Starting phenix.real_space_refine on Mon Mar 18 02:56:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o8y_0658/03_2024/6o8y_0658.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o8y_0658/03_2024/6o8y_0658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o8y_0658/03_2024/6o8y_0658.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o8y_0658/03_2024/6o8y_0658.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o8y_0658/03_2024/6o8y_0658.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o8y_0658/03_2024/6o8y_0658.pdb" } resolution = 4.14 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= 0.001 sd= 0.078 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 4541 5.49 5 S 130 5.16 5 C 69005 2.51 5 N 25587 2.21 5 O 38943 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 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "p PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 47": "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 "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" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 138210 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': 120, 'rna2p_pyr': 88, 'rna3p_pur': 737, 'rna3p_pyr': 583} Link IDs: {'rna2p': 208, 'rna3p': 1319} 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: 62176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2897, 62176 Classifications: {'RNA': 2897} Modifications used: {'rna2p_pur': 302, 'rna2p_pyr': 159, 'rna3p_pur': 1378, 'rna3p_pyr': 1054} Link IDs: {'rna2p': 461, 'rna3p': 2435} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 5 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 9 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': 6, 'rna3p_pur': 55, 'rna3p_pyr': 48} Link IDs: {'rna2p': 12, 'rna3p': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 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: 3 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: 6 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen planarities: 1 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 non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 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 non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 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 non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 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 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: "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: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 978 Classifications: {'peptide': 123} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 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} Link IDs: {'CIS': 2, 'PTRANS': 2, 'TRANS': 112} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 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: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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 non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen planarities: 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 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: "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 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: "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} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 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: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 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 non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 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 45166 SG CYS n 40 60.470 135.606 123.622 1.00 97.98 S ATOM A0S2R SG CYS 2 30 250.710 137.456 88.226 1.00165.41 S ATOM A0S5H SG CYS 2 43 248.750 140.250 89.519 1.00158.46 S ATOM A0S5Z SG CYS 2 46 253.206 139.176 90.274 1.00165.08 S ATOM A0TB7 SG CYS 6 11 142.313 125.069 49.874 1.00179.57 S ATOM A0TEU SG CYS 6 27 145.730 123.953 48.930 1.00175.43 S Time building chain proxies: 52.68, per 1000 atoms: 0.38 Number of scatterers: 138210 At special positions: 0 Unit cell: (286.317, 276.444, 230.37, 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 4541 15.00 O 38943 8.00 N 25587 7.00 C 69005 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: 64.30 Conformation dependent library (CDL) restraints added in 6.1 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 ZN 2 101 " - pdb=" SG CYS 2 43 " pdb=" ZN 6 101 " pdb="ZN ZN 6 101 " - pdb=" ND1 HIS 6 33 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 11 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 27 " pdb=" ZN n 101 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 40 " 10202 Ramachandran restraints generated. 5101 Oldfield, 0 Emsley, 5101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9540 Finding SS restraints... Warning! N1 atom is missing from residue G A2597 Was trying to link: G A2567 O6 with G A2597 N1, Saenger class: 6 Warning! N1 atom is missing from residue G A2597 Was trying to link: G A2567 N7 with G A2597 N1, Saenger class: 7 Secondary structure from input PDB file: 149 helices and 70 sheets defined 28.9% alpha, 12.8% beta 1439 base pairs and 2294 stacking pairs defined. Time for finding SS restraints: 46.99 Creating SS restraints... Processing helix chain 'c' and resid 6 through 11 Processing helix chain 'c' and resid 28 through 41 removed outlier: 3.563A pdb=" N LEU c 32 " --> pdb=" O TYR c 28 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE c 41 " --> pdb=" O ARG c 37 " (cutoff:3.500A) Processing helix chain 'c' and resid 42 through 49 removed outlier: 4.184A pdb=" N ASP c 48 " --> pdb=" O THR c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 95 removed outlier: 3.730A pdb=" N ASN c 85 " --> pdb=" O SER c 81 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU c 93 " --> pdb=" O GLU c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 125 removed outlier: 3.735A pdb=" N ASN c 125 " --> pdb=" O ARG c 121 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 Processing helix chain 'd' and resid 9 through 16 Processing helix chain 'd' and resid 45 through 59 removed outlier: 3.640A pdb=" N GLN d 50 " --> pdb=" O GLU d 46 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 75 removed outlier: 3.638A pdb=" N LYS d 74 " --> pdb=" O THR d 70 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA d 75 " --> pdb=" O LEU d 71 " (cutoff:3.500A) Processing helix chain 'd' and resid 82 through 93 removed outlier: 3.588A pdb=" N GLN d 93 " --> pdb=" O VAL d 89 " (cutoff:3.500A) Processing helix chain 'd' and resid 96 through 101 Processing helix chain 'd' and resid 107 through 117 removed outlier: 4.085A pdb=" N HIS d 117 " --> pdb=" O GLN d 113 " (cutoff:3.500A) Processing helix chain 'd' and resid 149 through 158 removed outlier: 3.534A pdb=" N LYS d 153 " --> pdb=" O ILE d 149 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU d 157 " --> pdb=" O LYS d 153 " (cutoff:3.500A) removed outlier: 3.754A 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: 4.347A pdb=" N VAL e 114 " --> pdb=" O PRO e 110 " (cutoff:3.500A) Processing helix chain 'e' and resid 132 through 147 removed outlier: 3.540A pdb=" N LEU e 147 " --> pdb=" O GLY e 143 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 157 Processing helix chain 'f' and resid 19 through 34 Processing helix chain 'f' and resid 35 through 37 No H-bonds generated for 'chain 'f' and resid 35 through 37' Processing helix chain 'f' and resid 77 through 85 removed outlier: 4.307A pdb=" N LYS f 85 " --> pdb=" O ASP f 81 " (cutoff:3.500A) Processing helix chain 'g' and resid 21 through 31 Processing helix chain 'g' and resid 35 through 53 removed outlier: 3.963A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.966A pdb=" N MET g 70 " --> pdb=" O MET g 66 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 110 removed outlier: 3.748A pdb=" N LEU g 110 " --> pdb=" O ASN g 106 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 127 removed outlier: 3.982A pdb=" N ARG g 119 " --> pdb=" O THR g 115 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU g 120 " --> pdb=" O MET g 116 " (cutoff:3.500A) Processing helix chain 'g' and resid 128 through 130 No H-bonds generated for 'chain 'g' and resid 128 through 130' Processing helix chain 'g' and resid 132 through 145 removed outlier: 3.686A pdb=" N ALA g 145 " --> pdb=" O THR g 141 " (cutoff:3.500A) Processing helix chain 'h' and resid 6 through 20 removed outlier: 4.110A pdb=" N PHE h 10 " --> pdb=" O PRO h 6 " (cutoff:3.500A) Processing helix chain 'h' and resid 31 through 43 Processing helix chain 'h' and resid 90 through 94 removed outlier: 3.742A pdb=" N VAL h 94 " --> pdb=" O ALA h 91 " (cutoff:3.500A) Processing helix chain 'h' and resid 115 through 120 Processing helix chain 'i' and resid 44 through 49 Processing helix chain 'i' and resid 49 through 55 removed outlier: 3.723A pdb=" N THR i 55 " --> pdb=" O PRO i 51 " (cutoff:3.500A) Processing helix chain 'i' and resid 73 through 78 Processing helix chain 'i' and resid 79 through 91 Processing helix chain 'i' and resid 94 through 102 Processing helix chain 'j' and resid 14 through 33 removed outlier: 4.250A pdb=" N LEU j 18 " --> pdb=" O GLU j 14 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP j 19 " --> pdb=" O HIS j 15 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.698A