASN 2 40 HIS 2 48 HIS 3 4 ASN 3 26 ASN 5 4 GLN 5 7 HIS 5 43 GLN 5 60 GLN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 150437 Z= 0.201 Angle : 0.651 11.594 225587 Z= 0.336 Chirality : 0.037 0.321 28933 Planarity : 0.005 0.104 11679 Dihedral : 23.742 179.768 76274 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.69 % Favored : 89.15 % Rotamer: Outliers : 4.11 % Allowed : 12.53 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.26 % Twisted Proline : 0.52 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.10), residues: 5097 helix: -1.31 (0.13), residues: 1281 sheet: -2.15 (0.16), residues: 931 loop : -3.00 (0.10), residues: 2885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP c 200 HIS 0.016 0.001 HIS C 142 PHE 0.025 0.002 PHE i 127 TYR 0.027 0.002 TYR g 107 ARG 0.011 0.001 ARG Z 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10194 Ramachandran restraints generated. 5097 Oldfield, 0 Emsley, 5097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10194 Ramachandran restraints generated. 5097 Oldfield, 0 Emsley, 5097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1231 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1052 time to evaluate : 5.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP 1 4 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 4 1 " (corrupted residue). Skipping it. REVERT: c 10 MET cc_start: 0.5557 (mmm) cc_final: 0.5294 (mmm) REVERT: c 62 ARG cc_start: 0.6920 (mtm110) cc_final: 0.6525 (mtt-85) REVERT: c 92 LYS cc_start: 0.8469 (mttt) cc_final: 0.8170 (ptpt) REVERT: c 133 GLN cc_start: 0.8285 (mt0) cc_final: 0.7497 (tm-30) REVERT: d 41 ARG cc_start: 0.6635 (ptm160) cc_final: 0.4901 (mtm180) REVERT: d 50 GLN cc_start: 0.7294 (mt0) cc_final: 0.6867 (mt0) REVERT: d 63 MET cc_start: 0.8708 (ptm) cc_final: 0.6868 (ppp) REVERT: d 88 MET cc_start: 0.9321 (mmt) cc_final: 0.9080 (mmm) REVERT: d 100 TYR cc_start: 0.8519 (t80) cc_final: 0.8306 (t80) REVERT: e 22 THR cc_start: 0.6166 (p) cc_final: 0.5531 (t) REVERT: e 37 VAL cc_start: 0.9391 (t) cc_final: 0.9171 (p) REVERT: f 7 TYR cc_start: 0.8289 (m-10) cc_final: 0.8027 (m-80) REVERT: f 20 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8531 (pm20) REVERT: f 79 GLU cc_start: 0.8768 (tp30) cc_final: 0.8409 (tp30) REVERT: f 83 LEU cc_start: 0.9431 (mt) cc_final: 0.9218 (mm) REVERT: g 56 ASN cc_start: 0.7941 (m-40) cc_final: 0.7501 (t0) REVERT: g 70 MET cc_start: 0.6963 (ttp) cc_final: 0.6536 (tmm) REVERT: g 85 TYR cc_start: 0.5781 (m-80) cc_final: 0.5420 (m-80) REVERT: h 35 ASP cc_start: 0.8859 (m-30) cc_final: 0.8535 (m-30) REVERT: h 61 ARG cc_start: 0.8620 (ttm170) cc_final: 0.8419 (ttm110) REVERT: h 76 ASN cc_start: 0.8351 (t0) cc_final: 0.8104 (t0) REVERT: i 98 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8377 (mt) REVERT: j 10 LEU cc_start: 0.8068 (mp) cc_final: 0.7862 (mt) REVERT: j 68 ARG cc_start: 0.6096 (mtt180) cc_final: 0.5456 (mtt-85) REVERT: k 14 LYS cc_start: 0.8190 (ttpt) cc_final: 0.7902 (ttpt) REVERT: k 15 ASN cc_start: 0.8468 (m-40) cc_final: 0.8039 (p0) REVERT: k 36 ASP cc_start: 0.8771 (m-30) cc_final: 0.8555 (m-30) REVERT: k 53 LYS cc_start: 0.8363 (tmtt) cc_final: 0.8085 (tmtt) REVERT: k 64 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8438 (pm20) REVERT: k 83 ASP cc_start: 0.8615 (m-30) cc_final: 0.8389 (m-30) REVERT: k 87 LYS cc_start: 0.9156 (ttmm) cc_final: 0.8915 (ttpt) REVERT: l 125 GLN cc_start: 0.8564 (tt0) cc_final: 0.8333 (mt0) REVERT: m 66 GLU cc_start: 0.8146 (tt0) cc_final: 0.7848 (tt0) REVERT: m 77 ILE cc_start: 0.8517 (pt) cc_final: 0.8299 (tp) REVERT: m 78 LYS cc_start: 0.7655 (tppt) cc_final: 0.7384 (mmtm) REVERT: o 13 LYS cc_start: 0.9131 (mttt) cc_final: 0.8723 (mptt) REVERT: o 14 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7866 (tm-30) REVERT: o 41 GLU cc_start: 0.9222 (mm-30) cc_final: 0.9003 (mm-30) REVERT: p 68 ASP cc_start: 0.8728 (p0) cc_final: 0.8340 (p0) REVERT: p 74 LEU cc_start: 0.9258 (mp) cc_final: 0.9036 (mt) REVERT: q 25 THR cc_start: 0.8065 (m) cc_final: 0.7838 (p) REVERT: q 54 ASN cc_start: 0.8808 (OUTLIER) cc_final: 0.8250 (t0) REVERT: q 80 GLU cc_start: 0.8204 (tp30) cc_final: 0.7929 (tm-30) REVERT: r 56 GLN cc_start: 0.9493 (tp-100) cc_final: 0.9247 (tp40) REVERT: r 64 LYS cc_start: 0.8884 (mttt) cc_final: 0.8169 (mtpt) REVERT: r 72 LEU cc_start: 0.8516 (tp) cc_final: 0.8060 (tt) REVERT: s 36 ARG cc_start: 0.5875 (mmt180) cc_final: 0.4907 (tpp-160) REVERT: s 66 MET cc_start: 0.8232 (ttp) cc_final: 0.7419 (mmp) REVERT: C 20 ASP cc_start: 0.7948 (m-30) cc_final: 0.7631 (m-30) REVERT: C 111 GLU cc_start: 0.7036 (pm20) cc_final: 0.5860 (pm20) REVERT: C 225 MET cc_start: 0.8416 (mmt) cc_final: 0.8173 (mmt) REVERT: D 85 ASN cc_start: 0.7927 (t0) cc_final: 0.7673 (t0) REVERT: E 16 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8142 (mm-30) REVERT: E 35 ASP cc_start: 0.8978 (t70) cc_final: 0.8733 (t0) REVERT: E 127 GLU cc_start: 0.7570 (mp0) cc_final: 0.7262 (mm-30) REVERT: E 157 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7334 (mp0) REVERT: E 158 ASN cc_start: 0.8030 (m-40) cc_final: 0.7547 (p0) REVERT: F 96 MET cc_start: 0.8262 (mmm) cc_final: 0.7918 (mmm) REVERT: F 97 TYR cc_start: 0.9255 (m-80) cc_final: 0.8857 (m-80) REVERT: F 99 PHE cc_start: 0.9521 (t80) cc_final: 0.9187 (t80) REVERT: F 137 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8876 (tt) REVERT: F 152 MET cc_start: 0.8248 (mmm) cc_final: 0.8047 (mmm) REVERT: F 175 MET cc_start: 0.8391 (mmm) cc_final: 0.8061 (mtt) REVERT: G 57 ASP cc_start: 0.8077 (m-30) cc_final: 0.7614 (t70) REVERT: G 115 MET cc_start: 0.7290 (mmm) cc_final: 0.6683 (mmm) REVERT: K 72 ASP cc_start: 0.8745 (m-30) cc_final: 0.8470 (m-30) REVERT: K 117 ARG cc_start: 0.9024 (mtt180) cc_final: 0.8823 (mtm180) REVERT: K 118 LYS cc_start: 0.8911 (mttt) cc_final: 0.8553 (ttpp) REVERT: L 23 LYS cc_start: 0.9024 (mtpp) cc_final: 0.8812 (mtpp) REVERT: L 31 LYS cc_start: 0.8873 (mttt) cc_final: 0.8458 (ptpp) REVERT: L 73 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8209 (p0) REVERT: L 89 ASP cc_start: 0.7716 (p0) cc_final: 0.7401 (p0) REVERT: L 105 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8694 (mm-30) REVERT: L 120 GLU cc_start: 0.8827 (tp30) cc_final: 0.8341 (mt-10) REVERT: M 7 LYS cc_start: 0.9174 (mmmt) cc_final: 0.8852 (mptt) REVERT: N 1 MET cc_start: 0.4013 (mmm) cc_final: 0.3708 (mmm) REVERT: P 9 LYS cc_start: 0.9053 (mttt) cc_final: 0.8819 (mtmt) REVERT: P 17 ARG cc_start: 0.8595 (mtt180) cc_final: 0.7888 (mtt90) REVERT: P 33 ILE cc_start: 0.8718 (mt) cc_final: 0.8480 (mm) REVERT: P 48 VAL cc_start: 0.8069 (OUTLIER) cc_final: 0.7834 (t) REVERT: P 77 LYS cc_start: 0.9505 (OUTLIER) cc_final: 0.8953 (ptpp) REVERT: P 78 LEU cc_start: 0.9373 (tt) cc_final: 0.8992 (tt) REVERT: P 116 LEU cc_start: 0.8853 (mt) cc_final: 0.8630 (mt) REVERT: P 117 GLU cc_start: 0.9231 (mt-10) cc_final: 0.8473 (mp0) REVERT: Q 65 SER cc_start: 0.9255 (p) cc_final: 0.8010 (p) REVERT: Q 71 GLU cc_start: 0.7735 (mp0) cc_final: 0.7507 (mp0) REVERT: R 49 ASP cc_start: 0.8435 (m-30) cc_final: 0.8100 (m-30) REVERT: R 102 ASP cc_start: 0.7959 (t0) cc_final: 0.7605 (t0) REVERT: S 1 MET cc_start: 0.8137 (mmm) cc_final: 0.7910 (tmm) REVERT: S 31 GLU cc_start: 0.8831 (mp0) cc_final: 0.8435 (mp0) REVERT: U 22 GLU cc_start: 0.7121 (pm20) cc_final: 0.6235 (tm-30) REVERT: U 30 ASP cc_start: 0.7635 (m-30) cc_final: 0.7303 (p0) REVERT: X 24 ASP cc_start: 0.7605 (t0) cc_final: 0.7229 (t0) REVERT: Y 17 ASN cc_start: 0.8335 (t0) cc_final: 0.7758 (t0) REVERT: Z 45 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8204 (mt-10) REVERT: 0 10 ARG cc_start: 0.8656 (tpp80) cc_final: 0.8434 (tpp80) REVERT: 0 18 ASN cc_start: 0.8562 (p0) cc_final: 0.7958 (p0) REVERT: 0 54 VAL cc_start: 0.9271 (t) cc_final: 0.8996 (p) REVERT: 4 11 LYS cc_start: 0.8265 (mttt) cc_final: 0.8054 (mttp) REVERT: 4 36 ARG cc_start: 0.8100 (mtt180) cc_final: 0.7324 (ttp-110) REVERT: 4 37 LYS cc_start: 0.8347 (mttt) cc_final: 0.8136 (mmmt) REVERT: 5 22 LEU cc_start: 0.8682 (mt) cc_final: 0.8266 (mt) outliers start: 179 outliers final: 106 residues processed: 1137 average time/residue: 1.1780 time to fit residues: 2328.7681 Evaluate side-chains 974 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 861 time to evaluate : 7.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain d residue 64 ASN Chi-restraints excluded: chain d residue 120 ILE Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 135 ASN Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain f residue 42 GLU Chi-restraints excluded: chain f residue 69 THR Chi-restraints excluded: chain g residue 26 LEU Chi-restraints excluded: chain g residue 67 LYS Chi-restraints excluded: chain g residue 140 ASP Chi-restraints excluded: chain h residue 70 GLU Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 27 LYS Chi-restraints excluded: chain i residue 49 ASN Chi-restraints excluded: chain i residue 98 LEU Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain k residue 24 HIS Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 64 GLN Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 19 SER Chi-restraints excluded: chain l residue 60 SER Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain o residue 3 ILE Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 27 SER Chi-restraints excluded: chain q residue 30 THR Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 54 ASN Chi-restraints excluded: chain q residue 78 LEU Chi-restraints excluded: chain r residue 37 ILE Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain s residue 61 TYR Chi-restraints excluded: chain t residue 18 ASN Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 62 THR Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 119 PHE Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 172 GLN Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 94 VAL Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 39 GLU Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain O residue 57 HIS Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 77 LYS Chi-restraints excluded: chain R residue 29 HIS Chi-restraints excluded: chain R residue 54 LYS Chi-restraints excluded: chain R residue 97 ASP Chi-restraints excluded: chain R residue 115 ASP Chi-restraints excluded: chain S residue 88 HIS Chi-restraints excluded: chain U residue 50 VAL Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 60 VAL Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 39 LEU Chi-restraints excluded: chain Z residue 5 GLU Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain 3 residue 48 THR Chi-restraints excluded: chain 4 residue 41 VAL Chi-restraints excluded: chain 6 residue 7 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 479 optimal weight: 10.0000 chunk 268 optimal weight: 6.9990 chunk 718 optimal weight: 9.9990 chunk 588 optimal weight: 10.0000 chunk 238 optimal weight: 10.0000 chunk 865 optimal weight: 5.9990 chunk 934 optimal weight: 30.0000 chunk 770 optimal weight: 5.9990 chunk 857 optimal weight: 5.9990 chunk 294 optimal weight: 30.0000 chunk 694 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 85 ASN ** c 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 50 GLN ** d 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 97 ASN k 24 HIS ** p 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 22 GLN ** s 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 21 ASN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN F 21 ASN G 6 ASN ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 86 GLN ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 53 GLN ** W 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 20 GLN 0 48 ASN ** 1 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 60 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 150437 Z= 0.315 Angle : 0.729 12.069 225587 Z= 0.372 Chirality : 0.041 0.327 28933 Planarity : 0.006 0.102 11679 Dihedral : 23.774 179.321 76272 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.20 % Favored : 86.64 % Rotamer: Outliers : 5.21 % Allowed : 15.91 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.26 % Twisted Proline : 0.52 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.11), residues: 5097 helix: -0.81 (0.13), residues: 1306 sheet: -2.03 (0.16), residues: 966 loop : -3.00 (0.10), residues: 2825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP g 103 HIS 0.024 0.002 HIS C 142 PHE 0.031 0.002 PHE M 58 TYR 0.029 0.002 TYR N 74 ARG 0.008 0.001 ARG C 215 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10194 Ramachandran restraints generated. 5097 Oldfield, 0 Emsley, 5097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10194 Ramachandran restraints generated. 5097 Oldfield, 0 Emsley, 5097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1108 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 881 time to evaluate : 7.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP 1 4 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 4 1 " (corrupted residue). Skipping it. REVERT: c 92 LYS cc_start: 0.8403 (mttt) cc_final: 0.8123 (ptpt) REVERT: c 133 GLN cc_start: 0.8306 (mt0) cc_final: 0.7509 (tm-30) REVERT: d 41 ARG cc_start: 0.6810 (ptm160) cc_final: 0.5013 (mtm180) REVERT: d 50 GLN cc_start: 0.7644 (mt0) cc_final: 0.7182 (mt0) REVERT: d 60 MET cc_start: 0.8383 (tpt) cc_final: 0.8147 (mmt) REVERT: d 63 MET cc_start: 0.8921 (ptm) cc_final: 0.8710 (ptm) REVERT: d 65 GLU cc_start: 0.9035 (tt0) cc_final: 0.8416 (tt0) REVERT: d 88 MET cc_start: 0.9500 (mmt) cc_final: 0.9233 (mmm) REVERT: e 37 VAL cc_start: 0.9533 (t) cc_final: 0.9316 (p) REVERT: f 6 LYS cc_start: 0.9428 (OUTLIER) cc_final: 0.9163 (pttp) REVERT: g 56 ASN cc_start: 0.7761 (m-40) cc_final: 0.7332 (t0) REVERT: g 70 MET cc_start: 0.7225 (ttp) cc_final: 0.6923 (tmm) REVERT: g 85 TYR cc_start: 0.5722 (m-80) cc_final: 0.5398 (m-80) REVERT: h 76 ASN cc_start: 0.8422 (t0) cc_final: 0.8149 (t0) REVERT: j 10 LEU cc_start: 0.7878 (mp) cc_final: 0.7624 (mt) REVERT: j 68 ARG cc_start: 0.6130 (mtt180) cc_final: 0.5479 (mtt-85) REVERT: j 98 ILE cc_start: 0.6185 (pt) cc_final: 0.5867 (mm) REVERT: k 14 LYS cc_start: 0.8135 (ttpt) cc_final: 0.7752 (ttpt) REVERT: k 15 ASN cc_start: 0.8442 (m-40) cc_final: 0.7849 (p0) REVERT: k 64 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8378 (pm20) REVERT: k 82 VAL cc_start: 0.8044 (OUTLIER) cc_final: 0.7742 (m) REVERT: k 83 ASP cc_start: 0.8673 (m-30) cc_final: 0.8336 (m-30) REVERT: k 87 LYS cc_start: 0.9277 (ttmm) cc_final: 0.9027 (ttpt) REVERT: k 112 ASP cc_start: 0.7337 (t0) cc_final: 0.7015 (t0) REVERT: m 66 GLU cc_start: 0.8158 (tt0) cc_final: 0.7908 (tt0) REVERT: m 77 ILE cc_start: 0.8548 (pt) cc_final: 0.8283 (tp) REVERT: o 13 LYS cc_start: 0.9313 (mttt) cc_final: 0.8925 (mptt) REVERT: o 41 GLU cc_start: 0.9314 (mm-30) cc_final: 0.9111 (mm-30) REVERT: p 65 GLN cc_start: 0.8461 (mp10) cc_final: 0.8108 (mp10) REVERT: p 68 ASP cc_start: 0.8853 (p0) cc_final: 0.8493 (p0) REVERT: p 74 LEU cc_start: 0.9335 (mp) cc_final: 0.9117 (mt) REVERT: q 25 THR cc_start: 0.8178 (m) cc_final: 0.7909 (p) REVERT: q 54 ASN cc_start: 0.8685 (OUTLIER) cc_final: 0.8260 (t0) REVERT: q 83 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7552 (tm-30) REVERT: r 58 LYS cc_start: 0.9486 (mtpp) cc_final: 0.8886 (mmtt) REVERT: r 64 LYS cc_start: 0.8880 (mttt) cc_final: 0.8513 (mtpt) REVERT: s 36 ARG cc_start: 0.5730 (mmt180) cc_final: 0.5282 (tpp-160) REVERT: s 66 MET cc_start: 0.8497 (ttp) cc_final: 0.7446 (mmp) REVERT: t 70 LYS cc_start: 0.8818 (mtmt) cc_final: 0.8431 (ttmm) REVERT: C 20 ASP cc_start: 0.8195 (m-30) cc_final: 0.7935 (m-30) REVERT: C 225 MET cc_start: 0.8497 (mmt) cc_final: 0.8133 (mmt) REVERT: C 276 LYS cc_start: 0.7019 (mmmm) cc_final: 0.5863 (tptm) REVERT: D 85 ASN cc_start: 0.8315 (t0) cc_final: 0.8090 (t0) REVERT: E 35 ASP cc_start: 0.9044 (t70) cc_final: 0.8822 (t0) REVERT: E 75 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7791 (mm110) REVERT: E 158 ASN cc_start: 0.8228 (m-40) cc_final: 0.7552 (p0) REVERT: E 161 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8407 (p0) REVERT: F 96 MET cc_start: 0.8256 (mmm) cc_final: 0.7774 (mmm) REVERT: F 97 TYR cc_start: 0.9307 (m-80) cc_final: 0.8952 (m-80) REVERT: F 99 PHE cc_start: 0.9541 (t80) cc_final: 0.9218 (t80) REVERT: F 152 MET cc_start: 0.8203 (mmm) cc_final: 0.7899 (mmm) REVERT: F 167 ARG cc_start: 0.9037 (ttm-80) cc_final: 0.8473 (ttm-80) REVERT: G 84 GLN cc_start: 0.7565 (pp30) cc_final: 0.7322 (pp30) REVERT: G 115 MET cc_start: 0.7483 (mmm) cc_final: 0.6756 (mmm) REVERT: K 1 MET cc_start: 0.6910 (mmp) cc_final: 0.5749 (pmm) REVERT: K 72 ASP cc_start: 0.8848 (m-30) cc_final: 0.8515 (m-30) REVERT: L 1 MET cc_start: 0.8523 (mmm) cc_final: 0.8319 (mmm) REVERT: L 31 LYS cc_start: 0.8902 (mttt) cc_final: 0.8400 (ptpt) REVERT: L 45 GLN cc_start: 0.8062 (mp10) cc_final: 0.7666 (mp10) REVERT: L 73 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8266 (p0) REVERT: L 105 GLU cc_start: 0.9177 (mt-10) cc_final: 0.8823 (mm-30) REVERT: L 120 GLU cc_start: 0.8761 (tp30) cc_final: 0.8433 (mt-10) REVERT: M 19 VAL cc_start: 0.9133 (OUTLIER) cc_final: 0.8842 (p) REVERT: N 35 GLN cc_start: 0.8878 (tt0) cc_final: 0.8204 (tp40) REVERT: N 106 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8788 (mm) REVERT: O 57 HIS cc_start: 0.7992 (OUTLIER) cc_final: 0.7215 (t-90) REVERT: P 17 ARG cc_start: 0.8531 (mtt180) cc_final: 0.7808 (mtt90) REVERT: P 45 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8620 (tp) REVERT: P 77 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.9207 (ptpp) REVERT: Q 65 SER cc_start: 0.9235 (p) cc_final: 0.8547 (p) REVERT: Q 71 GLU cc_start: 0.8071 (mp0) cc_final: 0.7544 (mp0) REVERT: R 49 ASP cc_start: 0.8624 (m-30) cc_final: 0.8202 (m-30) REVERT: R 76 TYR cc_start: 0.6311 (OUTLIER) cc_final: 0.6057 (m-80) REVERT: R 102 ASP cc_start: 0.8130 (t0) cc_final: 0.7669 (t0) REVERT: S 31 GLU cc_start: 0.8877 (mp0) cc_final: 0.8477 (mp0) REVERT: U 30 ASP cc_start: 0.7496 (m-30) cc_final: 0.7154 (p0) REVERT: X 79 GLU cc_start: 0.7839 (tp30) cc_final: 0.7584 (tp30) REVERT: Y 17 ASN cc_start: 0.8451 (t0) cc_final: 0.7897 (t0) REVERT: Z 45 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8265 (mt-10) REVERT: Z 59 GLU cc_start: 0.8228 (pp20) cc_final: 0.7561 (pp20) REVERT: 0 41 GLU cc_start: 0.8063 (tt0) cc_final: 0.7799 (tm-30) REVERT: 4 36 ARG cc_start: 0.8184 (mtt180) cc_final: 0.7412 (ttp-110) outliers start: 227 outliers final: 151 residues processed: 1004 average time/residue: 1.2642 time to fit residues: 2243.1328 Evaluate side-chains 972 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 809 time to evaluate : 5.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain d residue 64 ASN Chi-restraints excluded: chain d residue 120 ILE Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 135 ASN Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain f residue 6 LYS Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain f residue 42 GLU Chi-restraints excluded: chain f residue 50 ARG Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 69 THR Chi-restraints excluded: chain f residue 70 SER Chi-restraints excluded: chain g residue 26 LEU Chi-restraints excluded: chain g residue 67 LYS Chi-restraints excluded: chain g residue 86 GLN Chi-restraints excluded: chain g residue 140 ASP Chi-restraints excluded: chain g residue 144 MET Chi-restraints excluded: chain h residue 70 GLU Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 27 LYS Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 96 SER Chi-restraints excluded: chain j residue 14 GLU Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 64 GLN Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 19 SER Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 60 SER Chi-restraints excluded: chain l residue 62 LEU Chi-restraints excluded: chain o residue 3 ILE Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 60 ILE Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 27 SER Chi-restraints excluded: chain q residue 30 THR Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 54 ASN Chi-restraints excluded: chain q residue 78 LEU Chi-restraints excluded: chain r residue 37 ILE Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain s residue 61 TYR Chi-restraints excluded: chain t residue 18 ASN Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 62 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 119 PHE Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 172 GLN Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 48 HIS Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 39 GLU Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain O residue 57 HIS Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 77 LYS Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 24 ASP Chi-restraints excluded: chain R residue 29 HIS Chi-restraints excluded: chain R residue 54 LYS Chi-restraints excluded: chain R residue 76 TYR Chi-restraints excluded: chain R residue 97 ASP Chi-restraints excluded: chain R residue 115 ASP Chi-restraints excluded: chain S residue 2 TYR Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 81 HIS Chi-restraints excluded: chain S residue 88 HIS Chi-restraints excluded: chain T residue 36 ASP Chi-restraints excluded: chain T residue 44 THR Chi-restraints excluded: chain U residue 50 VAL Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 64 HIS Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 60 VAL Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 38 VAL Chi-restraints excluded: chain Z residue 5 GLU Chi-restraints excluded: chain Z residue 57 LEU Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 46 LEU Chi-restraints excluded: chain 3 residue 48 THR Chi-restraints excluded: chain 4 residue 41 VAL Chi-restraints excluded: chain 4 residue 43 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 854 optimal weight: 0.6980 chunk 650 optimal weight: 10.0000 chunk 449 optimal weight: 10.0000 chunk 95 optimal weight: 50.0000 chunk 412 optimal weight: 10.0000 chunk 580 optimal weight: 10.0000 chunk 868 optimal weight: 2.9990 chunk 919 optimal weight: 3.9990 chunk 453 optimal weight: 10.0000 chunk 822 optimal weight: 5.9990 chunk 247 optimal weight: 40.0000 overall best weight: 4.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 35 GLN ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 8 HIS e 43 ASN ** e 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 20 GLN k 24 HIS m 91 HIS n 52 GLN ** o 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 65 GLN p 84 HIS s 22 GLN C 86 ASN C 134 ASN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 ASN ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 HIS ** R 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 66 ASN V 64 HIS ** W 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 20 GLN 0 48 ASN ** 1 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 60 GLN 5 61 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 150437 Z= 0.223 Angle : 0.636 13.658 225587 Z= 0.326 Chirality : 0.037 0.320 28933 Planarity : 0.005 0.096 11679 Dihedral : 23.655 179.683 76272 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.69 % Favored : 89.17 % Rotamer: Outliers : 5.58 % Allowed : 16.90 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.26 % Twisted Proline : 0.52 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.11), residues: 5097 helix: -0.42 (0.14), residues: 1329 sheet: -1.80 (0.16), residues: 949 loop : -2.82 (0.11), residues: 2819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP g 103 HIS 0.020 0.001 HIS C 142 PHE 0.030 0.002 PHE M 58 TYR 0.026 0.002 TYR C 62 ARG 0.009 0.001 ARG Z 29 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10194 Ramachandran restraints generated. 5097 Oldfield, 0 Emsley, 5097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10194 Ramachandran restraints generated. 5097 Oldfield, 0 Emsley, 5097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1136 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 893 time to evaluate : 5.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP 1 4 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 4 1 " (corrupted residue). Skipping it. REVERT: c 10 MET cc_start: 0.4913 (mmm) cc_final: 0.4679 (mmm) REVERT: c 92 LYS cc_start: 0.8329 (mttt) cc_final: 0.8042 (ptpt) REVERT: c 133 GLN cc_start: 0.8283 (mt0) cc_final: 0.7576 (tm-30) REVERT: d 41 ARG cc_start: 0.6780 (ptm160) cc_final: 0.4992 (mtm180) REVERT: d 50 GLN cc_start: 0.7674 (mt0) cc_final: 0.7360 (mt0) REVERT: d 88 MET cc_start: 0.9487 (mmt) cc_final: 0.9192 (mmm) REVERT: e 37 VAL cc_start: 0.9501 (t) cc_final: 0.9273 (p) REVERT: e 146 GLN cc_start: 0.9321 (tt0) cc_final: 0.8846 (tm-30) REVERT: f 6 LYS cc_start: 0.9387 (OUTLIER) cc_final: 0.9180 (pttp) REVERT: f 28 ARG cc_start: 0.9080 (ptm160) cc_final: 0.8763 (tmm-80) REVERT: f 42 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7106 (pp20) REVERT: g 56 ASN cc_start: 0.7719 (m-40) cc_final: 0.7338 (t0) REVERT: g 85 TYR cc_start: 0.5764 (m-80) cc_final: 0.5471 (m-80) REVERT: h 76 ASN cc_start: 0.8425 (t0) cc_final: 0.8199 (t0) REVERT: j 10 LEU cc_start: 0.7968 (mp) cc_final: 0.7171 (mt) REVERT: j 68 ARG cc_start: 0.5976 (mtt180) cc_final: 0.5461 (mtt-85) REVERT: j 98 ILE cc_start: 0.6060 (pt) cc_final: 0.5796 (mm) REVERT: k 14 LYS cc_start: 0.8137 (ttpt) cc_final: 0.7704 (ttpt) REVERT: k 15 ASN cc_start: 0.8431 (m-40) cc_final: 0.7915 (p0) REVERT: k 64 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8410 (pm20) REVERT: k 80 LYS cc_start: 0.9491 (OUTLIER) cc_final: 0.9290 (mtpt) REVERT: k 83 ASP cc_start: 0.8576 (m-30) cc_final: 0.8348 (m-30) REVERT: k 112 ASP cc_start: 0.7287 (t0) cc_final: 0.6982 (t0) REVERT: m 77 ILE cc_start: 0.8432 (pt) cc_final: 0.8205 (tp) REVERT: o 10 GLU cc_start: 0.8860 (pp20) cc_final: 0.8635 (pp20) REVERT: o 13 LYS cc_start: 0.9348 (mttt) cc_final: 0.8915 (mptt) REVERT: o 14 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8261 (tm-30) REVERT: p 65 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8096 (mp10) REVERT: p 68 ASP cc_start: 0.8836 (p0) cc_final: 0.8485 (p0) REVERT: p 74 LEU cc_start: 0.9327 (mp) cc_final: 0.9072 (mt) REVERT: q 14 ARG cc_start: 0.8717 (ptm-80) cc_final: 0.8446 (ttm110) REVERT: q 20 MET cc_start: 0.8459 (mmm) cc_final: 0.8142 (mmt) REVERT: q 25 THR cc_start: 0.8148 (m) cc_final: 0.7895 (p) REVERT: q 54 ASN cc_start: 0.8665 (OUTLIER) cc_final: 0.8337 (t0) REVERT: r 58 LYS cc_start: 0.9487 (mtpp) cc_final: 0.8954 (mmtt) REVERT: r 64 LYS cc_start: 0.8863 (mttt) cc_final: 0.8468 (mtpt) REVERT: s 36 ARG cc_start: 0.5707 (mmt180) cc_final: 0.5253 (tpp-160) REVERT: s 66 MET cc_start: 0.8324 (ttp) cc_final: 0.7439 (mmp) REVERT: t 18 ASN cc_start: 0.8590 (OUTLIER) cc_final: 0.8140 (t0) REVERT: t 70 LYS cc_start: 0.8734 (ttmt) cc_final: 0.8383 (ttmm) REVERT: C 20 ASP cc_start: 0.8007 (m-30) cc_final: 0.7783 (m-30) REVERT: C 84 ASP cc_start: 0.8186 (t0) cc_final: 0.7747 (t0) REVERT: C 87 ARG cc_start: 0.9196 (OUTLIER) cc_final: 0.8933 (ptp90) REVERT: C 225 MET cc_start: 0.8489 (mmt) cc_final: 0.8148 (mmt) REVERT: C 276 LYS cc_start: 0.7139 (mmmm) cc_final: 0.6727 (mmmm) REVERT: D 85 ASN cc_start: 0.8285 (t0) cc_final: 0.8056 (t0) REVERT: E 158 ASN cc_start: 0.8160 (m-40) cc_final: 0.7665 (p0) REVERT: E 161 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8315 (p0) REVERT: F 96 MET cc_start: 0.8411 (mmm) cc_final: 0.7895 (mmm) REVERT: F 97 TYR cc_start: 0.9315 (m-80) cc_final: 0.8926 (m-80) REVERT: F 99 PHE cc_start: 0.9539 (t80) cc_final: 0.9181 (t80) REVERT: F 152 MET cc_start: 0.8102 (mmm) cc_final: 0.7861 (mmm) REVERT: F 164 GLU cc_start: 0.9252 (pm20) cc_final: 0.9021 (pm20) REVERT: F 167 ARG cc_start: 0.8864 (ttm-80) cc_final: 0.8411 (ttm-80) REVERT: G 54 ARG cc_start: 0.7481 (ttm110) cc_final: 0.5677 (ttt180) REVERT: G 84 GLN cc_start: 0.7441 (pp30) cc_final: 0.7105 (pp30) REVERT: G 115 MET cc_start: 0.7616 (mmm) cc_final: 0.6957 (mmm) REVERT: K 1 