pdb=" N LYS j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 57 Processing helix chain 'k' and resid 59 through 75 removed outlier: 3.776A pdb=" N VAL k 73 " --> pdb=" O ALA k 69 " (cutoff:3.500A) Processing helix chain 'k' and resid 76 through 78 No H-bonds generated for 'chain 'k' and resid 76 through 78' Processing helix chain 'k' and resid 92 through 102 removed outlier: 4.023A pdb=" N ILE k 97 " --> pdb=" O ARG k 93 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG k 98 " --> pdb=" O GLU k 94 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 9 Processing helix chain 'l' and resid 21 through 25 removed outlier: 3.899A pdb=" N LEU l 24 " --> pdb=" O SER l 21 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 21 removed outlier: 3.911A pdb=" N TYR m 21 " --> pdb=" O VAL m 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 28 through 37 removed outlier: 3.659A pdb=" N VAL m 33 " --> pdb=" O THR m 29 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL m 37 " --> pdb=" O VAL m 33 " (cutoff:3.500A) Processing helix chain 'm' and resid 50 through 62 removed outlier: 3.889A pdb=" N LYS m 62 " --> pdb=" O ALA m 58 " (cutoff:3.500A) Processing helix chain 'm' and resid 68 through 81 Processing helix chain 'm' and resid 87 through 93 removed outlier: 3.718A pdb=" N ARG m 92 " --> pdb=" O GLY m 88 " (cutoff:3.500A) Processing helix chain 'n' and resid 3 through 12 removed outlier: 3.903A pdb=" N ASN n 10 " --> pdb=" O MET n 6 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS n 11 " --> pdb=" O ILE n 7 " (cutoff:3.500A) Processing helix chain 'n' and resid 16 through 20 removed outlier: 3.706A pdb=" N GLN n 19 " --> pdb=" O HIS n 16 " (cutoff:3.500A) removed outlier: 3.522A 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 51 Processing helix chain 'o' and resid 4 through 9 Processing helix chain 'o' and resid 10 through 14 Processing helix chain 'o' and resid 25 through 46 removed outlier: 3.772A pdb=" N ILE o 29 " --> pdb=" O PRO o 25 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 72 removed outlier: 4.049A pdb=" N TYR o 53 " --> pdb=" O ASP o 49 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG o 71 " --> pdb=" O LEU o 67 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS o 72 " --> pdb=" O ALA o 68 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 85 Processing helix chain 'p' and resid 54 through 63 Processing helix chain 'p' and resid 67 through 76 Processing helix chain 'p' and resid 78 through 90 removed outlier: 3.791A pdb=" N LYS p 90 " --> pdb=" O ALA p 86 " (cutoff:3.500A) Processing helix chain 'r' and resid 29 through 34 Processing helix chain 'r' and resid 45 through 50 removed outlier: 3.883A pdb=" N GLY r 50 " --> pdb=" O ARG r 46 " (cutoff:3.500A) Processing helix chain 'r' and resid 52 through 67 removed outlier: 3.837A pdb=" N ARG r 57 " --> pdb=" O ALA r 53 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 25 removed outlier: 4.956A pdb=" N LYS s 18 " --> pdb=" O HIS s 14 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 45 removed outlier: 4.177A pdb=" N VAL s 45 " --> pdb=" O PRO s 42 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 74 removed outlier: 4.082A pdb=" N GLU s 73 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE s 74 " --> pdb=" O LEU s 71 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 70 through 74' Processing helix chain 't' and resid 7 through 42 removed outlier: 3.596A pdb=" N ALA t 38 " --> pdb=" O LYS t 34 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA t 41 " --> pdb=" O GLU t 37 " (cutoff:3.500A) Processing helix chain 't' and resid 45 through 63 removed outlier: 4.405A pdb=" N LEU t 49 " --> pdb=" O ASN t 45 " (cutoff:3.500A) Processing helix chain 't' and resid 69 through 83 removed outlier: 3.873A pdb=" N LYS t 83 " --> pdb=" O SER t 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 198 through 202 removed outlier: 4.054A pdb=" N GLU C 201 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 214 removed outlier: 3.827A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) 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 40 through 45 Processing helix chain 'D' and resid 62 through 70 Processing helix chain 'D' and resid 98 through 103 removed outlier: 3.866A pdb=" N VAL D 101 " --> pdb=" O LYS D 98 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN D 103 " --> pdb=" O ASP D 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 42 removed outlier: 3.528A pdb=" N VAL E 33 " --> pdb=" O ASN E 29 " (cutoff:3.500A) 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 119 removed outlier: 3.716A pdb=" N ARG E 106 " --> pdb=" O PRO E 102 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG E 107 " --> pdb=" O LYS E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 146 removed outlier: 3.617A pdb=" N PHE E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 189 Processing helix chain 'E' and resid 196 through 206 Processing helix chain 'F' and resid 3 through 11 Processing helix chain 'F' and resid 11 through 21 Processing helix chain 'F' and resid 24 through 28 Processing helix chain 'F' and resid 41 through 45 removed outlier: 3.629A pdb=" N VAL F 44 " --> pdb=" O GLY F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 61 Processing helix chain 'F' and resid 93 through 106 removed outlier: 3.737A pdb=" N TYR F 97 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE F 99 " --> pdb=" O ARG F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 111 removed outlier: 3.754A pdb=" N VAL F 111 " --> pdb=" O LEU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 172 Processing helix chain 'G' and resid 63 through 81 removed outlier: 4.053A pdb=" N THR G 67 " --> pdb=" O THR G 63 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL G 79 " --> pdb=" O MET G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 150 removed outlier: 3.761A pdb=" N GLY G 150 " --> pdb=" O ALA G 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 25 through 39 removed outlier: 3.537A pdb=" N LEU K 29 " --> pdb=" O PRO K 25 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG K 38 " --> pdb=" O ALA K 34 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY K 39 " --> pdb=" O SER K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 95 removed outlier: 3.912A pdb=" N LEU K 93 " --> pdb=" O ALA K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 106 removed outlier: 3.659A pdb=" N LEU K 101 " --> pdb=" O ASN K 97 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE K 102 " --> pdb=" O SER K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 110 removed outlier: 3.820A pdb=" N LEU K 110 " --> pdb=" O LYS K 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 107 through 110' Processing helix chain 'K' and resid 114 through 119 Processing helix chain 'K' and resid 133 through 137 removed outlier: 3.547A pdb=" N GLN K 137 " --> pdb=" O ALA K 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 110 removed outlier: 3.723A pdb=" N ASN L 110 " --> pdb=" O ARG L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 117 Processing helix chain 'M' and resid 2 through 6 removed outlier: 3.885A pdb=" N LEU M 6 " --> pdb=" O LEU M 3 " (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 GLN M 133 " --> pdb=" O SER M 129 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU M 134 " --> pdb=" O LYS M 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 56 removed outlier: 4.303A pdb=" N ILE N 47 " --> pdb=" O THR N 43 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU N 48 " --> pdb=" O ASN N 44 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 123 removed outlier: 3.638A pdb=" N ALA N 114 " --> pdb=" O PRO N 110 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 21 removed outlier: 3.876A pdb=" N ARG O 13 " --> pdb=" O THR O 9 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYS O 14 " --> pdb=" O SER O 10 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR O 21 " --> pdb=" O LEU O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 33 through 50 removed outlier: 3.660A pdb=" N ALA O 37 " --> pdb=" O THR O 33 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR O 49 " --> pdb=" O GLU O 45 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU O 50 " --> pdb=" O LYS O 46 " (cutoff:3.500A) Processing helix chain 'O' and resid 88 through 93 Processing helix chain 'P' and resid 7 through 22 Processing helix chain 'P' and resid 68 through 87 removed outlier: 3.904A pdb=" N ALA P 72 " --> pdb=" O LYS P 68 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS P 86 " --> pdb=" O ARG P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 113 removed outlier: 3.701A pdb=" N ALA P 110 " --> pdb=" O ALA P 106 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 9 Processing helix chain 'Q' and resid 97 through 101 removed outlier: 3.537A pdb=" N ARG Q 101 " --> pdb=" O TYR Q 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 104 through 108 Processing helix chain 'R' and resid 9 through 14 Processing helix chain 'R' and resid 26 through 30 removed outlier: 3.625A pdb=" N HIS R 29 " --> pdb=" O GLY R 26 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR R 30 " --> pdb=" O SER R 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 26 through 30' Processing helix chain 'R' and resid 31 through 72 removed outlier: 4.801A pdb=" N GLU R 37 " --> pdb=" O LYS