MET cc_start: 0.6875 (OUTLIER) cc_final: 0.5761 (pmm) REVERT: K 72 ASP cc_start: 0.8784 (m-30) cc_final: 0.8450 (m-30) REVERT: L 5 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8179 (pt0) REVERT: L 31 LYS cc_start: 0.8873 (mttt) cc_final: 0.8467 (ptpt) REVERT: L 45 GLN cc_start: 0.8036 (mp10) cc_final: 0.7579 (mp10) REVERT: L 73 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8359 (p0) REVERT: L 120 GLU cc_start: 0.8754 (tp30) cc_final: 0.8505 (mt-10) REVERT: M 19 VAL cc_start: 0.9107 (OUTLIER) cc_final: 0.8858 (p) REVERT: N 106 ILE cc_start: 0.9365 (mt) cc_final: 0.9002 (mm) REVERT: O 57 HIS cc_start: 0.7919 (OUTLIER) cc_final: 0.7421 (t-90) REVERT: P 17 ARG cc_start: 0.8528 (mtt180) cc_final: 0.7775 (mtt90) REVERT: P 45 ILE cc_start: 0.8963 (mp) cc_final: 0.8571 (tp) REVERT: P 48 VAL cc_start: 0.8254 (OUTLIER) cc_final: 0.7979 (t) REVERT: Q 10 GLN cc_start: 0.7831 (mp10) cc_final: 0.7610 (mm-40) REVERT: Q 65 SER cc_start: 0.9213 (p) cc_final: 0.8047 (p) REVERT: Q 71 GLU cc_start: 0.8098 (mp0) cc_final: 0.7830 (mp0) REVERT: R 49 ASP cc_start: 0.8571 (m-30) cc_final: 0.8201 (m-30) REVERT: R 102 ASP cc_start: 0.8111 (t0) cc_final: 0.7591 (t0) REVERT: S 28 GLU cc_start: 0.7757 (mp0) cc_final: 0.7542 (mp0) REVERT: S 31 GLU cc_start: 0.8955 (mp0) cc_final: 0.8651 (mp0) REVERT: U 20 MET cc_start: 0.8616 (tpp) cc_final: 0.7880 (tmm) REVERT: U 30 ASP cc_start: 0.7635 (m-30) cc_final: 0.7319 (p0) REVERT: X 79 GLU cc_start: 0.7945 (tp30) cc_final: 0.7575 (tp30) REVERT: Y 17 ASN cc_start: 0.8400 (t0) cc_final: 0.7811 (t0) REVERT: Y 36 VAL cc_start: 0.8981 (OUTLIER) cc_final: 0.8742 (p) REVERT: Z 59 GLU cc_start: 0.8024 (pp20) cc_final: 0.7659 (tm-30) REVERT: Z 60 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7859 (mp10) REVERT: 0 9 LYS cc_start: 0.9242 (pttt) cc_final: 0.9006 (ptmm) REVERT: 0 10 ARG cc_start: 0.8695 (tpp80) cc_final: 0.8392 (tpp80) REVERT: 0 19 GLN cc_start: 0.9005 (mp10) cc_final: 0.8472 (mp10) REVERT: 3 24 ARG cc_start: 0.8677 (ttp80) cc_final: 0.8098 (ptt-90) REVERT: 4 36 ARG cc_start: 0.8224 (mtt180) cc_final: 0.7504 (ttm110) outliers start: 243 outliers final: 159 residues processed: 1026 average time/residue: 1.2701 time to fit residues: 2305.3900 Evaluate side-chains 987 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 812 time to evaluate : 5.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain d residue 64 ASN Chi-restraints excluded: chain d residue 120 ILE Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 135 ASN Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain f residue 6 LYS Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain f residue 42 GLU Chi-restraints excluded: chain f residue 69 THR Chi-restraints excluded: chain f residue 70 SER Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain g residue 140 ASP Chi-restraints excluded: chain h residue 70 GLU Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 27 LYS Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 96 SER Chi-restraints excluded: chain j residue 14 GLU Chi-restraints excluded: chain j residue 17 ILE Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain k residue 64 GLN Chi-restraints excluded: chain k residue 80 LYS Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 19 SER Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 60 SER Chi-restraints excluded: chain l residue 62 LEU Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain o residue 3 ILE Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 60 ILE Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 27 SER Chi-restraints excluded: chain p residue 57 LEU Chi-restraints excluded: chain p residue 65 GLN Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 54 ASN Chi-restraints excluded: chain q residue 78 LEU Chi-restraints excluded: chain r residue 37 ILE Chi-restraints excluded: chain r residue 68 ILE Chi-restraints excluded: chain r residue 69 MET Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain t residue 18 ASN Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 62 THR Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 119 PHE Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 172 GLN Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 80 ARG Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 116 GLU Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 39 GLU Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain O residue 46 LYS Chi-restraints excluded: chain O residue 57 HIS Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 29 HIS Chi-restraints excluded: chain R residue 54 LYS Chi-restraints excluded: chain R residue 97 ASP Chi-restraints excluded: chain R residue 115 ASP Chi-restraints excluded: chain S residue 2 TYR Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 81 HIS Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain S residue 88 HIS Chi-restraints excluded: chain T residue 36 ASP Chi-restraints excluded: chain T residue 44 THR Chi-restraints excluded: chain U residue 21 ASP Chi-restraints excluded: chain U residue 40 GLN Chi-restraints excluded: chain U residue 50 VAL Chi-restraints excluded: chain U residue 89 ILE Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain W residue 43 PHE Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 60 VAL Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Z residue 4 LYS Chi-restraints excluded: chain Z residue 5 GLU Chi-restraints excluded: chain Z residue 57 LEU Chi-restraints excluded: chain Z residue 60 GLN Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 46 LEU Chi-restraints excluded: chain 3 residue 3 VAL Chi-restraints excluded: chain 3 residue 48 THR Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 41 VAL Chi-restraints excluded: chain 4 residue 43 SER Chi-restraints excluded: chain 5 residue 31 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 765 optimal weight: 4.9990 chunk 521 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 684 optimal weight: 8.9990 chunk 379 optimal weight: 20.0000 chunk 784 optimal weight: 7.9990 chunk 635 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 469 optimal weight: 10.0000 chunk 825 optimal weight: 0.8980 chunk 231 optimal weight: 2.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 24 HIS ** o 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 65 GLN s 22 GLN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 ASN ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 GLN ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 131 HIS N 35 GLN N 123 HIS ** R 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 64 HIS Z 20 GLN 0 48 ASN ** 1 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 55 HIS ** 3 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 4 GLN 5 60 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 150437 Z= 0.240 Angle : 0.649 11.573 225587 Z= 0.332 Chirality : 0.037 0.320 28933 Planarity : 0.005 0.096 11679 Dihedral : 23.645 179.585 76272 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.26 % Favored : 87.60 % Rotamer: Outliers : 5.90 % Allowed : 17.63 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.26 % Twisted Proline : 0.52 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.11), residues: 5097 helix: -0.22 (0.14), residues: 1323 sheet: -1.78 (0.16), residues: 950 loop : -2.74 (0.11), residues: 2824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP g 103 HIS 0.018 0.001 HIS C 142 PHE 0.031 0.002 PHE M 58 TYR 0.026 0.002 TYR C 62 ARG 0.012 0.001 ARG Z 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10194 Ramachandran restraints generated. 5097 Oldfield, 0 Emsley, 5097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10194 Ramachandran restraints generated. 5097 Oldfield, 0 Emsley, 5097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1086 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 829 time to evaluate : 5.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP 1 4 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET 4 1 " (corrupted residue). Skipping it. REVERT: c 10 MET cc_start: 0.5410 (mmm) cc_final: 0.5128 (mmp) REVERT: c 92 LYS cc_start: 0.8327 (mttt) cc_final: 0.8024 (ptpt) REVERT: c 133 GLN cc_start: 0.8276 (mt0) cc_final: 0.7584 (tm-30) REVERT: d 41 ARG cc_start: 0.6885 (ptm160) cc_final: 0.5087 (mtm180) REVERT: d 60 MET cc_start: 0.8495 (tpt) cc_final: 0.8116 (mmt) REVERT: d 88 MET cc_start: 0.9519 (mmt) cc_final: 0.9203 (mmm) REVERT: e 37 VAL cc_start: 0.9507 (t) cc_final: 0.9287 (p) REVERT: e 81 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7960 (pt) REVERT: e 146 GLN cc_start: 0.9329 (tt0) cc_final: 0.8867 (tm-30) REVERT: f 6 LYS cc_start: 0.9343 (OUTLIER) cc_final: 0.9053 (pttp) REVERT: f 28 ARG cc_start: 0.9084 (ptm160) cc_final: 0.8800 (tmm-80) REVERT: f 42 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7180 (pp20) REVERT: f 69 THR cc_start: 0.9350 (OUTLIER) cc_final: 0.9007 (t) REVERT: g 56 ASN cc_start: 0.7881 (m-40) cc_final: 0.7371 (t0) REVERT: g 70 MET cc_start: 0.6496 (ppp) cc_final: 0.5090 (tmm) REVERT: g 85 TYR cc_start: 0.5724 (m-80) cc_final: 0.5442 (m-80) REVERT: h 76 ASN cc_start: 0.8402 (t0) cc_final: 0.8176 (t0) REVERT: j 10 LEU cc_start: 0.7839 (mp) cc_final: 0.7607 (mt) REVERT: j 68 ARG cc_start: 0.6091 (mtt180) cc_final: 0.5451 (mtt-85) REVERT: j 98 ILE cc_start: 0.6268 (pt) cc_final: 0.5916 (mm) REVERT: k 15 ASN cc_start: 0.8467 (m-40) cc_final: 0.7974 (p0) REVERT: k 64 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8454 (pm20) REVERT: k 80 LYS cc_start: 0.9375 (OUTLIER) cc_final: 0.9138 (mtpt) REVERT: k 83 ASP cc_start: 0.8573 (m-30) cc_final: 0.8315 (m-30) REVERT: m 77 ILE cc_start: 0.8429 (pt) cc_final: 0.8213 (tp) REVERT: o 13 LYS cc_start: 0.9365 (mttt) cc_final: 0.8950 (mptt) REVERT: o 14 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8358 (tm-30) REVERT: p 65 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8066 (mp10) REVERT: p 68 ASP cc_start: 0.8766 (p0) cc_final: 0.8407 (p0) REVERT: p 74 LEU cc_start: 0.9281 (mp) cc_final: 0.9033 (mt) REVERT: p 80 MET cc_start: 0.8705 (mmm) cc_final: 0.8201 (tpp) REVERT: q 14 ARG cc_start: 0.8678 (ptm-80) cc_final: 0.8465 (ttm110) REVERT: q 20 MET cc_start: 0.8651 (mmm) cc_final: 0.8353 (mmt) REVERT: q 25 THR cc_start: 0.8205 (m) cc_final: 0.7937 (p) REVERT: q 54 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8336 (t0) REVERT: q 83 GLU cc_start: 0.7474 (tm-30) cc_final: 0.7057 (tm-30) REVERT: r 24 TYR cc_start: 0.8371 (t80) cc_final: 0.8155 (t80) REVERT: r 64 LYS cc_start: 0.8858 (mttt) cc_final: 0.8146 (mtpt) REVERT: s 36 ARG cc_start: 0.5734 (mmt180) cc_final: 0.5464 (tpp-160) REVERT: s 66 MET cc_start: 0.8254 (ttp) cc_final: 0.7214 (mmp) REVERT: s 69 HIS cc_start: 0.6981 (p-80) cc_final: 0.6057 (p-80) REVERT: t 18 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.8117 (t0) REVERT: t 70 LYS cc_start: 0.8728 (ttmt) cc_final: 0.8466 (ttmm) REVERT: C 20 ASP cc_start: 0.8072 (m-30) cc_final: 0.7839 (m-30) REVERT: C 84 ASP cc_start: 0.8157 (t0) cc_final: 0.7680 (t70) REVERT: C 225 MET cc_start: 0.8531 (mmt) cc_final: 0.8045 (mmt) REVERT: C 276 LYS cc_start: 0.7259 (mmmm) cc_final: 0.6900 (mmmm) REVERT: D 142 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8633 (mtt-85) REVERT: E 149 ASP cc_start: 0.8857 (p0) cc_final: 0.8632 (p0) REVERT: E 161 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8195 (p0) REVERT: F 96 MET cc_start: 0.8399 (mmm) cc_final: 0.7900 (mmm) REVERT: F 97 TYR cc_start: 0.9328 (m-80) cc_final: 0.8942 (m-80) REVERT: F 99 PHE cc_start: 0.9511 (t80) cc_final: 0.9196 (t80) REVERT: F 152 MET cc_start: 0.8160 (mmm) cc_final: 0.7840 (mmm) REVERT: F 164 GLU cc_start: 0.9260 (pm20) cc_final: 0.8932 (pm20) REVERT: F 167 ARG cc_start: 0.8881 (ttm-80) cc_final: 0.8499 (ttm-80) REVERT: G 54 ARG cc_start: 0.7433 (ttm110) cc_final: 0.5647 (ttt180) REVERT: G 84 GLN cc_start: 0.7448 (pp30) cc_final: 0.7047 (pp30) REVERT: G 115 MET cc_start: 0.7529 (mmm) cc_final: 0.6926 (mmm) REVERT: K 1 MET cc_start: 0.6495 (OUTLIER) cc_final: 0.5314 (pmm) REVERT: K 72 ASP cc_start: 0.8788 (m-30) cc_final: 0.8476 (m-30) REVERT: K 103 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7648 (mp0) REVERT: L 31 LYS cc_start: 0.8877 (mttt) cc_final: 0.8469 (ptpt) REVERT: L 45 GLN cc_start: 0.8187 (mp10) cc_final: 0.7700 (mp10) REVERT: L 73 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8304 (p0) REVERT: L 105 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8938 (mm-30) REVERT: L 120 GLU cc_start: 0.8767 (tp30) cc_final: 0.8524 (mt-10) REVERT: M 19 VAL cc_start: 0.9126 (OUTLIER) cc_final: 0.8852 (p) REVERT: O 57 HIS cc_start: 0.7966 (OUTLIER) cc_final: 0.7341 (t-90) REVERT: P 17 ARG cc_start: 0.8539 (mtt180) cc_final: 0.7762 (mtt90) REVERT: P 34 PHE cc_start: 0.8626 (t80) cc_final: 0.7915 (t80) REVERT: P 45 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8553 (tp) REVERT: P 48 VAL cc_start: 0.8281 (OUTLIER) cc_final: 0.8012 (t) REVERT: Q 10 GLN cc_start: 0.7908 (mp10) cc_final: 0.7638 (mm-40) REVERT: Q 65 SER cc_start: 0.9209 (p) cc_final: 0.8053 (p) REVERT: Q 71 GLU cc_start: 0.8136 (mp0) cc_final: 0.7851 (mp0) REVERT: R 49 ASP cc_start: 0.8602 (m-30) cc_final: 0.8228 (m-30) REVERT: R 102 ASP cc_start: 0.8126 (t0) cc_final: 0.7543 (t0) REVERT: S 31 GLU cc_start: 0.8982 (mp0) cc_final: 0.8662 (mp0) REVERT: T 68 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7529 (t0) REVERT: T 114 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7930 (mt-10) REVERT: U 20 MET cc_start: 0.8588 (tpp) cc_final: 0.7874 (tmm) REVERT: U 30 ASP cc_start: 0.7618 (m-30) cc_final: 0.7267 (p0) REVERT: V 7 ASP cc_start: 0.8202 (p0) cc_final: 0.7615 (p0) REVERT: X 79 GLU cc_start: 0.7999 (tp30) cc_final: 0.7632 (tp30) REVERT: Y 17 ASN cc_start: 0.8463 (t0) cc_final: 0.7907 (t0) REVERT: Y 36 VAL cc_start: 0.9015 (OUTLIER) cc_final: 0.8780 (p) REVERT: Z 59 GLU cc_start: 0.8047 (pp20) cc_final: 0.7732 (tm-30) REVERT: Z 60 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7769 (mp10) REVERT: 0 19 GLN cc_start: 0.9046 (mp10) cc_final: 0.8485 (mp10) REVERT: 0 41 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7071 (tm-30) REVERT: 2 36 MET cc_start: 0.8329 (mmm) cc_final: 0.7941 (mmm) REVERT: 3 14 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7924 (mm-30) REVERT: 3 21 LYS cc_start: 0.8572 (ptmm) cc_final: 0.8294 (ptmm) REVERT: 3 31 GLU cc_start: 0.5822 (mm-30) cc_final: 0.5536 (mm-30) REVERT: 3 32 LYS cc_start: 0.7851 (mmtt) cc_final: 0.6815 (mmtt) REVERT: 3 47 GLU cc_start: 0.8652 (tt0) cc_final: 0.8412 (tt0) REVERT: 4 36 ARG cc_start: 0.8205 (mtt180) cc_final: 0.7528 (ttm110) REVERT: 5 49 MET cc_start: 0.8364 (mmm) cc_final: 0.8062 (mmm) outliers start: 257 outliers final: 196 residues processed: 961 average time/residue: 1.1480 time to fit residues: 1942.3307 Evaluate side-chains 1012 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 796 time to evaluate : 5.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain d residue 64 ASN Chi-restraints excluded: chain d residue 120 ILE Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 122 ASP Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 135 ASN Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain f residue 6 LYS Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain f residue 42 GLU Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 69 THR Chi-restraints excluded: chain f residue 70 SER Chi-restraints excluded: chain f residue 83 LEU Chi-restraints excluded: chain g residue 26 LEU Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain g residue 86 GLN Chi-restraints excluded: chain g residue 140 ASP Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 27 LYS Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 96 SER Chi-restraints excluded: chain j residue 14 GLU Chi-restraints excluded: chain j residue 17 ILE Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 64 GLN Chi-restraints excluded: chain k residue 80 LYS Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 19 SER Chi-restraints excluded: chain l residue 39 ASN Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 48 THR Chi-restraints excluded: chain l residue 60 SER Chi-restraints excluded: chain l residue 62 LEU Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain o residue 3 ILE Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 47 LYS Chi-restraints excluded: chain o residue 60 ILE Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 27 SER Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 57 LEU Chi-restraints excluded: chain p residue 65 GLN Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 30 THR Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 54 ASN Chi-restraints excluded: chain q residue 78 LEU Chi-restraints excluded: chain r residue 37 ILE Chi-restraints excluded: chain r residue 68 ILE Chi-restraints excluded: chain r residue 69 MET Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 18 ASN Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 62 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 119 PHE Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 172 GLN Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 196 GLN Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 80 ARG Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 113 ASN Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 116 GLU Chi-restraints excluded: chain N residue 123 HIS Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 39 GLU Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain O residue 57 HIS Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain Q residue 24 ASP Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 29 HIS Chi-restraints excluded: chain R residue 54 LYS Chi-restraints excluded: chain R residue 76 TYR Chi-restraints excluded: chain R residue 97 ASP Chi-restraints excluded: chain R residue 115 ASP Chi-restraints excluded: chain S residue 2 TYR Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 81 HIS Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain S residue 88 HIS Chi-restraints excluded: chain T residue 36 ASP Chi-restraints excluded: chain T residue 44 THR Chi-restraints excluded: chain T residue 67 PHE Chi-restraints excluded: chain T residue 68 ASP Chi-restraints excluded: chain U residue 21 ASP Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 40 GLN Chi-restraints excluded: chain U residue 89 ILE Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 57 LEU Chi-restraints excluded: chain V residue 64 HIS Chi-restraints excluded: chain W residue 43 PHE Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 60 VAL Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Z residue 4 LYS Chi-restraints excluded: chain Z residue 5 GLU Chi-restraints excluded: chain Z residue 60 GLN Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 23 PHE Chi-restraints excluded: chain 1 residue 46 LEU Chi-restraints excluded: chain 3 residue 48 THR Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 41 VAL Chi-restraints excluded: chain 4 residue 43 SER Chi-restraints excluded: chain 5 residue 58 ILE Chi-restraints excluded: chain 6 residue 7 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 309 optimal weight: 9.9990 chunk 827 optimal weight: 6.9990 chunk 181 optimal weight: 9.9990 chunk 539 optimal weight: 20.0000 chunk 226 optimal weight: 8.9990 chunk 920 optimal weight: 0.9990 chunk 763 optimal weight: 3.9990 chunk 426 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 304 optimal weight: 0.0970 chunk 483 optimal weight: 10.0000 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 24 HIS o 65 ASN s 22 GLN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 90 GLN V 64 HIS Z 20 GLN ** 1 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 4 ASN 3 20 ASN 5 4 GLN 5 60 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 150437 Z= 0.202 Angle : 0.615 11.907 225587 Z= 0.315 Chirality : 0.036 0.318 28933 Planarity : 0.005 0.094 11679 Dihedral : 23.588 179.842 76272 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.61 % Favored : 89.25 % Rotamer: Outliers : 5.81 % Allowed : 19.17 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.26 % Twisted Proline : 0.52 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.11), residues: 5097 helix: -0.06 (0.14), residues: 1328 sheet: -1.70 (0.16), residues: 950 loop : -2.62 (0.11), residues: 2819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP g 103 HIS 0.018 0.001 HIS N 123 PHE 0.032 0.002 PHE M 58 TYR 0.041 0.002 TYR N 74 ARG 0.013 0.001 ARG j 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10194 Ramachandran restraints generated. 5097 Oldfield, 0 Emsley, 5097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10194 Ramachandran restraints generated. 5097 Oldfield, 0 Emsley, 5097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1101 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 848 time to evaluate : 5.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP 1 4 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 4 1 " (corrupted residue). Skipping it. REVERT: c 92 LYS cc_start: 0.8166 (mttt) cc_final: 0.7849 (ptpt) REVERT: c 133 GLN cc_start: 0.8237 (mt0) cc_final: 0.7552 (tm-30) REVERT: d 41 ARG cc_start: 0.6908 (ptm160) cc_final: 0.5047 (mtm180) REVERT: d 50 GLN cc_start: 0.7644 (mt0) cc_final: 0.7421 (mt0) REVERT: d 88 MET cc_start: 0.9488 (mmt) cc_final: 0.9163 (mmm) REVERT: e 37 VAL cc_start: 0.9499 (t) cc_final: 0.9277 (p) REVERT: e 81 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7911 (pt) REVERT: e 146 GLN cc_start: 0.9338 (tt0) cc_final: 0.8921 (tm-30) REVERT: f 6 LYS cc_start: 0.9330 (OUTLIER) cc_final: 0.9096 (pttp) REVERT: f 28 ARG cc_start: 0.9064 (ptm160) cc_final: 0.8767 (tmm-80) REVERT: f 42 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7329 (pp20) REVERT: f 69 THR cc_start: 0.9384 (OUTLIER) cc_final: 0.9015 (t) REVERT: g 56 ASN cc_start: 0.8075 (m-40) cc_final: 0.7581 (t0) REVERT: g 70 MET cc_start: 0.6285 (ppp) cc_final: 0.4692 (tmm) REVERT: g 85 TYR cc_start: 0.5784 (m-80) cc_final: 0.5555 (m-80) REVERT: h 76 ASN cc_start: 0.8354 (t0) cc_final: 0.8146 (t0) REVERT: j 68 ARG cc_start: 0.6052 (mtt180) cc_final: 0.5434 (mtt-85) REVERT: j 98 ILE cc_start: 0.6208 (pt) cc_final: 0.5901 (mm) REVERT: k 15 ASN cc_start: 0.8345 (m-40) cc_final: 0.7842 (p0) REVERT: k 83 ASP cc_start: 0.8513 (m-30) cc_final: 0.8311 (m-30) REVERT: m 78 LYS cc_start: 0.7633 (tppt) cc_final: 0.7405 (mmtm) REVERT: o 13 LYS cc_start: 0.9372 (mttt) cc_final: 0.8944 (mptt) REVERT: o 14 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8373 (tm-30) REVERT: p 65 GLN cc_start: 0.8381 (mp10) cc_final: 0.8039 (mp10) REVERT: p 68 ASP cc_start: 0.8706 (p0) cc_final: 0.8342 (p0) REVERT: p 74 LEU cc_start: 0.9307 (mp) cc_final: 0.9063 (mt) REVERT: p 80 MET cc_start: 0.8736 (mmm) cc_final: 0.8251 (tpp) REVERT: q 25 THR cc_start: 0.8248 (m) cc_final: 0.7961 (p) REVERT: q 54 ASN cc_start: 0.8624 (OUTLIER) cc_final: 0.8332 (t0) REVERT: r 36 PHE cc_start: 0.8822 (m-80) cc_final: 0.8514 (m-80) REVERT: r 64 LYS cc_start: 0.8846 (mttt) cc_final: 0.8009 (mtpt) REVERT: r 72 LEU cc_start: 0.8641 (tp) cc_final: 0.8117 (tt) REVERT: s 36 ARG cc_start: 0.5682 (mmt180) cc_final: 0.5473 (tpp-160) REVERT: s 66 MET cc_start: 0.8241 (ttp) cc_final: 0.7388 (mmp) REVERT: s 69 HIS cc_start: 0.6950 (p-80) cc_final: 0.6173 (p-80) REVERT: t 18 ASN cc_start: 0.8453 (OUTLIER) cc_final: 0.7930 (t0) REVERT: t 70 LYS cc_start: 0.8703 (ttmt) cc_final: 0.8395 (ttmm) REVERT: C 20 ASP cc_start: 0.7993 (m-30) cc_final: 0.7768 (m-30) REVERT: C 225 MET cc_start: 0.8513 (mmt) cc_final: 0.8011 (mmt) REVERT: C 276 LYS cc_start: 0.7112 (mmmm) cc_final: 0.6779 (mmmm) REVERT: D 85 ASN cc_start: 0.8042 (t0) cc_final: 0.7825 (p0) REVERT: D 142 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8602 (mtt-85) REVERT: D 191 ASN cc_start: 0.8623 (OUTLIER) cc_final: 0.8312 (m-40) REVERT: E 149 ASP cc_start: 0.8923 (p0) cc_final: 0.8704 (p0) REVERT: E 158 ASN cc_start: 0.8202 (m-40) cc_final: 0.7516 (p0) REVERT: E 161 ASP cc_start: 0.8630 (OUTLIER) cc_final: 0.8274 (p0) REVERT: F 96 MET cc_start: 0.8349 (mmm) cc_final: 0.7896 (mmm) REVERT: F 97 TYR cc_start: 0.9330 (m-80) cc_final: 0.8951 (m-80) REVERT: F 99 PHE cc_start: 0.9493 (t80) cc_final: 0.9134 (t80) REVERT: F 152 MET cc_start: 0.8067 (mmm) cc_final: 0.7801 (mmm) REVERT: F 164 GLU cc_start: 0.9268 (pm20) cc_final: 0.9065 (pm20) REVERT: G 54 ARG cc_start: 0.7183 (ttm110) cc_final: 0.5776 (ttt180) REVERT: G 84 GLN cc_start: 0.7407 (pp30) cc_final: 0.6967 (pp30) REVERT: K 1 MET cc_start: 0.6361 (OUTLIER) cc_final: 0.5429 (pmm) REVERT: K 72 ASP cc_start: 0.8749 (m-30) cc_final: 0.8451 (m-30) REVERT: K 103 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7655 (mp0) REVERT: L 5 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8206 (pt0) REVERT: L 31 LYS cc_start: 0.8884 (mttt) cc_final: 0.8455 (ptpt) REVERT: L 45 GLN cc_start: 0.8141 (mp10) cc_final: 0.7619 (mp10) REVERT: L 73 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.8173 (p0) REVERT: L 105 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8950 (mm-30) REVERT: L 120 GLU cc_start: 0.8726 (tp30) cc_final: 0.8434 (mt-10) REVERT: M 19 VAL cc_start: 0.9108 (OUTLIER) cc_final: 0.8844 (p) REVERT: M 144 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: N 35 GLN cc_start: 0.8796 (tt0) cc_final: 0.8245 (tp-100) REVERT: N 51 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8587 (ttp80) REVERT: O 57 HIS cc_start: 0.7862 (OUTLIER) cc_final: 0.7382 (t-90) REVERT: P 17 ARG cc_start: 0.8544 (mtt180) cc_final: 0.7912 (mtt90) REVERT: P 48 VAL cc_start: 0.8239 (OUTLIER) cc_final: 0.7963 (t) REVERT: P 117 GLU cc_start: 0.9317 (mt-10) cc_final: 0.8974 (mt-10) REVERT: Q 10 GLN cc_start: 0.8024 (mp10) cc_final: 0.7712 (mm-40) REVERT: Q 44 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8517 (mm-30) REVERT: Q 65 SER cc_start: 0.9192 (p) cc_final: 0.7915 (p) REVERT: R 49 ASP cc_start: 0.8595 (m-30) cc_final: 0.8181 (m-30) REVERT: R 102 ASP cc_start: 0.8072 (t0) cc_final: 0.7482 (t0) REVERT: S 31 GLU cc_start: 0.8969 (mp0) cc_final: 0.8653 (mp0) REVERT: T 68 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.7572 (t0) REVERT: T 114 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7868 (mt-10) REVERT: U 20 MET cc_start: 0.8571 (tpp) cc_final: 0.7861 (tmm) REVERT: U 30 ASP cc_start: 0.7626 (m-30) cc_final: 0.7301 (p0) REVERT: V 7 ASP cc_start: 0.8278 (p0) cc_final: 0.7553 (p0) REVERT: X 79 GLU cc_start: 0.8145 (tp30) cc_final: 0.7865 (tp30) REVERT: Y 17 ASN cc_start: 0.8475 (t0) cc_final: 0.7805 (t0) REVERT: Y 36 VAL cc_start: 0.8974 (OUTLIER) cc_final: 0.8740 (p) REVERT: 0 9 LYS cc_start: 0.9256 (pttt) cc_final: 0.9050 (ptmm) REVERT: 0 41 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7212 (tm-30) REVERT: 2 36 MET cc_start: 0.8320 (mmm) cc_final: 0.7766 (mmm) REVERT: 3 21 LYS cc_start: 0.8677 (ptmm) cc_final: 0.7893 (ptmm) REVERT: 3 31 GLU cc_start: 0.5860 (mm-30) cc_final: 0.5631 (mm-30) REVERT: 3 32 LYS cc_start: 0.7923 (mmtt) cc_final: 0.6883 (mmtt) REVERT: 4 36 ARG cc_start: 0.8189 (mtt180) cc_final: 0.7540 (ttm110) REVERT: 5 49 MET cc_start: 0.8329 (mmm) cc_final: 0.8016 (mmm) outliers start: 253 outliers final: 186 residues processed: 984 average time/residue: 1.2792 time to fit residues: 2232.4535 Evaluate side-chains 1001 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 797 time to evaluate : 5.