R 33 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N MET R 40 " --> pdb=" O LYS R 36 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN R 41 " --> pdb=" O GLU R 37 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG R 51 " --> pdb=" O PHE R 47 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS R 54 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS R 59 " --> pdb=" O ARG R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 86 Processing helix chain 'R' and resid 91 through 101 Processing helix chain 'R' and resid 102 through 117 Processing helix chain 'T' and resid 19 through 24 removed outlier: 3.941A pdb=" N LEU T 24 " --> pdb=" O ARG T 20 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 28 Processing helix chain 'T' and resid 33 through 42 removed outlier: 3.751A pdb=" N SER T 39 " --> pdb=" O ALA T 35 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 66 removed outlier: 3.785A pdb=" N GLU T 53 " --> pdb=" O ALA T 49 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS T 54 " --> pdb=" O GLY T 50 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN T 66 " --> pdb=" O ASN T 62 " (cutoff:3.500A) Processing helix chain 'T' and resid 70 through 74 removed outlier: 3.762A pdb=" N LEU T 74 " --> pdb=" O VAL T 71 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 20 Processing helix chain 'U' and resid 21 through 23 No H-bonds generated for 'chain 'U' and resid 21 through 23' Processing helix chain 'U' and resid 34 through 43 removed outlier: 3.828A pdb=" N VAL U 38 " --> pdb=" O ASN U 34 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 46 No H-bonds generated for 'chain 'U' and resid 45 through 46' 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 15 through 17 No H-bonds generated for 'chain 'W' and resid 15 through 17' Processing helix chain 'W' and resid 18 through 20 No H-bonds generated for 'chain 'W' and resid 18 through 20' Processing helix chain 'W' and resid 22 through 23 No H-bonds generated for 'chain 'W' and resid 22 through 23' Processing helix chain 'W' and resid 44 through 53 removed outlier: 4.022A pdb=" N LEU W 48 " --> pdb=" O GLU W 44 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER W 49 " --> pdb=" O GLU W 45 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LYS W 50 " --> pdb=" O LYS W 46 " (cutoff:3.500A) Processing helix chain 'Y' and resid 52 through 54 No H-bonds generated for 'chain 'Y' and resid 52 through 54' Processing helix chain 'Z' and resid 5 through 9 Processing helix chain 'Z' and resid 10 through 31 removed outlier: 3.649A pdb=" N GLN Z 31 " --> pdb=" O ASN Z 27 " (cutoff:3.500A) Processing helix chain 'Z' and resid 43 through 60 removed outlier: 3.537A pdb=" N ARG Z 47 " --> pdb=" O ILE Z 43 " (cutoff:3.500A) Processing helix chain '0' and resid 16 through 26 removed outlier: 3.688A pdb=" N ARG 0 20 " --> pdb=" O PRO 0 16 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA 0 21 " --> pdb=" O GLN 0 17 " (cutoff:3.500A) Processing helix chain '0' and resid 42 through 48 Processing helix chain '2' and resid 9 through 18 removed outlier: 3.771A pdb=" N LYS 2 13 " --> pdb=" O SER 2 9 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA 2 14 " --> pdb=" O LYS 2 10 " (cutoff:3.500A) Processing helix chain '4' and resid 10 through 14 Processing helix chain '4' and resid 18 through 22 Processing helix chain '4' and resid 27 through 36 Processing helix chain '5' and resid 7 through 12 Processing helix chain '5' and resid 37 through 43 removed outlier: 3.556A pdb=" N ARG 5 41 " --> pdb=" O THR 5 37 " (cutoff:3.500A) Processing helix chain '5' and resid 51 through 56 Processing sheet with id=AA1, first strand: chain 'c' and resid 54 through 56 Processing sheet with id=AA2, first strand: chain 'c' and resid 54 through 56 Processing sheet with id=AA3, first strand: chain 'c' and resid 166 through 170 removed outlier: 3.639A pdb=" N GLY c 147 " --> pdb=" O TYR c 202 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER c 153 " --> pdb=" O GLY c 196 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY c 196 " --> pdb=" O SER c 153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'd' and resid 121 through 122 Processing sheet with id=AA5, first strand: chain 'd' and resid 166 through 169 removed outlier: 3.603A pdb=" N SER d 167 " --> pdb=" O SER d 176 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP d 169 " --> pdb=" O GLU d 174 " (cutoff:3.500A) removed outlier: 3.567A 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 17 removed outlier: 5.962A pdb=" N ASP e 13 " --> pdb=" O GLY e 40 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLY e 40 " --> pdb=" O ASP e 13 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL e 15 " --> pdb=" O VAL e 38 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL e 38 " --> pdb=" O VAL e 15 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'e' and resid 21 through 24 Processing sheet with id=AA8, first strand: chain 'e' and resid 85 through 87 removed outlier: 3.899A pdb=" N LEU e 95 " --> pdb=" O LYS e 126 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS e 126 " --> pdb=" O LEU e 95 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ALA e 106 " --> pdb=" O SER e 125 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N SER e 127 " --> pdb=" O ALA e 106 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'f' and resid 39 through 50 removed outlier: 6.572A pdb=" N ASN f 67 " --> pdb=" O ILE f 41 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N SER f 43 " --> pdb=" O ILE f 65 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE f 65 " --> pdb=" O SER f 43 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ASP f 45 " --> pdb=" O TYR f 63 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N TYR f 63 " --> pdb=" O ASP f 45 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N GLU f 47 " --> pdb=" O GLY f 61 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLY f 61 " --> pdb=" O GLU f 47 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER f 70 " --> pdb=" O THR f 5 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL f 96 " --> pdb=" O GLU f 8 " (cutoff:3.500A) removed outlier: 3.511A 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 76 Processing sheet with id=AB2, first strand: chain 'h' and resid 24 through 27 removed outlier: 3.644A pdb=" N GLU h 50 " --> pdb=" O ARG h 61 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'h' and resid 76 through 79 removed outlier: 3.525A pdb=" N TRP h 132 " --> pdb=" O ASN h 76 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS h 78 " --> pdb=" O TYR h 130 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE h 105 " --> pdb=" O ILE h 128 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N TYR h 130 " --> pdb=" O ILE h 103 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE h 103 " --> pdb=" O TYR h 130 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE h 106 " --> pdb=" O ILE h 113 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'i' and resid 16 through 21 removed outlier: 5.183A pdb=" N LYS i 27 " --> pdb=" O VAL i 63 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL i 65 " --> pdb=" O LYS i 27 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N THR i 29 " --> pdb=" O VAL i 65 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL i 67 " --> pdb=" O THR i 29 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'j' and resid 5 through 11 removed outlier: 4.019A pdb=" N ILE j 6 " --> pdb=" O ILE j 76 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU j 10 " --> pdb=" O ARG j 72 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N THR j 69 " --> pdb=" O THR j 44 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N THR j 44 " --> pdb=" O THR j 69 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'j' and resid 49 through 52 removed outlier: 3.758A pdb=" N LYS n 57 " --> pdb=" O GLU j 66 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'k' and resid 41 through 45 removed outlier: 3.891A pdb=" N ALA k 43 " --> pdb=" O ILE k 34 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL k 82 " --> pdb=" O GLU k 106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'l' and resid 75 through 79 removed outlier: 6.971A pdb=" N ARG l 63 " --> pdb=" O THR l 52 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N THR l 52 " --> pdb=" O ARG l 63 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N TYR l 65 " --> pdb=" O VAL l 50 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N VAL l 50 " --> pdb=" O TYR l 65 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ARG l 67 " --> pdb=" O THR l 48 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS l 43 " --> pdb=" O LEU l 95 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'p' and resid 3 through 6 removed outlier: 3.711A pdb=" N LYS p 4 " --> pdb=" O ALA p 23 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N TYR p 18 " --> pdb=" O THR p 39 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N THR p 39 " --> pdb=" O TYR p 18 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE p 20 " --> pdb=" O VAL p 37 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU p 35 " --> pdb=" O VAL p 22 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'q' and resid 11 through 15 removed outlier: 8.103A pdb=" N GLN q 12 " --> pdb=" O GLU q 29 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLU q 