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain d residue 64 ASN Chi-restraints excluded: chain d residue 120 ILE Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 135 ASN Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain f residue 6 LYS Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain f residue 42 GLU Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 69 THR Chi-restraints excluded: chain f residue 70 SER Chi-restraints excluded: chain f residue 83 LEU Chi-restraints excluded: chain g residue 26 LEU Chi-restraints excluded: chain g residue 27 ILE Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain g residue 86 GLN Chi-restraints excluded: chain g residue 140 ASP Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 27 LYS Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 96 SER Chi-restraints excluded: chain j residue 14 GLU Chi-restraints excluded: chain j residue 17 ILE Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain k residue 80 LYS Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 39 ASN Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 48 THR Chi-restraints excluded: chain l residue 60 SER Chi-restraints excluded: chain l residue 62 LEU Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain m residue 21 TYR Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain n residue 7 ILE Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 47 LYS Chi-restraints excluded: chain o residue 60 ILE Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 27 SER Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 57 LEU Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 54 ASN Chi-restraints excluded: chain q residue 78 LEU Chi-restraints excluded: chain r residue 37 ILE Chi-restraints excluded: chain r residue 68 ILE Chi-restraints excluded: chain r residue 69 MET Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain s residue 41 PHE Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 18 ASN Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 62 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 119 PHE Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 172 GLN Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 80 ARG Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 113 ASN Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 51 ARG Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 39 GLU Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain O residue 57 HIS Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 24 ASP Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain R residue 29 HIS Chi-restraints excluded: chain R residue 54 LYS Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 76 TYR Chi-restraints excluded: chain R residue 97 ASP Chi-restraints excluded: chain R residue 115 ASP Chi-restraints excluded: chain S residue 2 TYR Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 81 HIS Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain S residue 88 HIS Chi-restraints excluded: chain T residue 36 ASP Chi-restraints excluded: chain T residue 44 THR Chi-restraints excluded: chain T residue 67 PHE Chi-restraints excluded: chain T residue 68 ASP Chi-restraints excluded: chain U residue 21 ASP Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 40 GLN Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain W residue 43 PHE Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 60 VAL Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Z residue 4 LYS Chi-restraints excluded: chain Z residue 5 GLU Chi-restraints excluded: chain Z residue 30 PHE Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 22 LYS Chi-restraints excluded: chain 1 residue 23 PHE Chi-restraints excluded: chain 1 residue 46 LEU Chi-restraints excluded: chain 3 residue 3 VAL Chi-restraints excluded: chain 3 residue 23 LYS Chi-restraints excluded: chain 3 residue 48 THR Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 41 VAL Chi-restraints excluded: chain 4 residue 43 SER Chi-restraints excluded: chain 5 residue 58 ILE Chi-restraints excluded: chain 6 residue 7 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 887 optimal weight: 5.9990 chunk 103 optimal weight: 40.0000 chunk 524 optimal weight: 10.0000 chunk 671 optimal weight: 9.9990 chunk 520 optimal weight: 10.0000 chunk 774 optimal weight: 0.8980 chunk 513 optimal weight: 10.0000 chunk 916 optimal weight: 0.8980 chunk 573 optimal weight: 10.0000 chunk 558 optimal weight: 20.0000 chunk 423 optimal weight: 10.0000 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 8 HIS ** f 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 142 HIS ** j 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 131 HIS N 123 HIS ** R 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 20 ASN 5 4 GLN 6 35 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 150437 Z= 0.252 Angle : 0.654 13.532 225587 Z= 0.333 Chirality : 0.037 0.329 28933 Planarity : 0.005 0.095 11679 Dihedral : 23.599 179.776 76272 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.54 % Favored : 87.33 % Rotamer: Outliers : 6.04 % Allowed : 19.70 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.26 % Twisted Proline : 0.52 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.11), residues: 5097 helix: -0.08 (0.14), residues: 1336 sheet: -1.75 (0.16), residues: 966 loop : -2.69 (0.11), residues: 2795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP g 103 HIS 0.018 0.001 HIS C 142 PHE 0.033 0.002 PHE M 58 TYR 0.025 0.002 TYR C 62 ARG 0.010 0.001 ARG j 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10194 Ramachandran restraints generated. 5097 Oldfield, 0 Emsley, 5097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10194 Ramachandran restraints generated. 5097 Oldfield, 0 Emsley, 5097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1067 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 804 time to evaluate : 5.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP 1 4 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 4 1 " (corrupted residue). Skipping it. REVERT: c 10 MET cc_start: 0.5075 (mmm) cc_final: 0.4653 (mmp) REVERT: c 62 ARG cc_start: 0.7047 (mtm110) cc_final: 0.6773 (mtt-85) REVERT: c 92 LYS cc_start: 0.8198 (mttt) cc_final: 0.7879 (ptpt) REVERT: c 133 GLN cc_start: 0.8196 (mt0) cc_final: 0.7456 (tm-30) REVERT: d 41 ARG cc_start: 0.6952 (ptm160) cc_final: 0.5048 (mtm180) REVERT: d 50 GLN cc_start: 0.7880 (mt0) cc_final: 0.7644 (mt0) REVERT: d 60 MET cc_start: 0.8516 (tpt) cc_final: 0.8136 (mmt) REVERT: d 88 MET cc_start: 0.9516 (mmt) cc_final: 0.9180 (mmm) REVERT: e 37 VAL cc_start: 0.9523 (t) cc_final: 0.9306 (p) REVERT: e 81 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7968 (pt) REVERT: e 146 GLN cc_start: 0.9325 (tt0) cc_final: 0.8920 (tm-30) REVERT: f 6 LYS cc_start: 0.9354 (OUTLIER) cc_final: 0.9123 (pttp) REVERT: f 22 LYS cc_start: 0.8862 (ptmt) cc_final: 0.8652 (ptmm) REVERT: f 28 ARG cc_start: 0.9085 (ptm160) cc_final: 0.8739 (tmm-80) REVERT: f 42 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7462 (pp20) REVERT: f 69 THR cc_start: 0.9360 (OUTLIER) cc_final: 0.8984 (t) REVERT: g 56 ASN cc_start: 0.8170 (m-40) cc_final: 0.7692 (t0) REVERT: g 70 MET cc_start: 0.6395 (ppp) cc_final: 0.4813 (tmm) REVERT: g 85 TYR cc_start: 0.5817 (m-80) cc_final: 0.5586 (m-80) REVERT: g 144 MET cc_start: 0.6219 (tmm) cc_final: 0.6018 (tmm) REVERT: h 12 THR cc_start: 0.9050 (p) cc_final: 0.8721 (t) REVERT: j 30 LYS cc_start: 0.7366 (ptmm) cc_final: 0.7158 (ptmm) REVERT: j 68 ARG cc_start: 0.6034 (mtt180) cc_final: 0.5377 (mtt-85) REVERT: j 98 ILE cc_start: 0.6266 (pt) cc_final: 0.5954 (mm) REVERT: k 15 ASN cc_start: 0.8402 (m-40) cc_final: 0.7928 (p0) REVERT: k 23 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8833 (tp) REVERT: k 83 ASP cc_start: 0.8501 (m-30) cc_final: 0.8263 (m-30) REVERT: m 77 ILE cc_start: 0.8413 (pt) cc_final: 0.8213 (tp) REVERT: o 13 LYS cc_start: 0.9377 (mttt) cc_final: 0.8963 (mptt) REVERT: o 14 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8389 (tm-30) REVERT: p 65 GLN cc_start: 0.8305 (mp10) cc_final: 0.7989 (mp10) REVERT: p 68 ASP cc_start: 0.8748 (p0) cc_final: 0.8418 (p0) REVERT: p 74 LEU cc_start: 0.9308 (mp) cc_final: 0.9065 (mt) REVERT: p 80 MET cc_start: 0.8737 (mmm) cc_final: 0.8305 (tpp) REVERT: q 25 THR cc_start: 0.8259 (m) cc_final: 0.7942 (p) REVERT: q 54 ASN cc_start: 0.8663 (OUTLIER) cc_final: 0.8400 (t0) REVERT: r 36 PHE cc_start: 0.8831 (m-80) cc_final: 0.8531 (m-80) REVERT: r 64 LYS cc_start: 0.8849 (mttt) cc_final: 0.8157 (mtpt) REVERT: r 72 LEU cc_start: 0.8670 (tp) cc_final: 0.8141 (tt) REVERT: s 66 MET cc_start: 0.8273 (ttp) cc_final: 0.7369 (mmp) REVERT: s 69 HIS cc_start: 0.6993 (p-80) cc_final: 0.5940 (p-80) REVERT: t 18 ASN cc_start: 0.8401 (OUTLIER) cc_final: 0.8040 (t0) REVERT: t 70 LYS cc_start: 0.8742 (ttmt) cc_final: 0.8438 (ttmm) REVERT: C 20 ASP cc_start: 0.8024 (m-30) cc_final: 0.7794 (m-30) REVERT: C 225 MET cc_start: 0.8562 (mmt) cc_final: 0.7959 (mmt) REVERT: C 276 LYS cc_start: 0.7324 (mmmm) cc_final: 0.6997 (mmmm) REVERT: D 142 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8654 (mtt-85) REVERT: D 191 ASN cc_start: 0.8645 (OUTLIER) cc_final: 0.8335 (m-40) REVERT: E 158 ASN cc_start: 0.8226 (m-40) cc_final: 0.7571 (p0) REVERT: E 161 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8277 (p0) REVERT: F 96 MET cc_start: 0.8346 (mmm) cc_final: 0.7877 (mmm) REVERT: F 97 TYR cc_start: 0.9346 (m-80) cc_final: 0.8976 (m-80) REVERT: F 99 PHE cc_start: 0.9482 (t80) cc_final: 0.9134 (t80) REVERT: F 152 MET cc_start: 0.8101 (mmm) cc_final: 0.7889 (mmt) REVERT: G 54 ARG cc_start: 0.7076 (ttm110) cc_final: 0.5575 (ttt180) REVERT: G 84 GLN cc_start: 0.7447 (pp30) cc_final: 0.6951 (pp30) REVERT: G 115 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6883 (mmm) REVERT: K 1 MET cc_start: 0.6495 (OUTLIER) cc_final: 0.5676 (pmm) REVERT: K 72 ASP cc_start: 0.8776 (m-30) cc_final: 0.8506 (m-30) REVERT: K 103 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7669 (mp0) REVERT: L 5 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8118 (pt0) REVERT: L 31 LYS cc_start: 0.8847 (mttt) cc_final: 0.8436 (ptpt) REVERT: L 45 GLN cc_start: 0.8202 (mp10) cc_final: 0.7686 (mp10) REVERT: L 73 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8188 (p0) REVERT: L 105 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8945 (mm-30) REVERT: M 19 VAL cc_start: 0.9130 (OUTLIER) cc_final: 0.8846 (p) REVERT: M 144 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: N 51 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8527 (ttp80) REVERT: O 57 HIS cc_start: 0.7914 (OUTLIER) cc_final: 0.7393 (t-90) REVERT: P 17 ARG cc_start: 0.8598 (mtt180) cc_final: 0.7944 (mtt90) REVERT: P 34 PHE cc_start: 0.8619 (t80) cc_final: 0.7892 (t80) REVERT: P 48 VAL cc_start: 0.8171 (OUTLIER) cc_final: 0.7905 (t) REVERT: P 117 GLU cc_start: 0.9339 (mt-10) cc_final: 0.8979 (mt-10) REVERT: Q 10 GLN cc_start: 0.8214 (mp10) cc_final: 0.7898 (mm-40) REVERT: Q 44 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8472 (mm-30) REVERT: Q 65 SER cc_start: 0.9190 (p) cc_final: 0.7982 (p) REVERT: R 49 ASP cc_start: 0.8616 (m-30) cc_final: 0.8180 (m-30) REVERT: R 102 ASP cc_start: 0.8157 (t0) cc_final: 0.7553 (t0) REVERT: S 31 GLU cc_start: 0.8977 (mp0) cc_final: 0.8651 (mp0) REVERT: T 114 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7940 (mt-10) REVERT: U 20 MET cc_start: 0.8564 (tpp) cc_final: 0.7800 (tmm) REVERT: U 30 ASP cc_start: 0.7611 (m-30) cc_final: 0.7246 (p0) REVERT: U 85 ASP cc_start: 0.7045 (OUTLIER) cc_final: 0.6772 (t0) REVERT: Y 17 ASN cc_start: 0.8434 (t0) cc_final: 0.7849 (t0) REVERT: Y 36 VAL cc_start: 0.8972 (OUTLIER) cc_final: 0.8732 (p) REVERT: Z 45 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7957 (pm20) REVERT: 0 9 LYS cc_start: 0.9220 (pttt) cc_final: 0.9000 (ptmm) REVERT: 0 41 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7274 (tm-30) REVERT: 2 36 MET cc_start: 0.8374 (mmm) cc_final: 0.7862 (mmm) REVERT: 3 21 LYS cc_start: 0.8767 (ptmm) cc_final: 0.7970 (ptmm) REVERT: 5 49 MET cc_start: 0.8413 (mmm) cc_final: 0.8068 (mmm) outliers start: 263 outliers final: 214 residues processed: 949 average time/residue: 1.1355 time to fit residues: 1894.9375 Evaluate side-chains 1007 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 772 time to evaluate : 5.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain d residue 64 ASN Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 120 ILE Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 135 ASN Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain f residue 6 LYS Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain f residue 42 GLU Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 69 THR Chi-restraints excluded: chain f residue 70 SER Chi-restraints excluded: chain f residue 83 LEU Chi-restraints excluded: chain g residue 26 LEU Chi-restraints excluded: chain g residue 27 ILE Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain g residue 86 GLN Chi-restraints excluded: chain g residue 140 ASP Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 27 LYS Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 96 SER Chi-restraints excluded: chain j residue 14 GLU Chi-restraints excluded: chain j residue 17 ILE Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain k residue 23 ILE Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 42 LEU Chi-restraints excluded: chain k residue 80 LYS Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 19 SER Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 39 ASN Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 48 THR Chi-restraints excluded: chain l residue 60 SER Chi-restraints excluded: chain l residue 62 LEU Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain n residue 7 ILE Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 47 LYS Chi-restraints excluded: chain o residue 60 ILE Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 27 SER Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 57 LEU Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain q residue 14 ARG Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 54 ASN Chi-restraints excluded: chain q residue 78 LEU Chi-restraints excluded: chain r residue 37 ILE Chi-restraints excluded: chain r residue 68 ILE Chi-restraints excluded: chain r residue 69 MET Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain s residue 41 PHE Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 18 ASN Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 62 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 119 PHE Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 172 GLN Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 80 ARG Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 113 ASN Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 51 ARG Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 116 GLU Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 39 GLU Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain O residue 46 LYS Chi-restraints excluded: chain O residue 57 HIS Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 37 ASN Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain Q residue 24 ASP Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 29 HIS Chi-restraints excluded: chain R residue 54 LYS Chi-restraints excluded: chain R residue 76 TYR Chi-restraints excluded: chain R residue 97 ASP Chi-restraints excluded: chain R residue 115 ASP Chi-restraints excluded: chain S residue 2 TYR Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 81 HIS Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain S residue 88 HIS Chi-restraints excluded: chain T residue 36 ASP Chi-restraints excluded: chain T residue 44 THR Chi-restraints excluded: chain T residue 67 PHE Chi-restraints excluded: chain U residue 5 ASP Chi-restraints excluded: chain U residue 21 ASP Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 40 GLN Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain W residue 43 PHE Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 60 VAL Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Z residue 4 LYS Chi-restraints excluded: chain Z residue 5 GLU Chi-restraints excluded: chain Z residue 30 PHE Chi-restraints excluded: chain Z residue 45 GLU Chi-restraints excluded: chain Z residue 57 LEU Chi-restraints excluded: chain 0 residue 58 GLU Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 22 LYS Chi-restraints excluded: chain 1 residue 23 PHE Chi-restraints excluded: chain 1 residue 46 LEU Chi-restraints excluded: chain 3 residue 23 LYS Chi-restraints excluded: chain 3 residue 48 THR Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 41 VAL Chi-restraints excluded: chain 4 residue 43 SER Chi-restraints excluded: chain 5 residue 58 ILE Chi-restraints excluded: chain 6 residue 7 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 567 optimal weight: 50.0000 chunk 366 optimal weight: 20.0000 chunk 547 optimal weight: 10.0000 chunk 276 optimal weight: 0.0970 chunk 180 optimal weight: 9.9990 chunk 177 optimal weight: 8.9990 chunk 582 optimal weight: 20.0000 chunk 624 optimal weight: 10.0000 chunk 453 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 720 optimal weight: 0.0980 overall best weight: 5.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 8 HIS ** j 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 HIS ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 GLN ** G 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 131 HIS N 123 HIS Q 66 ASN R 38 GLN ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 20 ASN 5 4 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 150437 Z= 0.263 Angle : 0.668 15.260 225587 Z= 0.340 Chirality : 0.038 0.346 28933 Planarity : 0.005 0.095 11679 Dihedral : 23.619 179.559 76272 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.40 % Favored : 87.46 % Rotamer: Outliers : 5.92 % Allowed : 19.93 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.26 % Twisted Proline : 0.52 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.11), residues: 5097 helix: -0.10 (0.14), residues: 1348 sheet: -1.80 (0.16), residues: 961 loop : -2.74 (0.11), residues: 2788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP g 103 HIS 0.018 0.001 HIS C 142 PHE 0.034 0.002 PHE M 58 TYR 0.024 0.002 TYR C 62 ARG 0.014 0.001 ARG j 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10194 Ramachandran restraints generated. 5097 Oldfield, 0 Emsley, 5097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10194 Ramachandran restraints generated. 5097 Oldfield, 0 Emsley, 5097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1063 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 805 time to evaluate : 5.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP 1 4 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 4 1 " (corrupted residue). Skipping it. REVERT: c 10 MET cc_start: 0.4922 (mmm) cc_final: 0.4407 (mmm) REVERT: c 30 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8298 (tm-30) REVERT: c 62 ARG cc_start: 0.7045 (mtm110) cc_final: 0.6773 (mtt-85) REVERT: c 92 LYS cc_start: 0.8168 (mttt) cc_final: 0.7941 (pttp) REVERT: c 133 GLN cc_start: 0.8168 (mt0) cc_final: 0.7479 (tm-30) REVERT: d 41 ARG cc_start: 0.6999 (ptm160) cc_final: 0.5011 (mtm180) REVERT: d 50 GLN cc_start: 0.7829 (mt0) cc_final: 0.7594 (mt0) REVERT: d 88 MET cc_start: 0.9515 (mmt) cc_final: 0.9178 (mmm) REVERT: e 22 THR cc_start: 0.6252 (p) cc_final: 0.5581 (t) REVERT: e 37 VAL cc_start: 0.9540 (t) cc_final: 0.9325 (p) REVERT: e 81 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.8034 (pt) REVERT: e 146 GLN cc_start: 0.9304 (tt0) cc_final: 0.8903 (tm-30) REVERT: f 22 LYS cc_start: 0.8833 (ptmt) cc_final: 0.8580 (ptmm) REVERT: f 28 ARG cc_start: 0.9109 (ptm160) cc_final: 0.8766 (tmm-80) REVERT: f 42 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7401 (pp20) REVERT: g 70 MET cc_start: 0.6301 (ppp) cc_final: 0.4797 (tmm) REVERT: g 85 TYR cc_start: 0.5805 (m-80) cc_final: 0.5598 (m-80) REVERT: h 12 THR cc_start: 0.9057 (p) cc_final: 0.8746 (t) REVERT: j 30 LYS cc_start: 0.7419 (ptmm) cc_final: 0.7211 (ptmm) REVERT: j 68 ARG cc_start: 0.6010 (mtt180) cc_final: 0.5226 (mtt-85) REVERT: j 98 ILE cc_start: 0.6155 (pt) cc_final: 0.5741 (mm) REVERT: k 15 ASN cc_start: 0.8421 (m-40) cc_final: 0.7962 (p0) REVERT: k 23 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8842 (tp) REVERT: k 83 ASP cc_start: 0.8511 (m-30) cc_final: 0.8265 (m-30) REVERT: m 78 LYS cc_start: 0.7626 (tppt) cc_final: 0.7401 (mmtm) REVERT: m 105 ASN cc_start: 0.5926 (p0) cc_final: 0.5689 (p0) REVERT: o 13 LYS cc_start: 0.9387 (mttt) cc_final: 0.8984 (mptt) REVERT: o 14 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8440 (tm-30) REVERT: p 65 GLN cc_start: 0.8333 (mp10) cc_final: 0.7989 (mp10) REVERT: p 68 ASP cc_start: 0.8758 (p0) cc_final: 0.8401 (p0) REVERT: p 74 LEU cc_start: 0.9325 (mp) cc_final: 0.9081 (mt) REVERT: p 80 MET cc_start: 0.8729 (mmm) cc_final: 0.8297 (tpp) REVERT: q 25 THR cc_start: 0.8218 (m) cc_final: 0.7893 (p) REVERT: q 54 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8439 (t0) REVERT: r 64 LYS cc_start: 0.8856 (mttt) cc_final: 0.8017 (mtpt) REVERT: r 72 LEU cc_start: 0.8730 (tp) cc_final: 0.8241 (tt) REVERT: s 66 MET cc_start: 0.8250 (ttp) cc_final: 0.7272 (mmp) REVERT: s 69 HIS cc_start: 0.7041 (p-80) cc_final: 0.6138 (p-80) REVERT: t 52 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8320 (tp30) REVERT: t 70 LYS cc_start: 0.8756 (ttmt) cc_final: 0.8451 (ttmm) REVERT: C 20 ASP cc_start: 0.8099 (m-30) cc_final: 0.7879 (m-30) REVERT: C 225 MET cc_start: 0.8585 (mmt) cc_final: 0.7933 (mmt) REVERT: C 276 LYS cc_start: 0.7388 (mmmm) cc_final: 0.7082 (mmmm) REVERT: D 142 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8734 (mtt-85) REVERT: D 191 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.8309 (m-40) REVERT: E 158 ASN cc_start: 0.8315 (m-40) cc_final: 0.7627 (p0) REVERT: E 161 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8326 (p0) REVERT: F 96 MET cc_start: 0.8339 (mmm) cc_final: 0.7842 (mmm) REVERT: F 97 TYR cc_start: 0.9339 (m-80) cc_final: 0.9012 (m-80) REVERT: F 99 PHE cc_start: 0.9494 (t80) cc_final: 0.9152 (t80) REVERT: F 167 ARG cc_start: 0.8983 (ttm-80) cc_final: 0.8542 (ttm-80) REVERT: G 54 ARG cc_start: 0.7077 (ttm110) cc_final: 0.5684 (ttt180) REVERT: G 84 GLN cc_start: 0.7351 (pp30) cc_final: 0.6815 (pp30) REVERT: K 1 MET cc_start: 0.6301 (OUTLIER) cc_final: 0.5478 (pmm) REVERT: K 72 ASP cc_start: 0.8796 (m-30) cc_final: 0.8544 (m-30) REVERT: K 103 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7702 (mp0) REVERT: L 5 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8224 (pt0) REVERT: L 31 LYS cc_start: 0.8835 (mttt) cc_final: 0.8431 (ptpt) REVERT: L 45 GLN cc_start: 0.8161 (mp10) cc_final: 0.7659 (mm-40) REVERT: L 73 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8176 (p0) REVERT: L 105 GLU cc_start: 0.9230 (mm-30) cc_final: 0.9017 (mm-30) REVERT: N 35 GLN cc_start: 0.8866 (tt0) cc_final: 0.8154 (tm-30) REVERT: N 51 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8392 (mmm-85) REVERT: N 69 PHE cc_start: 0.8845 (t80) cc_final: 0.8336 (t80) REVERT: O 57 HIS cc_start: 0.7905 (OUTLIER) cc_final: 0.7425 (t-90) REVERT: O 125 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.7805 (m-80) REVERT: P 17 ARG cc_start: 0.8502 (mtt180) cc_final: 0.7815 (mtt90) REVERT: P 34 PHE cc_start: 0.8612 (t80) cc_final: 0.7831 (t80) REVERT: P 48 VAL cc_start: 0.8193 (OUTLIER) cc_final: 0.7924 (t) REVERT: P 117 GLU cc_start: 0.9326 (mt-10) cc_final: 0.8943 (mt-10) REVERT: Q 43 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7750 (m-80) REVERT: R 49 ASP cc_start: 0.8654 (m-30) cc_final: 0.8236 (m-30) REVERT: R 102 ASP cc_start: 0.8158 (t0) cc_final: 0.7550 (t0) REVERT: S 31 GLU cc_start: 0.8985 (mp0) cc_final: 0.8644 (mp0) REVERT: T 20 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8775 (mtt180) REVERT: U 20 MET cc_start: 0.8568 (tpp) cc_final: 0.7856 (tmm) REVERT: U 30 ASP cc_start: 0.7604 (m-30) cc_final: 0.7249 (p0) REVERT: Y 17 ASN cc_start: 0.8409 (t0) cc_final: 0.7811 (t0) REVERT: Y 36 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8717 (p) REVERT: 0 41 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7331 (tm-30) REVERT: 2 36 MET cc_start: 0.8403 (mmm) cc_final: 0.7843 (mmm) REVERT: 3 21 LYS cc_start: 0.8851 (ptmm) cc_final: 0.8096 (ptmm) REVERT: 5 49 MET cc_start: 0.8383 (mmm) cc_final: 0.8147 (mmm) outliers start: 258 outliers final: 219 residues processed: 949 average time/residue: 1.2509 time to fit residues: 2098.4753 Evaluate side-chains 1010 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 774 time to evaluate : 5.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 123 LEU Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain d residue 64 ASN Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 120 ILE Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 135 ASN Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain f residue 42 GLU Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 69 THR Chi-restraints excluded: chain f residue 70 SER Chi-restraints excluded: chain f residue 83 LEU Chi-restraints excluded: chain g residue 26 LEU Chi-restraints excluded: chain g residue 27 ILE Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain g residue 140 ASP Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 27 LYS Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 96 SER Chi-restraints excluded: chain j residue 14 GLU Chi-restraints excluded: chain j residue 17 ILE Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain k residue 23 ILE Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 80 LYS Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 97 ILE Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 19 SER Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 39 ASN Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 48 THR Chi-restraints excluded: chain l residue 60 SER Chi-restraints excluded: chain l residue 62 LEU Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain m residue 21 TYR Chi-restraints excluded: chain m residue 70 ARG Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain n residue 7 ILE Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 47 LYS Chi-restraints excluded: chain o residue 60 ILE Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 27 SER Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 57 LEU Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain q residue 14 ARG Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 54 ASN Chi-restraints excluded: chain q residue 78 LEU Chi-restraints excluded: chain r residue 37 ILE Chi-restraints excluded: chain r residue 68 ILE Chi-restraints excluded: chain r residue 69 MET Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain s residue 41 PHE Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 52 GLU Chi-restraints excluded: chain t residue 62 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 119 PHE Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 172 GLN Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 80 ARG Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 113 ASN Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 109 ASN Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 51 ARG Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 116 GLU Chi-restraints excluded: chain N residue 123 HIS Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 39 GLU Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain O residue 46 LYS Chi-restraints excluded: chain O residue 57 HIS Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 125 PHE Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 37 ASN Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain Q residue 24 ASP Chi-restraints excluded: chain Q residue 43 PHE Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 29 HIS Chi-restraints excluded: chain R residue 54 LYS Chi-restraints excluded: chain R residue 88 ILE Chi-restraints excluded: chain R residue 97 ASP Chi-restraints excluded: chain R residue 115 ASP Chi-restraints excluded: chain S residue 2 TYR Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 81 HIS Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain S residue 88 HIS Chi-restraints excluded: chain T residue 20 ARG Chi-restraints excluded: chain T residue 36 ASP Chi-restraints excluded: chain T residue 44 THR Chi-restraints