29 " --> pdb=" O GLN q 12 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS q 45 " --> pdb=" O VAL q 28 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE q 76 " --> pdb=" O LYS q 48 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU q 78 " --> pdb=" O HIS q 50 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS q 63 " --> pdb=" O LEU q 79 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VAL q 81 " --> pdb=" O ILE q 61 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE q 61 " --> pdb=" O VAL q 81 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'q' and resid 32 through 33 Processing sheet with id=AC3, first strand: chain 's' and resid 48 through 52 removed outlier: 3.847A pdb=" N VAL s 60 " --> pdb=" O ILE s 49 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 3 through 4 removed outlier: 3.588A 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 35 Processing sheet with id=AC6, first strand: chain 'C' and resid 95 through 96 removed outlier: 3.909A 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 removed outlier: 3.530A pdb=" N ILE C 91 " --> pdb=" O GLU C 82 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 129 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: 3.564A pdb=" N GLY C 251 " --> pdb=" O SER C 248 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 9 through 14 removed outlier: 4.046A pdb=" N GLY D 11 " --> pdb=" O VAL D 27 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 34 through 39 removed outlier: 3.952A pdb=" N VAL D 34 " --> pdb=" O GLY D 52 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLN D 50 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N VAL D 38 " --> pdb=" O ALA D 48 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA D 48 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE D 79 " --> pdb=" O TYR D 53 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 170 through 174 removed outlier: 5.408A pdb=" N GLN D 172 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL D 110 " --> pdb=" O GLN D 172 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP D 109 " --> pdb=" O LYS D 203 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS D 203 " --> pdb=" O ASP D 109 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR D 201 " --> pdb=" O THR D 111 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 176 through 180 removed outlier: 6.880A pdb=" N LEU D 187 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N VAL D 179 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL D 185 " --> pdb=" O VAL D 179 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 16 through 18 removed outlier: 3.550A pdb=" N ILE E 17 " --> pdb=" O VAL E 4 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL E 4 " --> pdb=" O ILE E 17 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LEU E 123 " --> pdb=" O ASN E 3 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA E 5 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA E 125 " --> pdb=" O ALA E 5 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL E 124 " --> pdb=" O ALA E 194 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU E 153 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR E 195 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N VAL E 155 " --> pdb=" O THR E 195 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL E 176 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N VAL E 154 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 88 through 91 removed outlier: 4.135A pdb=" N ILE F 34 " --> pdb=" O LEU F 91 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 16 through 20 removed outlier: 3.644A pdb=" N GLU G 16 " --> pdb=" O LYS G 27 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS G 18 " --> pdb=" O THR G 25 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 83 through 84 removed outlier: 3.536A pdb=" N GLY G 135 " --> pdb=" O PHE G 83 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 88 through 89 Processing sheet with id=AE2, first strand: chain 'G' and resid 96 through 99 removed outlier: 3.780A pdb=" N GLN G 99 " --> pdb=" O LYS G 102 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS G 102 " --> pdb=" O GLN G 99 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 123 through 126 removed outlier: 4.890A pdb=" N ALA K 60 " --> pdb=" O ALA K 21 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP K 16 " --> pdb=" O GLU K 139 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 16 through 21 removed outlier: 6.502A pdb=" N ALA L 16 " --> pdb=" O ALA L 46 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ALA L 46 " --> pdb=" O ALA L 16 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLU L 18 " --> pdb=" O LYS L 44 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR L 42 " --> pdb=" O LEU L 20 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL L 61 " --> pdb=" O VAL L 85 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 76 through 78 removed outlier: 3.562A pdb=" N TYR L 76 " --> pdb=" O THR Q 73 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 102 through 103 removed outlier: 6.732A pdb=" N VAL L 102 " --> pdb=" O LEU L 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'M' and resid 110 through 111 removed outlier: 3.666A pdb=" N VAL M 111 " --> pdb=" O LYS M 127 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'M' and resid 122 through 125 removed outlier: 3.549A pdb=" N ALA M 125 " --> pdb=" O GLU M 144 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 63 through 66 removed outlier: 3.654A pdb=" N ALA N 107 " --> pdb=" O LYS N 63 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N PHE N 104 " --> pdb=" O LEU N 34 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU N 34 " --> pdb=" O PHE N 104 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 72 through 73 removed outlier: 3.726A pdb=" N LYS N 72 " --> pdb=" O VAL N 94 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 30 through 32 removed outlier: 3.502A pdb=" N ILE O 30 " --> pdb=" O ILE O 123 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 30 through 31 Processing sheet with id=AF4, first strand: chain 'P' and resid 30 through 31 removed outlier: 6.993A pdb=" N ALA P 42 " --> pdb=" O SER P 55 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N SER P 55 " --> pdb=" O ALA P 42 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL P 44 " --> pdb=" O LEU P 53 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 43 through 45 removed outlier: 3.572A pdb=" N GLY Q 45 " --> pdb=" O VAL Q 26 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL Q 26 " --> pdb=" O GLY Q 45 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 32 through 34 removed outlier: 3.521A pdb=" N GLU Q 34 " --> pdb=" O ARG Q 37 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'S' and resid 10 through 13 removed outlier: 6.719A pdb=" N ILE S 4 " --> pdb=" O ILE S 39 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'S' and resid 18 through 22 removed outlier: 4.114A pdb=" N GLN S 18 " --> pdb=" O ILE S 97 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'S' and resid 18 through 22 removed outlier: 4.114A pdb=" N GLN S 18 " --> pdb=" O ILE S 97 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'T' and resid 8 through 15 removed outlier: 3.783A pdb=" N ALA T 10 " --> pdb=" O VAL T 110 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N SER T 106 " --> pdb=" O THR T 14 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N THR T 113 " --> pdb=" O VAL T 76 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N VAL T 76 " --> pdb=" O THR T 113 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'T' and resid 87 through 90 removed outlier: 3.735A pdb=" N ARG T 89 " --> pdb=" O ILE T 101 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE T 101 " --> pdb=" O ARG T 89 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'U' and resid 25 through 28 removed outlier: 3.575A pdb=" N ASN U 54 " --> pdb=" O ILE U 79 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'V' and resid 23 through 26 removed outlier: 6.450A pdb=" N ILE V 34 " --> pdb=" O LEU V 24 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ALA V 26 " --> pdb=" O LYS V 32 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N LYS V 32 " --> pdb=" O ALA V 26 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'V' and resid 40 through 43 removed outlier: 3.688A pdb=" N VAL V 59 " --> pdb=" O VAL V 41 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS V 43 " --> pdb=" O LEU V 57 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU V 57 " --> pdb=" O LYS V 43 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'V' and resid 81 through 82 removed outlier: 3.504A pdb=" N VAL V 93 " --> pdb=" O ALA V 82 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'W' and resid 38 through 39 removed outlier: 3.549A pdb=" N VAL W 31 " --> pdb=" O THR W 39 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ILE W 30 " --> pdb=" O PHE W 91 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'X' and resid 31 through 32 removed outlier: 3.741A pdb=" N GLY X 31 " --> pdb=" O ARG X 48 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG X 48 " --> pdb=" O GLY X 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'X' and resid 54 through 55 removed outlier: 3.686A pdb=" N VAL X 88 " --> pdb=" O TYR X 55 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Y' and resid 33 through 40 Processing sheet with id=AH2, first strand: chain '0' and resid 34 through 38 removed outlier: 3.507A pdb=" N ASP 0 55 " --> pdb=" O THR 0 7 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain '2' and resid 27 through 28 Processing sheet with id=AH4, first strand: chain '3' and resid 4 through 5 Processing sheet with id=AH5, first strand: chain '3' and resid 7 through 9 Processing sheet with id=AH6, first strand: chain '5' and resid 14 through 16 Processing sheet with id=AH7, first strand: chain '6' and resid 24 through 25 1158 hydrogen bonds defined for protein. 