excluded: chain T residue 67 PHE Chi-restraints excluded: chain U residue 5 ASP Chi-restraints excluded: chain U residue 21 ASP Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 40 GLN Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain W residue 43 PHE Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 60 VAL Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Z residue 4 LYS Chi-restraints excluded: chain Z residue 5 GLU Chi-restraints excluded: chain Z residue 30 PHE Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 22 LYS Chi-restraints excluded: chain 1 residue 23 PHE Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 46 LEU Chi-restraints excluded: chain 3 residue 23 LYS Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 3 residue 48 THR Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 41 VAL Chi-restraints excluded: chain 4 residue 43 SER Chi-restraints excluded: chain 5 residue 58 ILE Chi-restraints excluded: chain 6 residue 7 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 833 optimal weight: 9.9990 chunk 878 optimal weight: 8.9990 chunk 801 optimal weight: 8.9990 chunk 854 optimal weight: 5.9990 chunk 877 optimal weight: 7.9990 chunk 514 optimal weight: 20.0000 chunk 372 optimal weight: 10.0000 chunk 670 optimal weight: 2.9990 chunk 262 optimal weight: 0.9990 chunk 771 optimal weight: 4.9990 chunk 807 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 8 HIS g 129 ASN ** j 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 56 GLN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 HIS ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 30 GLN ** W 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 20 ASN 5 4 GLN ** 5 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 60 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 150437 Z= 0.216 Angle : 0.631 15.820 225587 Z= 0.321 Chirality : 0.036 0.320 28933 Planarity : 0.005 0.094 11679 Dihedral : 23.566 179.832 76272 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.40 % Favored : 88.46 % Rotamer: Outliers : 5.53 % Allowed : 21.10 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.26 % Twisted Proline : 0.52 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.11), residues: 5097 helix: 0.05 (0.14), residues: 1339 sheet: -1.72 (0.16), residues: 946 loop : -2.64 (0.11), residues: 2812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP g 103 HIS 0.016 0.001 HIS C 142 PHE 0.040 0.002 PHE c 31 TYR 0.025 0.002 TYR C 62 ARG 0.010 0.001 ARG j 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10194 Ramachandran restraints generated. 5097 Oldfield, 0 Emsley, 5097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10194 Ramachandran restraints generated. 5097 Oldfield, 0 Emsley, 5097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1044 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 803 time to evaluate : 5.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP 1 4 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 4 1 " (corrupted residue). Skipping it. REVERT: c 10 MET cc_start: 0.4889 (mmm) cc_final: 0.4381 (mmm) REVERT: c 62 ARG cc_start: 0.7050 (mtm110) cc_final: 0.6762 (mtt-85) REVERT: c 92 LYS cc_start: 0.8146 (mttt) cc_final: 0.7922 (pttp) REVERT: c 133 GLN cc_start: 0.8177 (mt0) cc_final: 0.7507 (tm-30) REVERT: d 41 ARG cc_start: 0.6963 (ptm160) cc_final: 0.5011 (mtm180) REVERT: d 50 GLN cc_start: 0.7781 (mt0) cc_final: 0.7571 (mt0) REVERT: d 60 MET cc_start: 0.8378 (tpt) cc_final: 0.8006 (mmt) REVERT: d 65 GLU cc_start: 0.9225 (tt0) cc_final: 0.8860 (mm-30) REVERT: d 88 MET cc_start: 0.9527 (mmt) cc_final: 0.9196 (mmm) REVERT: e 22 THR cc_start: 0.6225 (p) cc_final: 0.5558 (t) REVERT: e 37 VAL cc_start: 0.9511 (t) cc_final: 0.9286 (p) REVERT: e 81 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7987 (pt) REVERT: e 146 GLN cc_start: 0.9317 (tt0) cc_final: 0.8921 (tm-30) REVERT: f 22 LYS cc_start: 0.8839 (ptmt) cc_final: 0.8591 (ptmm) REVERT: f 28 ARG cc_start: 0.9107 (ptm160) cc_final: 0.8752 (tmm-80) REVERT: f 42 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7773 (pp20) REVERT: g 70 MET cc_start: 0.6247 (ppp) cc_final: 0.4645 (tmm) REVERT: h 12 THR cc_start: 0.9040 (p) cc_final: 0.8697 (t) REVERT: j 30 LYS cc_start: 0.7407 (ptmm) cc_final: 0.7183 (ptmm) REVERT: j 68 ARG cc_start: 0.5930 (mtt180) cc_final: 0.5257 (mtt-85) REVERT: j 98 ILE cc_start: 0.6095 (pt) cc_final: 0.5671 (mm) REVERT: k 15 ASN cc_start: 0.8399 (m-40) cc_final: 0.7932 (p0) REVERT: k 83 ASP cc_start: 0.8480 (m-30) cc_final: 0.8258 (m-30) REVERT: m 78 LYS cc_start: 0.7427 (tppt) cc_final: 0.7200 (mmtm) REVERT: o 13 LYS cc_start: 0.9357 (mttt) cc_final: 0.8945 (mptt) REVERT: o 14 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8433 (tm-30) REVERT: o 35 ASP cc_start: 0.9373 (OUTLIER) cc_final: 0.8943 (t0) REVERT: o 48 LYS cc_start: 0.9255 (mmmt) cc_final: 0.9047 (mmmm) REVERT: p 65 GLN cc_start: 0.8255 (mp10) cc_final: 0.7916 (mp10) REVERT: p 68 ASP cc_start: 0.8738 (p0) cc_final: 0.8307 (p0) REVERT: p 74 LEU cc_start: 0.9317 (mp) cc_final: 0.9071 (mt) REVERT: p 80 MET cc_start: 0.8737 (mmm) cc_final: 0.8295 (tpp) REVERT: q 25 THR cc_start: 0.8211 (m) cc_final: 0.7886 (p) REVERT: q 54 ASN cc_start: 0.8679 (OUTLIER) cc_final: 0.8438 (t0) REVERT: r 36 PHE cc_start: 0.8834 (m-80) cc_final: 0.8627 (m-80) REVERT: r 64 LYS cc_start: 0.8829 (mttt) cc_final: 0.8021 (mtpt) REVERT: r 72 LEU cc_start: 0.8682 (tp) cc_final: 0.8163 (tt) REVERT: s 66 MET cc_start: 0.8254 (ttp) cc_final: 0.7257 (mmp) REVERT: s 69 HIS cc_start: 0.7058 (p-80) cc_final: 0.6265 (p-80) REVERT: t 70 LYS cc_start: 0.8753 (ttmt) cc_final: 0.8415 (ttmm) REVERT: C 20 ASP cc_start: 0.7994 (m-30) cc_final: 0.7769 (m-30) REVERT: C 225 MET cc_start: 0.8540 (mmt) cc_final: 0.7879 (mmt) REVERT: C 229 ASP cc_start: 0.8448 (t0) cc_final: 0.8030 (t0) REVERT: C 276 LYS cc_start: 0.6990 (mmmm) cc_final: 0.6693 (mmmm) REVERT: D 85 ASN cc_start: 0.8325 (t0) cc_final: 0.8063 (p0) REVERT: D 119 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.8210 (t80) REVERT: D 142 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8635 (mtt-85) REVERT: D 191 ASN cc_start: 0.8638 (OUTLIER) cc_final: 0.8323 (m-40) REVERT: E 158 ASN cc_start: 0.8350 (m-40) cc_final: 0.7694 (p0) REVERT: E 161 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8300 (p0) REVERT: F 96 MET cc_start: 0.8360 (mmm) cc_final: 0.7846 (mmm) REVERT: F 97 TYR cc_start: 0.9358 (m-80) cc_final: 0.9005 (m-80) REVERT: F 99 PHE cc_start: 0.9480 (t80) cc_final: 0.9142 (t80) REVERT: F 152 MET cc_start: 0.8106 (mmm) cc_final: 0.7755 (mmm) REVERT: G 54 ARG cc_start: 0.7129 (ttm110) cc_final: 0.5765 (ttt180) REVERT: G 84 GLN cc_start: 0.7435 (pp30) cc_final: 0.6907 (pp30) REVERT: G 130 GLN cc_start: 0.8888 (mt0) cc_final: 0.8322 (mp10) REVERT: K 1 MET cc_start: 0.6036 (OUTLIER) cc_final: 0.5353 (pmm) REVERT: K 72 ASP cc_start: 0.8763 (m-30) cc_final: 0.8486 (m-30) REVERT: K 103 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7697 (mp0) REVERT: L 5 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8183 (pt0) REVERT: L 31 LYS cc_start: 0.8827 (mttt) cc_final: 0.8425 (ptpt) REVERT: L 45 GLN cc_start: 0.8131 (mp10) cc_final: 0.7625 (mm-40) REVERT: L 73 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8119 (p0) REVERT: L 120 GLU cc_start: 0.7769 (mp0) cc_final: 0.7568 (mp0) REVERT: M 19 VAL cc_start: 0.9124 (OUTLIER) cc_final: 0.8823 (p) REVERT: N 51 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8483 (ttp80) REVERT: N 69 PHE cc_start: 0.8890 (t80) cc_final: 0.8353 (t80) REVERT: N 74 TYR cc_start: 0.5430 (m-80) cc_final: 0.5086 (m-80) REVERT: N 103 MET cc_start: 0.7978 (mmm) cc_final: 0.7480 (mmt) REVERT: O 57 HIS cc_start: 0.7857 (OUTLIER) cc_final: 0.7348 (t-90) REVERT: O 125 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.7987 (m-80) REVERT: P 17 ARG cc_start: 0.8514 (mtt180) cc_final: 0.7682 (mtt90) REVERT: P 48 VAL cc_start: 0.8068 (OUTLIER) cc_final: 0.7802 (t) REVERT: P 78 LEU cc_start: 0.9259 (tt) cc_final: 0.8918 (tt) REVERT: P 117 GLU cc_start: 0.9338 (mt-10) cc_final: 0.8962 (mt-10) REVERT: Q 10 GLN cc_start: 0.8366 (mp10) cc_final: 0.8148 (mm-40) REVERT: Q 44 GLU cc_start: 0.8862 (tp30) cc_final: 0.8634 (mm-30) REVERT: Q 71 GLU cc_start: 0.8180 (mp0) cc_final: 0.7867 (mp0) REVERT: R 49 ASP cc_start: 0.8624 (m-30) cc_final: 0.8178 (m-30) REVERT: R 102 ASP cc_start: 0.8096 (t0) cc_final: 0.7463 (t0) REVERT: S 31 GLU cc_start: 0.8976 (mp0) cc_final: 0.8648 (mp0) REVERT: S 75 GLN cc_start: 0.7717 (tm-30) cc_final: 0.7478 (tm-30) REVERT: T 20 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8756 (mtt180) REVERT: T 23 ARG cc_start: 0.8552 (mtt180) cc_final: 0.8289 (mtt180) REVERT: U 20 MET cc_start: 0.8592 (tpp) cc_final: 0.7852 (tmm) REVERT: U 30 ASP cc_start: 0.7616 (m-30) cc_final: 0.7284 (p0) REVERT: U 85 ASP cc_start: 0.6968 (OUTLIER) cc_final: 0.6730 (t0) REVERT: Y 17 ASN cc_start: 0.8408 (t0) cc_final: 0.7796 (t0) REVERT: Y 36 VAL cc_start: 0.8965 (OUTLIER) cc_final: 0.8733 (p) REVERT: Z 24 GLU cc_start: 0.9246 (mm-30) cc_final: 0.9026 (mm-30) REVERT: 0 5 LYS cc_start: 0.8421 (mmmm) cc_final: 0.8074 (mmmm) REVERT: 0 9 LYS cc_start: 0.9237 (pttt) cc_final: 0.8997 (ptmm) REVERT: 0 41 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7302 (tm-30) REVERT: 2 36 MET cc_start: 0.8361 (mmm) cc_final: 0.7670 (mmm) REVERT: 3 21 LYS cc_start: 0.8932 (ptmm) cc_final: 0.8226 (ptmm) REVERT: 3 32 LYS cc_start: 0.7757 (mmtt) cc_final: 0.6310 (mmtm) REVERT: 5 49 MET cc_start: 0.8364 (mmm) cc_final: 0.8111 (mmm) outliers start: 241 outliers final: 196 residues processed: 941 average time/residue: 1.1485 time to fit residues: 1902.8285 Evaluate side-chains 991 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 777 time to evaluate : 5.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 123 LEU Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain d residue 64 ASN Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 135 ASN Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain f residue 42 GLU Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 70 SER Chi-restraints excluded: chain f residue 83 LEU Chi-restraints excluded: chain g residue 26 LEU Chi-restraints excluded: chain g residue 27 ILE Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain g residue 140 ASP Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 27 LYS Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain j residue 14 GLU Chi-restraints excluded: chain j residue 17 ILE Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 42 LEU Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 97 ILE Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 39 ASN Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 48 THR Chi-restraints excluded: chain l residue 60 SER Chi-restraints excluded: chain l residue 62 LEU Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain m residue 21 TYR Chi-restraints excluded: chain m residue 70 ARG Chi-restraints excluded: chain n residue 7 ILE Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 35 ASP Chi-restraints excluded: chain o residue 47 LYS Chi-restraints excluded: chain o residue 60 ILE Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 27 SER Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 57 LEU Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain q residue 14 ARG Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 54 ASN Chi-restraints excluded: chain r residue 37 ILE Chi-restraints excluded: chain r residue 68 ILE Chi-restraints excluded: chain r residue 69 MET Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain s residue 41 PHE Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 62 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 119 PHE Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 172 GLN Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 80 ARG Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 113 ASN Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 109 ASN Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 51 ARG Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 39 GLU Chi-restraints excluded: chain O residue 46 LYS Chi-restraints excluded: chain O residue 57 HIS Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 125 PHE Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 29 HIS Chi-restraints excluded: chain R residue 54 LYS Chi-restraints excluded: chain R residue 88 ILE Chi-restraints excluded: chain R residue 97 ASP Chi-restraints excluded: chain R residue 115 ASP Chi-restraints excluded: chain S residue 2 TYR Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 81 HIS Chi-restraints excluded: chain S residue 88 HIS Chi-restraints excluded: chain T residue 20 ARG Chi-restraints excluded: chain T residue 36 ASP Chi-restraints excluded: chain T residue 44 THR Chi-restraints excluded: chain T residue 67 PHE Chi-restraints excluded: chain U residue 5 ASP Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 40 GLN Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain W residue 43 PHE Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 60 VAL Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Z residue 5 GLU Chi-restraints excluded: chain Z residue 30 PHE Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 23 PHE Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 46 LEU Chi-restraints excluded: chain 3 residue 23 LYS Chi-restraints excluded: chain 3 residue 48 THR Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 41 VAL Chi-restraints excluded: chain 4 residue 43 SER Chi-restraints excluded: chain 5 residue 58 ILE Chi-restraints excluded: chain 6 residue 7 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 851 optimal weight: 4.9990 chunk 560 optimal weight: 10.0000 chunk 903 optimal weight: 5.9990 chunk 551 optimal weight: 10.0000 chunk 428 optimal weight: 10.0000 chunk 627 optimal weight: 10.0000 chunk 947 optimal weight: 5.9990 chunk 872 optimal weight: 4.9990 chunk 754 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 582 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 8 HIS ** k 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 HIS ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 131 HIS N 123 HIS ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 20 ASN 5 4 GLN ** 5 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 150437 Z= 0.275 Angle : 0.677 16.352 225587 Z= 0.343 Chirality : 0.038 0.356 28933 Planarity : 0.005 0.102 11679 Dihedral : 23.586 179.797 76272 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.81 % Favored : 87.05 % Rotamer: Outliers : 5.21 % Allowed : 21.72 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.26 % Twisted Proline : 0.52 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.11), residues: 5097 helix: -0.08 (0.14), residues: 1354 sheet: -1.76 (0.16), residues: 941 loop : -2.73 (0.11), residues: 2802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.094 0.003 TRP g 103 HIS 0.018 0.002 HIS C 142 PHE 0.040 0.002 PHE n 44 TYR 0.024 0.002 TYR C 62 ARG 0.012 0.001 ARG j 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10194 Ramachandran restraints generated. 5097 Oldfield, 0 Emsley, 5097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10194 Ramachandran restraints generated. 5097 Oldfield, 0 Emsley, 5097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1010 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 783 time to evaluate : 5.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP 1 4 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET 4 1 " (corrupted residue). Skipping it. REVERT: c 10 MET cc_start: 0.4889 (mmm) cc_final: 0.4396 (mmm) REVERT: c 62 ARG cc_start: 0.7052 (mtm110) cc_final: 0.6765 (mtt-85) REVERT: c 92 LYS cc_start: 0.8161 (mttt) cc_final: 0.7959 (pttp) REVERT: c 133 GLN cc_start: 0.8181 (mt0) cc_final: 0.7503 (tm-30) REVERT: d 41 ARG cc_start: 0.6998 (ptm160) cc_final: 0.5024 (mtm180) REVERT: d 50 GLN cc_start: 0.7848 (mt0) cc_final: 0.7635 (mt0) REVERT: d 60 MET cc_start: 0.8421 (tpt) cc_final: 0.8030 (mmt) REVERT: d 88 MET cc_start: 0.9530 (mmt) cc_final: 0.9213 (mmm) REVERT: e 22 THR cc_start: 0.6061 (p) cc_final: 0.5364 (t) REVERT: e 37 VAL cc_start: 0.9551 (t) cc_final: 0.9335 (p) REVERT: e 81 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.8028 (pt) REVERT: e 146 GLN cc_start: 0.9285 (tt0) cc_final: 0.8861 (tm-30) REVERT: f 22 LYS cc_start: 0.8811 (ptmt) cc_final: 0.8561 (ptmm) REVERT: f 28 ARG cc_start: 0.9109 (ptm160) cc_final: 0.8760 (tmm-80) REVERT: f 42 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7764 (pp20) REVERT: g 70 MET cc_start: 0.6506 (ppp) cc_final: 0.5182 (tmm) REVERT: h 12 THR cc_start: 0.9053 (p) cc_final: 0.8744 (t) REVERT: j 30 LYS cc_start: 0.7431 (ptmm) cc_final: 0.7213 (ptmm) REVERT: j 68 ARG cc_start: 0.5917 (mtt180) cc_final: 0.5224 (mtt-85) REVERT: j 98 ILE cc_start: 0.6182 (pt) cc_final: 0.5750 (mm) REVERT: k 15 ASN cc_start: 0.8383 (m-40) cc_final: 0.7874 (p0) REVERT: k 83 ASP cc_start: 0.8492 (m-30) cc_final: 0.8205 (m-30) REVERT: m 78 LYS cc_start: 0.7592 (tppt) cc_final: 0.7357 (mmtm) REVERT: o 13 LYS cc_start: 0.9363 (mttt) cc_final: 0.8965 (mptt) REVERT: o 14 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8469 (tm-30) REVERT: o 48 LYS cc_start: 0.9228 (mmmt) cc_final: 0.9027 (mmmm) REVERT: p 65 GLN cc_start: 0.8287 (mp10) cc_final: 0.7953 (mp10) REVERT: p 68 ASP cc_start: 0.8760 (p0) cc_final: 0.8434 (p0) REVERT: p 74 LEU cc_start: 0.9334 (mp) cc_final: 0.9093 (mt) REVERT: p 80 MET cc_start: 0.8705 (mmm) cc_final: 0.8280 (tpp) REVERT: q 25 THR cc_start: 0.8211 (m) cc_final: 0.7885 (p) REVERT: q 29 GLU cc_start: 0.9088 (pm20) cc_final: 0.8871 (pm20) REVERT: q 54 ASN cc_start: 0.8703 (OUTLIER) cc_final: 0.8475 (t0) REVERT: r 36 PHE cc_start: 0.8907 (m-80) cc_final: 0.8653 (m-80) REVERT: r 64 LYS cc_start: 0.8845 (mttt) cc_final: 0.8009 (mtpt) REVERT: r 72 LEU cc_start: 0.8725 (tp) cc_final: 0.8229 (tt) REVERT: s 66 MET cc_start: 0.8282 (ttp) cc_final: 0.7304 (mmp) REVERT: s 69 HIS cc_start: 0.7072 (p-80) cc_final: 0.6288 (p-80) REVERT: t 70 LYS cc_start: 0.8778 (ttmt) cc_final: 0.8438 (ttmm) REVERT: C 20 ASP cc_start: 0.8054 (m-30) cc_final: 0.7829 (m-30) REVERT: C 225 MET cc_start: 0.8580 (mmt) cc_final: 0.7852 (mmt) REVERT: C 229 ASP cc_start: 0.8480 (t0) cc_final: 0.8160 (t0) REVERT: C 276 LYS cc_start: 0.7249 (mmmm) cc_final: 0.6947 (mmmm) REVERT: D 119 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.8223 (t80) REVERT: D 142 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8726 (mtt-85) REVERT: D 191 ASN cc_start: 0.8647 (OUTLIER) cc_final: 0.8317 (m-40) REVERT: E 158 ASN cc_start: 0.8357 (m-40) cc_final: 0.7680 (p0) REVERT: E 161 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8338 (p0) REVERT: F 96 MET cc_start: 0.8341 (mmm) cc_final: 0.7833 (mmm) REVERT: F 97 TYR cc_start: 0.9347 (m-80) cc_final: 0.9015 (m-80) REVERT: F 99 PHE cc_start: 0.9494 (t80) cc_final: 0.9148 (t80) REVERT: F 167 ARG cc_start: 0.9040 (ttm-80) cc_final: 0.8612 (ttm-80) REVERT: G 54 ARG cc_start: 0.7063 (ttm110) cc_final: 0.5855 (ttt180) REVERT: G 84 GLN cc_start: 0.7434 (pp30) cc_final: 0.6883 (pp30) REVERT: G 130 GLN cc_start: 0.8860 (mt0) cc_final: 0.8293 (mp10) REVERT: K 1 MET cc_start: 0.6250 (OUTLIER) cc_final: 0.5500 (pmm) REVERT: K 72 ASP cc_start: 0.8803 (m-30) cc_final: 0.8526 (m-30) REVERT: K 103 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7733 (mp0) REVERT: L 5 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8218 (pt0) REVERT: L 31 LYS cc_start: 0.8838 (mttt) cc_final: 0.8385 (ptpt) REVERT: L 45 GLN cc_start: 0.8201 (mp10) cc_final: 0.7641 (mp10) REVERT: L 73 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.8240 (p0) REVERT: M 19 VAL cc_start: 0.9142 (OUTLIER) cc_final: 0.8834 (p) REVERT: N 35 GLN cc_start: 0.8848 (tt0) cc_final: 0.8143 (tm-30) REVERT: N 51 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8403 (mmm-85) REVERT: N 69 PHE cc_start: 0.8884 (t80) cc_final: 0.8370 (t80) REVERT: N 74 TYR cc_start: 0.5371 (m-80) cc_final: 0.5001 (m-80) REVERT: N 106 ILE cc_start: 0.9280 (pt) cc_final: 0.8750 (mm) REVERT: N 112 GLU cc_start: 0.8965 (mp0) cc_final: 0.8674 (pm20) REVERT: O 57 HIS cc_start: 0.7891 (OUTLIER) cc_final: 0.7386 (t-90) REVERT: O 125 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.7631 (m-80) REVERT: P 17 ARG cc_start: 0.8560 (mtt180) cc_final: 0.7721 (mtt90) REVERT: P 34 PHE cc_start: 0.8606 (t80) cc_final: 0.7895 (t80) REVERT: P 48 VAL cc_start: 0.8057 (OUTLIER) cc_final: 0.7788 (t) REVERT: P 117 GLU cc_start: 0.9338 (mt-10) cc_final: 0.9001 (mt-10) REVERT: Q 71 GLU cc_start: 0.8220 (mp0) cc_final: 0.7889 (mp0) REVERT: R 49 ASP cc_start: 0.8670 (m-30) cc_final: 0.8258 (m-30) REVERT: R 102 ASP cc_start: 0.8186 (t0) cc_final: 0.7562 (t0) REVERT: S 31 GLU cc_start: 0.8999 (mp0) cc_final: 0.8561 (mp0) REVERT: T 20 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8778 (mtt180) REVERT: U 20 MET cc_start: 0.8621 (tpp) cc_final: 0.7913 (tmm) REVERT: U 30 ASP cc_start: 0.7608 (m-30) cc_final: 0.7261 (p0) REVERT: U 85 ASP cc_start: 0.6974 (OUTLIER) cc_final: 0.6724 (t0) REVERT: Y 17 ASN cc_start: 0.8439 (t0) cc_final: 0.7824 (t0) REVERT: Y 36 VAL cc_start: 0.8968 (OUTLIER) cc_final: 0.8731 (p) REVERT: Z 24 GLU cc_start: 0.9277 (mm-30) cc_final: 0.9065 (mm-30) REVERT: 0 5 LYS cc_start: 0.8446 (mmmm) cc_final: 0.8109 (mmmm) REVERT: 0 41 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7350 (tm-30) REVERT: 2 36 MET cc_start: 0.8258 (mmm) cc_final: 0.7721 (mmm) REVERT: 3 21 LYS cc_start: 0.8978 (ptmm) cc_final: 0.8221 (ptmm) REVERT: 3 32 LYS cc_start: 0.7777 (mmtt) cc_final: 0.6350 (mmtm) REVERT: 5 49 MET cc_start: 0.8373 (mmm) cc_final: 0.8116 (mmm) outliers start: 227 outliers final: 204 residues processed: 911 average time/residue: 1.1764 time to fit residues: 1887.6557 Evaluate side-chains 991 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 770 time to evaluate : 5.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 28 TYR Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 123 LEU Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain d residue 64 ASN Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 135 ASN Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain f residue 30 ASP Chi-restraints excluded: chain f residue 42 GLU Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 70 SER Chi-restraints excluded: chain f residue 83 LEU Chi-restraints excluded: chain g residue 26 LEU Chi-restraints excluded: chain g residue 27 ILE Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain g residue 140 ASP Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 27 LYS Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 14 GLU Chi-restraints excluded: chain j residue 17 ILE Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 97 ILE Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 19 SER Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 39 ASN Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 60 SER Chi-restraints excluded: chain l residue 62 LEU Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain m residue 21 TYR Chi-restraints excluded: chain m residue 70 ARG Chi-restraints excluded: chain n residue 7 ILE Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 47 LYS Chi-restraints excluded: chain o residue 60 ILE Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 27 SER Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 57 LEU Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain q residue 14 ARG Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 54 ASN Chi-restraints excluded: chain q residue 78 LEU Chi-restraints excluded: chain r residue 37 ILE Chi-restraints excluded: chain r residue 68 ILE Chi-restraints excluded: chain r residue 69 MET Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain s residue 41 PHE Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 62 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 119 PHE Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 172 GLN Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 80 ARG Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 113 ASN Chi-restraints excluded: chain K residue 131 HIS Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 109 ASN Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 51 ARG Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 123 HIS Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 39 GLU Chi-restraints excluded: chain O residue 57 HIS Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 125 PHE Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 29 HIS Chi-restraints excluded: chain R residue 54 LYS Chi-restraints excluded: chain R residue 88 ILE Chi-restraints excluded: chain R residue 97 ASP Chi-restraints excluded: chain R residue 115 ASP Chi-restraints excluded: chain S residue 2 TYR Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 81 HIS Chi-restraints excluded: chain S residue 88 HIS Chi-restraints excluded: chain T residue 20 ARG Chi-restraints excluded: chain T residue 36 ASP Chi-restraints excluded: chain T residue 44 THR Chi-restraints excluded: chain T residue 67 PHE Chi-restraints excluded: chain U residue 5 ASP Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 40 GLN Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain W residue 43 PHE Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 60 VAL Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Z residue 5 GLU Chi-restraints excluded: chain Z residue 30 PHE Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 23 PHE Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 46 LEU Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 23 LYS Chi-restraints excluded: chain 3 residue 48 THR Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 41 VAL Chi-restraints excluded: chain 4 residue 43 SER Chi-restraints excluded: chain 5 residue 58 ILE Chi-restraints excluded: chain 6 residue 7 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 462 optimal weight: 50.0000 chunk 599 optimal weight: 20.0000 chunk 803 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 chunk 695 optimal weight: 6.9990 chunk 111 optimal weight: 50.0000 chunk 209 optimal weight: 0.0070 chunk 755 optimal weight: 4.9990 chunk 316 optimal weight: 0.5980 chunk 775 optimal weight: 4.9990 chunk 95 optimal weight: 50.0000 overall best weight: 2.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 8 HIS ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 HIS ** F 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS G 147 ASN ** K 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 131 HIS K 136 GLN ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 HIS ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 41 ASN 3 20 ASN 5 4 GLN ** 5 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.068579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.052687 restraints weight = 728441.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.054112 restraints weight = 238829.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.054975 restraints weight = 124369.576| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 150437 Z= 0.152 Angle : 0.583 16.653 225587 Z= 0.296 Chirality : 0.033 0.416 28933 Planarity : 0.004 0.094 11679 Dihedral : 23.470 179.484 76272 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.14 % Favored : 89.76 % Rotamer: Outliers : 4.16 % Allowed : 23.03 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.26 % Twisted Proline : 0.52 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.12), residues: 5097 helix: 0.22 (0.14), residues: 1341 sheet: -1.57 (0.17), residues: 956 loop : -2.52 (0.11), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.002 TRP g 103 HIS 0.044 0.001 HIS N 123 PHE 0.040 0.001 PHE c 31 TYR 0.031 0.001 TYR g 107 ARG 0.010 0.000 ARG j 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32033.24 seconds wall clock time: 562 minutes 31.87 seconds (33751.87 seconds total)