3213 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3612 hydrogen bonds 5836 hydrogen bond angles 0 basepair planarities 1439 basepair parallelities 2294 stacking parallelities Total time for adding SS restraints: 208.42 Time building geometry restraints manager: 68.55 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: 15961 1.32 - 1.44: 65279 1.44 - 1.57: 59857 1.57 - 1.69: 9075 1.69 - 1.81: 241 Bond restraints: 150413 Sorted by residual: bond pdb=" C ARG d 29 " pdb=" N PRO d 30 " ideal model delta sigma weight residual 1.337 1.399 -0.063 9.80e-03 1.04e+04 4.09e+01 bond pdb=" C THR K 46 " pdb=" N PRO K 47 " ideal model delta sigma weight residual 1.333 1.300 0.033 7.80e-03 1.64e+04 1.78e+01 bond pdb=" C PHE Q 20 " pdb=" N ARG Q 21 " ideal model delta sigma weight residual 1.331 1.228 0.103 2.83e-02 1.25e+03 1.33e+01 bond pdb=" C LYS i 114 " pdb=" N LYS i 115 " ideal model delta sigma weight residual 1.331 1.296 0.035 1.36e-02 5.41e+03 6.59e+00 bond pdb=" CZ ARG 4 19 " pdb=" NH2 ARG 4 19 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 5.98e+00 ... (remaining 150408 not shown) Histogram of bond angle deviations from ideal: 96.97 - 105.04: 21491 105.04 - 113.10: 92993 113.10 - 121.17: 70849 121.17 - 129.23: 36384 129.23 - 137.30: 3826 Bond angle restraints: 225543 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 121.80 137.21 -15.41 2.44e+00 1.68e-01 3.99e+01 angle pdb=" C VAL M 15 " pdb=" N ARG M 16 " pdb=" CA ARG M 16 " ideal model delta sigma weight residual 121.54 133.27 -11.73 1.91e+00 2.74e-01 3.77e+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 97.78 13.52 2.30e+00 1.89e-01 3.45e+01 angle pdb=" C VAL U 50 " pdb=" N ALA U 51 " pdb=" CA ALA U 51 " ideal model delta sigma weight residual 121.54 132.40 -10.86 1.91e+00 2.74e-01 3.23e+01 angle pdb=" C HIS k 38 " pdb=" N GLY k 39 " pdb=" CA GLY k 39 " ideal model delta sigma weight residual 121.70 131.69 -9.99 1.80e+00 3.09e-01 3.08e+01 ... (remaining 225538 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 84409 35.89 - 71.78: 10553 71.78 - 107.67: 1201 107.67 - 143.56: 19 143.56 - 179.45: 26 Dihedral angle restraints: 96208 sinusoidal: 81378 harmonic: 14830 Sorted by residual: 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 -120.39 -59.61 0 5.00e+00 4.00e-02 1.42e+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 180.00 120.91 59.09 0 5.00e+00 4.00e-02 1.40e+02 dihedral pdb=" CA GLU G 46 " pdb=" C GLU G 46 " pdb=" N GLY G 47 " pdb=" CA GLY G 47 " ideal model delta harmonic sigma weight residual -180.00 -131.16 -48.84 0 5.00e+00 4.00e-02 9.54e+01 ... (remaining 96205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 26019 0.083 - 0.166: 2642 0.166 - 0.249: 224 0.249 - 0.333: 27 0.333 - 0.416: 11 Chirality restraints: 28923 Sorted by residual: chirality pdb=" CB ILE i 28 " pdb=" CA ILE i 28 " pdb=" CG1 ILE i 28 " pdb=" CG2 ILE i 28 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.32e+00 chirality pdb=" C3' C A 963 " pdb=" C4' C A 963 " pdb=" O3' C A 963 " pdb=" C2' C A 963 " both_signs ideal model delta sigma weight residual False -2.48 -2.06 -0.42 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" C1' G A1359 " pdb=" O4' G A1359 " pdb=" C2' G A1359 " pdb=" N9 G A1359 " both_signs ideal model delta sigma weight residual False 2.46 2.06 0.40 2.00e-01 2.50e+01 4.02e+00 ... (remaining 28920 not shown) Planarity restraints: 11684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP V 72 " 0.076 5.00e-02 4.00e+02 1.15e-01 2.12e+01 pdb=" N PRO V 73 " -0.199 5.00e-02 4.00e+02 pdb=" CA PRO V 73 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO V 73 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U A1507 " -0.055 2.00e-02 2.50e+03 2.77e-02 1.73e+01 pdb=" N1 U A1507 " 0.052 2.00e-02 2.50e+03 pdb=" C2 U A1507 " 0.010 2.00e-02 2.50e+03 pdb=" O2 U A1507 " 0.008 2.00e-02 2.50e+03 pdb=" N3 U A1507 " -0.004 2.00e-02 2.50e+03 pdb=" C4 U A1507 " -0.017 2.00e-02 2.50e+03 pdb=" O4 U A1507 " -0.006 2.00e-02 2.50e+03 pdb=" C5 U A1507 " -0.011 2.00e-02 2.50e+03 pdb=" C6 U A1507 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A2044 " -0.045 2.00e-02 2.50e+03 2.41e-02 1.60e+01 pdb=" N9 A A2044 " 0.053 2.00e-02 2.50e+03 pdb=" C8 A A2044 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A A2044 " 0.008 2.00e-02 2.50e+03 pdb=" C5 A A2044 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A A2044 " -0.037 2.00e-02 2.50e+03 pdb=" N6 A A2044 " 0.002 2.00e-02 2.50e+03 pdb=" N1 A A2044 " 0.006 2.00e-02 2.50e+03 pdb=" C2 A A2044 " 0.006 2.00e-02 2.50e+03 pdb=" N3 A A2044 " 0.007 2.00e-02 2.50e+03 pdb=" C4 A A2044 " 0.005 2.00e-02 2.50e+03 ... (remaining 11681 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 16130 2.72 - 3.26: 120161 3.26 - 3.81: 295794 3.81 - 4.35: 339921 4.35 - 4.90: 454756 Nonbonded interactions: 1226762 Sorted by model distance: nonbonded pdb=" OE1 GLU 3 39 " pdb="ZN ZN 3 101 " model vdw 2.169 2.230 nonbonded pdb=" OP2 G A 451 " pdb=" O2' C A2420 " model vdw 2.170 2.440 nonbonded pdb=" N9 A A2778 " pdb=" C5 A A2778 " model vdw 2.191 2.672 nonbonded pdb=" CD2 HIS 1 6 " pdb=" CE1 HIS 1 6 " model vdw 2.192 2.784 nonbonded pdb=" OG1 THR 3 43 " pdb="ZN ZN 3 101 " model vdw 2.196 2.230 ... (remaining 1226757 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: 4.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 21.730 Check model and map are aligned: 1.480 Set scattering table: 0.950 Process input model: 485.890 Find NCS groups from input model: 2.640 Set up NCS constraints: 0.360 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:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 519.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 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 0.107 150413 Z= 0.421 Angle : 1.046 16.438 225543 Z= 0.518 Chirality : 0.052 0.416 28923 Planarity : 0.007 0.115 11684 Dihedral : 23.442 179.455 86668 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.20 % Allowed : 14.78 % Favored : 85.02 % Rotamer: Outliers : 0.39 % Allowed : 2.36 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.28 % Twisted Proline : 1.55 % Twisted General : 0.54 % 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: -4.58 (0.09), residues: 5101 helix: -2.86 (0.10), residues: 1347 sheet: -2.35 (0.17), residues: 844 loop : -3.49 (0.09), residues: 2910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.004 TRP R 61 HIS 0.024 0.003 HIS C 142 PHE 0.041 0.004 PHE U 62 TYR 0.054 0.004 TYR C 62 ARG 0.022 0.001 ARG Q 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10202 Ramachandran restraints generated. 5101 Oldfield, 0 Emsley, 5101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10202 Ramachandran restraints generated. 5101 Oldfield, 0 Emsley, 5101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1252 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 1235 time to evaluate : 5.839 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 revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS K 118 " (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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 22 TRP cc_start: 0.6604 (m-10) cc_final: 0.5684 (m-10) REVERT: c 26 LYS cc_start: 0.7703 (ttpp) cc_final: 0.7357 (tptt) REVERT: c 99 HIS cc_start: 0.7756 (m-70) cc_final: 0.7303 (m90) REVERT: c 101 ASN cc_start: 0.7337 (t0) cc_final: 0.7126 (t0) REVERT: c 109 ASP cc_start: 0.3941 (t0) cc_final: 0.0208 (t0) REVERT: c 129 PHE cc_start: 0.8338 (p90) cc_final: 0.8057 (p90) REVERT: c 200 TRP cc_start: 0.6118 (m100) cc_final: 0.5862 (m-10) REVERT: d 41 ARG cc_start: 0.5928 (ptm-80) cc_final: 0.5726 (mtt180) REVERT: d 47 TYR cc_start: 0.7521 (t80) cc_final: 0.7154 (t80) REVERT: d 67 GLN cc_start: 0.9280 (tt0) cc_final: 0.8991 (mp10) REVERT: f 14 ARG cc_start: 0.7805 (mtm180) cc_final: 0.7528 (mtm-85) REVERT: f 31 THR cc_start: 0.9627 (p) cc_final: 0.9324 (p) REVERT: f 48 LYS cc_start: 0.9180 (tptt) cc_final: 0.8820 (tptp) REVERT: f 94 MET cc_start: 0.8725 (ttm) cc_final: 0.8248 (tmm) REVERT: g 33 ASP cc_start: 0.9009 (m-30) cc_final: 0.8519 (t70) REVERT: g 110 LEU cc_start: 0.7518 (mt) cc_final: 0.7102 (pp) REVERT: h 70 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8461 (tp30) REVERT: i 95 ARG cc_start: 0.9056 (ttp-170) cc_final: 0.8836 (ttp80) REVERT: i 103 LEU cc_start: 0.8199 (mt) cc_final: 0.7690 (tt) REVERT: i 104 LEU cc_start: 0.8083 (tp) cc_final: 0.7830 (pt) REVERT: i 107 ASP cc_start: 0.9126 (m-30) cc_final: 0.8631 (t0) REVERT: j 46 ARG cc_start: 0.7673 (ttp80) cc_final: 0.7343 (tmm160) REVERT: j 67 MET cc_start: 0.6656 (mmm) cc_final: 0.6288 (mmm) REVERT: j 88 MET cc_start: 0.7106 (ptm) cc_final: 0.6856 (ptm) REVERT: k 68 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8235 (mt-10) REVERT: k 77 HIS cc_start: 0.9317 (m-70) cc_final: 0.8755 (m-70) REVERT: l 21 SER cc_start: 0.9297 (m) cc_final: 0.8816 (p) REVERT: l 42 GLN cc_start: 0.8992 (pt0) cc_final: 0.8788 (pm20) REVERT: l 59 ASN cc_start: 0.8740 (m-40) cc_final: 0.8412 (m-40) REVERT: l 116 ASP cc_start: 0.7980 (t70) cc_final: 0.7711 (t0) REVERT: l 122 ASP cc_start: 0.7922 (t0) cc_final: 0.7292 (m-30) REVERT: o 8 LYS cc_start: 0.9334 (tptm) cc_final: 0.8755 (tmtt) REVERT: o 10 GLU cc_start: 0.9293 (tp30) cc_final: 0.8809 (tp30) REVERT: o 13 LYS cc_start: 0.9643 (mttt) cc_final: 0.9437 (mtmm) REVERT: o 37 ASN cc_start: 0.9044 (m110) cc_final: 0.8814 (t0) REVERT: o 38 GLN cc_start: 0.9510 (mt0) cc_final: 0.9090 (mp10) REVERT: o 57 MET cc_start: 0.9075 (mmm) cc_final: 0.8858 (tmm) REVERT: o 75 ILE cc_start: 0.9564 (pt) cc_final: 0.9341 (mt) REVERT: o 76 GLN cc_start: 0.9429 (tt0) cc_final: 0.8956 (tp-100) REVERT: p 18 TYR cc_start: 0.8671 (m-10) cc_final: 0.8087 (m-10) REVERT: p 68 ASP cc_start: 0.9209 (p0) cc_final: 0.8946 (p0) REVERT: q 20 MET cc_start: 0.8831 (mtm) cc_final: 0.8063 (mmp) REVERT: q 52 GLU cc_start: 0.9553 (mm-30) cc_final: 0.9283 (pt0) REVERT: r 15 ASP cc_start: 0.8807 (m-30) cc_final: 0.8409 (p0) REVERT: r 25 ILE cc_start: 0.7437 (pp) cc_final: 0.7073 (pp) REVERT: s 74 PHE cc_start: 0.3040 (m-80) cc_final: 0.2761 (m-80) REVERT: t 59 MET cc_start: 0.8533 (mmm) cc_final: 0.8042 (mmm) REVERT: t 75 LYS cc_start: 0.9356 (mtmm) cc_final: 0.9136 (mttp) REVERT: C 5 LYS cc_start: 0.9677 (mttt) cc_final: 0.9291 (tptt) REVERT: C 114 MET cc_start: 0.8600 (mmm) cc_final: 0.8267 (mmm) REVERT: D 21 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8569 (mm-30) REVERT: D 100 ASP cc_start: 0.9080 (m-30) cc_final: 0.8804 (p0) REVERT: D 152 ASN cc_start: 0.9235 (m-40) cc_final: 0.8755 (p0) REVERT: E 83 TRP cc_start: 0.8290 (m100) cc_final: 0.7997 (m100) REVERT: E 141 GLN cc_start: 0.9336 (tp-100) cc_final: 0.8973 (tp-100) REVERT: F 10 LYS cc_start: 0.9749 (mttt) cc_final: 0.9263 (pttp) REVERT: F 11 GLU cc_start: 0.9288 (mt-10) cc_final: 0.9047 (mm-30) REVERT: F 96 MET cc_start: 0.9129 (mmm) cc_final: 0.8676 (mmm) REVERT: G 99 GLN cc_start: 0.9000 (mt0) cc_final: 0.8762 (mp10) REVERT: K 77 ARG cc_start: 0.8248 (mtt180) cc_final: 0.7573 (mtm180) REVERT: K 100 ARG cc_start: 0.8943 (tpp80) cc_final: 0.8725 (tpp80) REVERT: K 103 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7970 (mt-10) REVERT: K 109 MET cc_start: 0.9173 (mmm) cc_final: 0.8890 (mmm) REVERT: K 124 ASN cc_start: 0.8612 (m-40) cc_final: 0.8221 (m-40) REVERT: L 53 LYS cc_start: 0.9105 (mttt) cc_final: 0.8587 (mttt) REVERT: L 54 LYS cc_start: 0.8641 (mttt) cc_final: 0.8238 (ttmt) REVERT: L 110 ASN cc_start: 0.9273 (m-40) cc_final: 0.8531 (t0) REVERT: L 120 GLU cc_start: 0.8547 (tt0) cc_final: 0.7928 (mp0) REVERT: L 122 LEU cc_start: 0.8626 (mt) cc_final: 0.8252 (mp) REVERT: M 27 ASN cc_start: 0.9134 (m-40) cc_final: 0.8825 (p0) REVERT: M 51 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7614 (tm-30) REVERT: N 1 MET cc_start: -0.1497 (mmm) cc_final: -0.2880 (mmm) REVERT: N 63 LYS cc_start: 0.9113 (mttt) cc_final: 0.8907 (tppp) REVERT: O 23 ASP cc_start: 0.8181 (m-30) cc_final: 0.7968 (t0) REVERT: O 30 ILE cc_start: 0.8649 (mt) cc_final: 0.8352 (tp) REVERT: O 80 ILE cc_start: 0.8474 (mt) cc_final: 0.7932 (tp) REVERT: P 45 ILE cc_start: 0.8883 (mt) cc_final: 0.8509 (mt) REVERT: P 46 ASP cc_start: 0.8644 (m-30) cc_final: 0.8042 (p0) REVERT: Q 4 LEU cc_start: 0.9248 (mt) cc_final: 0.8756 (tt) REVERT: Q 58 THR cc_start: 0.8552 (p) cc_final: 0.8115 (p) REVERT: Q 85 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7521 (tm-30) REVERT: R 49 ASP cc_start: 0.8531 (m-30) cc_final: 0.8308 (m-30) REVERT: R 70 ARG cc_start: 0.9171 (tpp80) cc_final: 0.8559 (tpp-160) REVERT: R 71 MET cc_start: 0.9495 (mmm) cc_final: 0.9097 (mmm) REVERT: T 20 ARG cc_start: 0.8436 (mtt180) cc_final: 0.8192 (mtt-85) REVERT: T 87 MET cc_start: 0.8274 (mmm) cc_final: 0.7431 (mmm) REVERT: T 114 GLU cc_start: 0.6336 (mt-10) cc_final: 0.5905 (mt-10) REVERT: U 3 LEU cc_start: 0.9328 (mt) cc_final: 0.9007 (tt) REVERT: V 79 THR cc_start: 0.6716 (p) cc_final: 0.5904 (p) REVERT: W 76 LYS cc_start: 0.6680 (mttt) cc_final: 0.6184 (tttp) REVERT: X 53 LYS cc_start: 0.9479 (mttt) cc_final: 0.9274 (mmmm) REVERT: Y 49 VAL cc_start: 0.9315 (t) cc_final: 0.9005 (m) REVERT: 0 55 ASP cc_start: 0.8917 (m-30) cc_final: 0.8705 (m-30) REVERT: 2 49 TYR cc_start: 0.7532 (OUTLIER) cc_final: 0.6900 (m-10) REVERT: 4 6 GLN cc_start: 0.9102 (mt0) cc_final: 0.8814 (tm-30) REVERT: 4 25 LYS cc_start: 0.8997 (mttt) cc_final: 0.8400 (mtmt) REVERT: 5 64 ARG cc_start: 0.8676 (mtt180) cc_final: 0.8449 (mmt180) outliers start: 17 outliers final: 6 residues processed: 1247 average time/residue: 1.2511 time to fit residues: 2625.6011 Evaluate side-chains 695 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 688 time to evaluate : 5.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 803 optimal weight: 6.9990 chunk 720 optimal weight: 8.9990 chunk 399 optimal weight: 20.0000 chunk 246 optimal weight: 50.0000 chunk 486 optimal weight: 10.0000 chunk 385 optimal weight: 20.0000 chunk 745 optimal weight: 0.5980 chunk 288 optimal weight: 10.0000 chunk 453 optimal weight: 10.0000 chunk 554 optimal weight: 10.0000 chunk 863 optimal weight: 0.9990 overall best weight: 5.5190 ------------------------------------------------------------------------------- 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 d 147 GLN d 200 ASN g 28 ASN ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 106 ASN g 142 HIS ** i 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 66 ASN i 75 GLN i 89 GLN i 126 GLN l 39 ASN l 86 ASN ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 9 ASN o 28 GLN q 7 GLN ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 50 HIS q 54 ASN r 56 GLN s 22 GLN t 18 ASN t 21 ASN ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 72 ASN C 15 ASN C 40 ASN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN C 177 ASN C 197 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN E 20 ASN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 HIS E 67 GLN E 75 GLN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 ASN G 73 ASN G 147 ASN K 119 GLN L 110 ASN M 54 GLN N 40 HIS O 68 ASN ** P 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 ASN Q 12 GLN ** Q 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 81 HIS ** S 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 101 ASN ** T 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 88 HIS X 38 GLN X 59 ASN X 87 GLN ** 0 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 40 ASN 0 48 ASN ** 2 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 40 HIS 3 4 ASN ** 3 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 150413 Z= 0.216 Angle : 0.684 16.203 225543 Z= 0.353 Chirality : 0.038 0.369 28923 Planarity : 0.005 0.105 11684 Dihedral : 24.420 179.434 76255 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.94 % Favored : 87.94 % Rotamer: Outliers : 0.07 % Allowed : 2.80 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.28 % Twisted Proline : 0.52 % Twisted General : 0.32 % 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: -3.72 (0.10), residues: 5101 helix: -1.54 (0.12), residues: 1390 sheet: -2.02 (0.17), residues: 869 loop : -3.23 (0.10), residues: 2842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 93 HIS 0.009 0.001 HIS s 14 PHE 0.021 0.002 PHE G 123 TYR 0.029 0.002 TYR N 74 ARG 0.014 0.001 ARG 3 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10202 Ramachandran restraints generated. 5101 Oldfield, 0 Emsley, 5101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10202 Ramachandran restraints generated. 5101 Oldfield, 0 Emsley, 5101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 911 time to evaluate : 5.877 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 TARDY: cannot create tardy model for: "LYS K 118 " (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 TARDY: cannot create tardy model for: "TYR R 43 " (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: c 22 TRP cc_start: 0.6405 (m-10) cc_final: 0.5858 (m-10) REVERT: c 26 LYS cc_start: 0.7655 (ttpp) cc_final: 0.7230 (tptt) REVERT: c 101 ASN cc_start: 0.7346 (t0) cc_final: 0.7095 (t0) REVERT: c 111 ASP cc_start: 0.7921 (t0) cc_final: 0.7714 (t0) REVERT: d 47 TYR cc_start: 0.7526 (t80) cc_final: 0.7187 (t80) REVERT: d 88 MET cc_start: 0.9145 (mmp) cc_final: 0.8858 (mmm) REVERT: d 201 GLN cc_start: 0.7526 (mt0) cc_final: 0.7153 (pm20) REVERT: e 76 MET cc_start: 0.8522 (tpp) cc_final: 0.8263 (tpp) REVERT: f 48 LYS cc_start: 0.8993 (tptt) cc_final: 0.8661 (tptp) REVERT: f 94 MET cc_start: 0.8390 (ttm) cc_final: 0.8024 (tmm) REVERT: g 9 LYS cc_start: 0.8285 (ptmm) cc_final: 0.7890 (pptt) REVERT: g 33 ASP cc_start: 0.8933 (m-30) cc_final: 0.8519 (t70) REVERT: g 110 LEU cc_start: 0.7610 (mt) cc_final: 0.7147 (pp) REVERT: h 5 ASP cc_start: 0.8671 (t0) cc_final: 0.8160 (p0) REVERT: h 61 ARG cc_start: 0.8669 (mtt180) cc_final: 0.8385 (mtt90) REVERT: h 70 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8426 (tp30) REVERT: h 76 ASN cc_start: 0.8414 (t0) cc_final: 0.8077 (t0) REVERT: i 46 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8525 (tt0) REVERT: i 103 LEU cc_start: 0.8210 (mt) cc_final: 0.7686 (tt) REVERT: i 107 ASP cc_start: 0.9143 (m-30) cc_final: 0.8567 (t0) REVERT: j 10 LEU cc_start: 0.5130 (mp) cc_final: 0.4673 (mp) REVERT: j 85 ASP cc_start: 0.7768 (m-30) cc_final: 0.7554 (m-30) REVERT: j 88 MET cc_start: 0.6991 (ptm) cc_final: 0.6490 (ppp) REVERT: k 17 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8068 (mm-30) REVERT: k 33 MET cc_start: 0.7608 (tpt) cc_final: 0.7267 (tpt) REVERT: k 34 ILE cc_start: 0.9209 (mp) cc_final: 0.8957 (tp) REVERT: k 68 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8314 (mt-10) REVERT: k 77 HIS cc_start: 0.9255 (m-70) cc_final: 0.8654 (m-70) REVERT: k 122 ARG cc_start: 0.9061 (mtp180) cc_final: 0.8629 (mtp-110) REVERT: l 21 SER cc_start: 0.9057 (m) cc_final: 0.8831 (p) REVERT: l 42 GLN cc_start: 0.8975 (pt0) cc_final: 0.8751 (pm20) REVERT: l 59 ASN cc_start: 0.8774 (m-40) cc_final: 0.8503 (m-40) REVERT: l 103 LEU cc_start: 0.8630 (tt) cc_final: 0.8269 (mm) REVERT: l 116 ASP cc_start: 0.8291 (t70) cc_final: 0.7960 (t0) REVERT: l 122 ASP cc_start: 0.7747 (t0) cc_final: 0.7294 (m-30) REVERT: o 8 LYS cc_start: 0.9233 (tptm) cc_final: 0.8996 (tmtt) REVERT: o 34 GLU cc_start: 0.8669 (mp0) cc_final: 0.8434 (mp0) REVERT: o 38 GLN cc_start: 0.9375 (mt0) cc_final: 0.9153 (mp10) REVERT: o 75 ILE cc_start: 0.9468 (pt) cc_final: 0.9166 (mt) REVERT: o 76 GLN cc_start: 0.9506 (tt0) cc_final: 0.9046 (tp-100) REVERT: o 79 ARG cc_start: 0.8964 (mtm180) cc_final: 0.8492 (mtm180) REVERT: p 68 ASP cc_start: 0.9113 (p0) cc_final: 0.8861 (p0) REVERT: p 73 ILE cc_start: 0.9201 (pt) cc_final: 0.8846 (pt) REVERT: q 14 ARG cc_start: 0.8366 (ptm-80) cc_final: 0.7633 (ptm-80) REVERT: q 20 MET cc_start: 0.8869 (mtm) cc_final: 0.8104 (mmt) REVERT: r 15 ASP cc_start: 0.8946 (m-30) cc_final: 0.8574 (p0) REVERT: s 66 MET cc_start: 0.6473 (ttm) cc_final: 0.5689 (ttt) REVERT: t 59 MET cc_start: 0.8492 (mmm) cc_final: 0.7981 (mmt) REVERT: t 80 LYS cc_start: 0.9669 (mtmt) cc_final: 0.9448 (mmtt) REVERT: C 5 LYS cc_start: 0.9656 (mttt) cc_final: 0.9261 (tptt) REVERT: D 152 ASN cc_start: 0.9244 (m-40) cc_final: 0.8816 (p0) REVERT: E 83 TRP cc_start: 0.8088 (m100) cc_final: 0.7645 (m100) REVERT: E 141 GLN cc_start: 0.9297 (tp-100) cc_final: 0.8951 (tp-100) REVERT: E 185 ASP cc_start: 0.8983 (m-30) cc_final: 0.8724 (p0) REVERT: F 10 LYS cc_start: 0.9743 (mttt) cc_final: 0.9361 (pttp) REVERT: F 26 MET cc_start: 0.7987 (mmm) cc_final: 0.7784 (mmm) REVERT: F 96 MET cc_start: 0.9026 (mmm) cc_final: 0.8788 (mmm) REVERT: K 77 ARG cc_start: 0.8149 (mtt180) cc_final: 0.7469 (mtm180) REVERT: K 124 ASN cc_start: 0.8366 (m-40) cc_final: 0.7854 (m-40) REVERT: L 81 GLU cc_start: 0.8398 (mp0) cc_final: 0.7938 (mp0) REVERT: L 110 ASN cc_start: 0.9379 (m110) cc_final: 0.8518 (t0) REVERT: L 112 MET cc_start: 0.8751 (pmm) cc_final: 0.7883 (pmm) REVERT: L 120 GLU cc_start: 0.8526 (tt0) cc_final: 0.7877 (mp0) REVERT: L 122 LEU cc_start: 0.8739 (mt) cc_final: 0.8527 (mp) REVERT: M 27 ASN cc_start: 0.9078 (m-40) cc_final: 0.8773 (p0) REVERT: N 1 MET cc_start: -0.1194 (mmm) cc_final: -0.2644 (mmm) REVERT: N 54 MET cc_start: 0.8673 (mtp) cc_final: 0.8356 (mtp) REVERT: N 63 LYS cc_start: 0.8957 (mttt) cc_final: 0.8645 (tppp) REVERT: N 64 VAL cc_start: 0.8837 (t) cc_final: 0.8421 (t) REVERT: O 23 ASP cc_start: 0.8324 (m-30) cc_final: 0.7997 (t0) REVERT: O 47 MET cc_start: 0.8296 (tmm) cc_final: 0.8063 (tmm) REVERT: O 80 ILE cc_start: 0.8297 (mt) cc_final: 0.7791 (tp) REVERT: Q 4 LEU cc_start: 0.9388 (mt) cc_final: 0.8889 (tt) REVERT: R 71 MET cc_start: 0.9473 (mmm) cc_final: 0.9002 (mmm) REVERT: S 31 GLU cc_start: 0.8652 (mp0) cc_final: 0.8167 (mp0) REVERT: T 70 ASP cc_start: 0.9102 (t0) cc_final: 0.8756 (t0) REVERT: T 72 GLU cc_start: 0.9085 (mp0) cc_final: 0.8750 (pm20) REVERT: T 114 GLU cc_start: 0.6143 (mt-10) cc_final: 0.5686 (mt-10) REVERT: U 20 MET cc_start: 0.8930 (mmm) cc_final: 0.8728 (mmm) REVERT: U 59 ARG cc_start: 0.7596 (mtt180) cc_final: 0.7368 (mtt180) REVERT: W 76 LYS cc_start: 0.6639 (mttt) cc_final: 0.5938 (tptm) REVERT: W 80 ASP cc_start: 0.8880 (t0) cc_final: 0.8183 (p0) REVERT: X 53 LYS cc_start: 0.9459 (mttt) cc_final: 0.9219 (mmmm) REVERT: Y 49 VAL cc_start: 0.9137 (t) cc_final: 0.8727 (m) REVERT: Z 14 MET cc_start: 0.6748 (mtt) cc_final: 0.6329 (mtp) REVERT: 0 15 ARG cc_start: 0.8566 (tpp80) cc_final: 0.8199 (mtt-85) REVERT: 0 46 MET cc_start: 0.8646 (mmt) cc_final: 0.8381 (mmt) REVERT: 0 55 ASP cc_start: 0.9003 (m-30) cc_final: 0.8768 (m-30) REVERT: 2 36 MET cc_start: 0.8938 (mmp) cc_final: 0.8733 (mmm) REVERT: 2 53 ASP cc_start: 0.9157 (t0) cc_final: 0.8791 (t0) REVERT: 3 46 ARG cc_start: 0.9154 (ptm160) cc_final: 0.8689 (ptm160) REVERT: 4 11 LYS cc_start: 0.7677 (mttt) cc_final: 0.7428 (mttm) REVERT: 4 25 LYS cc_start: 0.8863 (mttt) cc_final: 0.8323 (mtmt) REVERT: 5 64 ARG cc_start: 0.8723 (mtt180) cc_final: 0.8428 (mmt180) outliers start: 3 outliers final: 0 residues processed: 912 average time/residue: 1.3252 time to fit residues: 2100.9294 Evaluate side-chains 669 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 669 time to evaluate : 5.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 479 optimal weight: 20.0000 chunk 268 optimal weight: 20.0000 chunk 718 optimal weight: 20.0000 chunk 588 optimal weight: 20.0000 chunk 238 optimal weight: 7.9990 chunk 865 optimal weight: 7.9990 chunk 934 optimal weight: 0.0370 chunk 770 optimal weight: 2.9990 chunk 857 optimal weight: 30.0000 chunk 294 optimal weight: 40.0000 chunk 694 optimal weight: 0.6980 overall best weight: 3.9464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 6 HIS ** d 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 142 HIS ** i 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 75 GLN k 38 HIS n 10 ASN ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 38 HIS n 52 GLN o 28 GLN o 46 HIS ** p 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 18 ASN t 69 ASN C 15 ASN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 HIS D 184 ASN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 ASN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 131 HIS L 110 ASN M 38 GLN N 9 HIS N 35 GLN ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 65 ASN U 57 ASN Y 23 ASN 2 32 ASN 3 25 ASN 3 26 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 150413 Z= 0.169 Angle : 0.606 17.378 225543 Z= 0.311 Chirality : 0.035 0.350 28923 Planarity : 0.005 0.099 11684 Dihedral : 24.205 179.990 76255 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.61 % Favored : 88.30 % Rotamer: Outliers : 0.05 % Allowed : 3.95 % Favored : 96.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.28 % Twisted Proline : 0.52 % Twisted General : 0.26 % 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: -3.13 (0.11), residues: 5101 helix: -0.75 (0.13), residues: 1389 sheet: -1.60 (0.18), residues: 816 loop : -3.05 (0.10), residues: 2896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP c 200 HIS 0.008 0.001 HIS C 142 PHE 0.021 0.002 PHE s 41 TYR 0.027 0.002 TYR N 74 ARG 0.011 0.001 ARG c 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10202 Ramachandran restraints generated. 5101 Oldfield, 0 Emsley, 5101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10202 Ramachandran restraints generated. 5101 Oldfield, 0 Emsley, 5101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 872 time to evaluate : 7.527 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 TARDY: cannot create tardy model for: "LYS K 118 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR R 43 " (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: c 22 TRP cc_start: 0.6270 (m-10) cc_final: 0.5540 (m-10) REVERT: c 111 ASP cc_start: 0.7727 (t0) cc_final: 0.7500 (t0) REVERT: c 123 LEU cc_start: 0.8670 (tp) cc_final: 0.8202 (pp) REVERT: d 47 TYR cc_start: 0.7389 (t80) cc_final: 0.7097 (t80) REVERT: e 76 MET cc_start: 0.8482 (tpp) cc_final: 0.8276 (tpp) REVERT: f 10 MET cc_start: 0.7829 (tmm) cc_final: 0.7589 (tmm) REVERT: f 48 LYS cc_start: 0.9053 (tptt) cc_final: 0.8652 (tptp) REVERT: f 51 LEU cc_start: 0.8896 (mm) cc_final: 0.8097 (mt) REVERT: g 33 ASP cc_start: 0.8943 (m-30) cc_final: 0.8523 (t70) REVERT: g 110 LEU cc_start: 0.7533 (mt) cc_final: 0.7089 (pp) REVERT: h 5 ASP cc_start: 0.8656 (t0) cc_final: 0.7429 (p0) REVERT: h 42 ARG cc_start: 0.9349 (ttm110) cc_final: 0.8975 (ptp-110) REVERT: h 70 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8379 (tp30) REVERT: h 76 ASN cc_start: 0.8479 (t0) cc_final: 0.8162 (t0) REVERT: i 46 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8792 (tt0) REVERT: i 103 LEU cc_start: 0.8062 (mt) cc_final: 0.7792 (tt) REVERT: i 107 ASP cc_start: 0.9155 (m-30) cc_final: 0.8522 (t0) REVERT: k 77 HIS cc_start: 0.9170 (m-70) cc_final: 0.8672 (m-70) REVERT: l 59 ASN cc_start: 0.8566 (m-40) cc_final: 0.8256 (m-40) REVERT: l 116 ASP cc_start: 0.8348 (t70) cc_final: 0.8072 (t0) REVERT: l 122 ASP cc_start: 0.7776 (t0) cc_final: 0.7327 (m-30) REVERT: m 46 ARG cc_start: 0.6575 (ttp80) cc_final: 0.5806 (ttm110) REVERT: o 34 GLU cc_start: 0.8637 (mp0) cc_final: 0.8364 (mp0) REVERT: o 37 ASN cc_start: 0.9357 (t0) cc_final: 0.8961 (t0) REVERT: o 41 GLU cc_start: 0.9215 (tp30) cc_final: 0.8831 (tp30) REVERT: o 75 ILE cc_start: 0.9471 (pt) cc_final: 0.9200 (mt) REVERT: o 76 GLN cc_start: 0.9556 (tt0) cc_final: 0.9203 (tp-100) REVERT: o 79 ARG cc_start: 0.9010 (mtm180) cc_final: 0.8528 (mtm180) REVERT: p 18 TYR cc_start: 0.8797 (m-10) cc_final: 0.8220 (m-10) REVERT: p 68 ASP cc_start: 0.9136 (p0) cc_final: 0.8909 (p0) REVERT: p 73 ILE cc_start: 0.9171 (pt) cc_final: 0.8933 (mm) REVERT: q 14 ARG cc_start: 0.8584 (ptm-80) cc_final: 0.8265 (ttp80) REVERT: q 20 MET cc_start: 0.8576 (mtm) cc_final: 0.7717 (mmp) REVERT: q 21 ASP cc_start: 0.9272 (m-30) cc_final: 0.9048 (p0) REVERT: r 15 ASP cc_start: 0.8991 (m-30) cc_final: 0.8611 (p0) REVERT: r 55 ASN cc_start: 0.9233 (m-40) cc_final: 0.9013 (m-40) REVERT: t 59 MET cc_start: 0.8496 (mmm) cc_final: 0.8018 (mmm) REVERT: t 70 LYS cc_start: 0.8917 (ttmt) cc_final: 0.8690 (ttmm) REVERT: t 80 LYS cc_start: 0.9633 (mtmt) cc_final: 0.9426 (mmtt) REVERT: C 5 LYS cc_start: 0.9635 (mttt) cc_final: 0.9399 (mmmt) REVERT: C 16 MET cc_start: 0.7926 (mmt) cc_final: 0.7715 (mmt) REVERT: D 37 GLN cc_start: 0.8791 (tp-100) cc_final: 0.8378 (tp40) REVERT: D 152 ASN cc_start: 0.9180 (m-40) cc_final: 0.8849 (p0) REVERT: D 180 ASP cc_start: 0.9476 (m-30) cc_final: 0.8499 (t0) REVERT: E 13 GLN cc_start: 0.8906 (tp-100) cc_final: 0.8687 (tp-100) REVERT: E 83 TRP cc_start: 0.8036 (m100) cc_final: 0.7768 (m-10) REVERT: E 141 GLN cc_start: 0.9168 (tp-100) cc_final: 0.8827 (tp-100) REVERT: E 161 ASP cc_start: 0.9096 (m-30) cc_final: 0.8829 (p0) REVERT: F 7 LYS cc_start: 0.9644 (mttt) cc_final: 0.9403 (ttpp) REVERT: F 97 TYR cc_start: 0.9147 (m-80) cc_final: 0.8937 (m-10) REVERT: K 75 TYR cc_start: 0.9001 (m-80) cc_final: 0.8666 (m-80) REVERT: K 77 ARG cc_start: 0.8215 (mtt180) cc_final: 0.7592 (mtm180) REVERT: L 1 MET cc_start: 0.7414 (mmt) cc_final: 0.6968 (mmp) REVERT: L 81 GLU cc_start: 0.8602 (mp0) cc_final: 0.8173 (mp0) REVERT: L 120 GLU cc_start: 0.8532 (tt0) cc_final: 0.7810 (mp0) REVERT: N 1 MET cc_start: -0.1146 (mmm) cc_final: -0.2581 (mmm) REVERT: N 46 GLN cc_start: 0.8576 (mt0) cc_final: 0.7811 (mm-40) REVERT: N 54 MET cc_start: 0.8908 (mtp) cc_final: 0.8701 (mtm) REVERT: N 58 MET cc_start: 0.8830 (tpt) cc_final: 0.8141 (tpt) REVERT: N 63 LYS cc_start: 0.8985 (mttt) cc_final: 0.8638 (tppp) REVERT: N 64 VAL cc_start: 0.9020 (t) cc_final: 0.8504 (t) REVERT: N 69 PHE cc_start: 0.8008 (m-80) cc_final: 0.7721 (m-80) REVERT: O 80 ILE cc_start: 0.8338 (mt) cc_final: 0.7793 (tp) REVERT: P 45 ILE cc_start: 0.9020 (mm) cc_final: 0.8492 (mm) REVERT: P 46 ASP cc_start: 0.8330 (m-30) cc_final: 0.8041 (t70) REVERT: Q 4 LEU cc_start: 0.9368 (mt) cc_final: 0.8847 (tt) REVERT: T 23 ARG cc_start: 0.7647 (mtt180) cc_final: 0.6949 (mtt90) REVERT: T 114 GLU cc_start: 0.6449 (mt-10) cc_final: 0.6242 (mt-10) REVERT: U 20 MET cc_start: 0.9007 (mmm) cc_final: 0.8721 (mmm) REVERT: U 59 ARG cc_start: 0.7252 (mtt180) cc_final: 0.7008 (ttt180) REVERT: W 76 LYS cc_start: 0.7114 (mttt) cc_final: 0.6320 (tptm) REVERT: W 80 ASP cc_start: 0.8526 (t0) cc_final: 0.7956 (p0) REVERT: W 89 VAL cc_start: 0.7057 (t) cc_final: 0.6806 (t) REVERT: X 53 LYS cc_start: 0.9434 (mttt) cc_final: 0.9009 (mtmm) REVERT: Y 34 GLN cc_start: 0.9086 (mp10) cc_final: 0.8770 (mp10) REVERT: Z 23 GLU cc_start: 0.9328 (pt0) cc_final: 0.8969 (pp20) REVERT: Z 24 GLU cc_start: 0.9420 (mm-30) cc_final: 0.8972 (mm-30) REVERT: 0 4 LEU cc_start: 0.8653 (mm) cc_final: 0.8427 (mm) REVERT: 0 15 ARG cc_start: 0.8517 (tpp80) cc_final: 0.8269 (mmt90) REVERT: 2 53 ASP cc_start: 0.9260 (t0) cc_final: 0.8971 (t0) REVERT: 3 46 ARG cc_start: 0.9171 (ptm160) cc_final: 0.8652 (ptm160) REVERT: 4 20 LYS cc_start: 0.9290 (mmmt) cc_final: 0.8834 (tppp) REVERT: 4 25 LYS cc_start: 0.8763 (mttt) cc_final: 0.8286 (ttmt) REVERT: 5 10 LEU cc_start: 0.9502 (mm) cc_final: 0.9265 (mm) REVERT: 5 64 ARG cc_start: 0.8658 (mtt180) cc_final: 0.8424 (mmt180) outliers start: 2 outliers final: 1 residues processed: 874 average time/residue: 1.2629 time to fit residues: 1921.0977 Evaluate side-chains 633 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 632 time to evaluate : 5.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 854 optimal weight: 0.0870 chunk 650 optimal weight: 20.0000 chunk 449 optimal weight: 20.0000 chunk 95 optimal weight: 50.0000 chunk 412 optimal weight: 20.0000 chunk 580 optimal weight: 20.0000 chunk 868 optimal weight: 20.0000 chunk 919 optimal weight: 10.0000 chunk 453 optimal weight: 10.0000 chunk 822 optimal weight: 9.9990 chunk 247 optimal weight: 30.0000 overall best weight: 10.0172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 6 HIS c 64 ASN c 85 ASN d 83 HIS d 147 GLN f 93 HIS ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 122 ASN ** i 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 18 HIS o 28 GLN ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 65 ASN ** p 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 55 ASN r 56 GLN s 23 GLN ** s 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 69 HIS t 18 ASN ** t 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 HIS C 86 ASN ** C 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN D 184 ASN F 2 ASN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 GLN G 71 ASN K 131 HIS L 110 ASN M 27 ASN ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 38 GLN X 59 ASN ** 0 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 40 HIS ** 3 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 26 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 150413 Z= 0.338 Angle : 0.778 16.163 225543 Z= 0.395 Chirality : 0.042 0.380 28923 Planarity : 0.006 0.104 11684 Dihedral : 24.482 179.722 76255 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 28.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 14.31 % Favored : 85.55 % Rotamer: Outliers : 0.09 % Allowed : 3.35 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.28 % Twisted Proline : 0.52 % Twisted General : 0.28 % 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: -3.25 (0.11), residues: 5101 helix: -0.74 (0.13), residues: 1369 sheet: -1.88 (0.17), residues: 864 loop : -3.11 (0.10), residues: 2868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP N 93 HIS 0.013 0.002 HIS C 53 PHE 0.036 0.003 PHE S 74 TYR 0.031 0.002 TYR f 53 ARG 0.015 0.001 ARG Z 29 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10202 Ramachandran restraints generated. 5101 Oldfield, 0 Emsley, 5101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10202 Ramachandran restraints generated. 5101 Oldfield, 0 Emsley, 5101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 749 time to evaluate : 8.115 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 TARDY: cannot create tardy model for: "LYS K 118 " (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 TARDY: cannot create tardy model for: "TYR R 43 " (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: c 22 TRP cc_start: 0.6611 (m-10) cc_final: 0.6141 (m-10) REVERT: c 74 MET cc_start: 0.8689 (mtp) cc_final: 0.8073 (ttm) REVERT: c 123 LEU cc_start: 0.8718 (tp) cc_final: 0.8287 (pp) REVERT: d 47 TYR cc_start: 0.7641 (t80) cc_final: 0.7293 (t80) REVERT: d 88 MET cc_start: 0.9170 (mmp) cc_final: 0.8926 (mmm) REVERT: d 201 GLN cc_start: 0.8308 (pm20) cc_final: 0.7597 (pm20) REVERT: f 10 MET cc_start: 0.7959 (tmm) cc_final: 0.7676 (tmm) REVERT: f 48 LYS cc_start: 0.8975 (tptt) cc_final: 0.8680 (tptp) REVERT: g 33 ASP cc_start: 0.8774 (m-30) cc_final: 0.8386 (t70) REVERT: g 110 LEU cc_start: 0.7586 (mt) cc_final: 0.7178 (pp) REVERT: h 5 ASP cc_start: 0.8694 (t0) cc_final: 0.8253 (t0) REVERT: h 76 ASN cc_start: 0.8601 (t0) cc_final: 0.8147 (t0) REVERT: h 98 LEU cc_start: 0.8455 (tp) cc_final: 0.8209 (tp) REVERT: i 103 LEU cc_start: 0.8043 (mt) cc_final: 0.7729 (tt) REVERT: i 107 ASP cc_start: 0.9090 (m-30) cc_final: 0.8528 (t0) REVERT: j 85 ASP cc_start: 0.8196 (m-30) cc_final: 0.7905 (m-30) REVERT: j 88 MET cc_start: 0.7114 (ptm) cc_final: 0.6702 (ppp) REVERT: k 33 MET cc_start: 0.8710 (tpp) cc_final: 0.8450 (tpp) REVERT: k 65 MET cc_start: 0.8189 (mtm) cc_final: 0.7912 (ptp) REVERT: k 94 GLU cc_start: 0.9046 (tt0) cc_final: 0.8811 (tt0) REVERT: k 122 ARG cc_start: 0.9144 (mtp180) cc_final: 0.8564 (mtp-110) REVERT: l 116 ASP cc_start: 0.8051 (t70) cc_final: 0.7702 (t0) REVERT: l 122 ASP cc_start: 0.7894 (t0) cc_final: 0.7291 (m-30) REVERT: m 9 ILE cc_start: 0.3212 (mm) cc_final: 0.2731 (mm) REVERT: o 34 GLU cc_start: 0.8680 (mp0) cc_final: 0.8463 (mp0) REVERT: o 37 ASN cc_start: 0.9445 (t0) cc_final: 0.8931 (t0) REVERT: o 41 GLU cc_start: 0.9322 (tp30) cc_final: 0.9002 (tp30) REVERT: o 76 GLN cc_start: 0.9569 (tt0) cc_final: 0.9273 (tp-100) REVERT: p 68 ASP cc_start: 0.9110 (p0) cc_final: 0.8869 (p0) REVERT: q 20 MET cc_start: 0.8902 (mtm) cc_final: 0.8074 (mmt) REVERT: r 15 ASP cc_start: 0.9043 (m-30) cc_final: 0.8675 (p0) REVERT: r 36 PHE cc_start: 0.8256 (m-80) cc_final: 0.7981 (m-80) REVERT: t 59 MET cc_start: 0.8384 (mmm) cc_final: 0.7963 (mmt) REVERT: C 5 LYS cc_start: 0.9665 (mttt) cc_final: 0.9277 (tptt) REVERT: C 273 ARG cc_start: 0.8020 (mtm110) cc_final: 0.7799 (ttp80) REVERT: D 152 ASN cc_start: 0.9235 (m-40) cc_final: 0.8883 (p0) REVERT: D 164 MET cc_start: 0.7792 (mmm) cc_final: 0.6424 (tpt) REVERT: E 83 TRP cc_start: 0.8151 (m100) cc_final: 0.7805 (m-10) REVERT: E 141 GLN cc_start: 0.9236 (tp-100) cc_final: 0.8924 (tp-100) REVERT: F 96 MET cc_start: 0.8929 (mmm) cc_final: 0.8586 (mmm) REVERT: F 97 TYR cc_start: 0.9107 (m-10) cc_final: 0.8865 (m-10) REVERT: K 75 TYR cc_start: 0.9068 (m-80) cc_final: 0.8725 (m-80) REVERT: K 77 ARG cc_start: 0.8316 (mtt180) cc_final: 0.7526 (mtm180) REVERT: K 103 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8072 (mt-10) REVERT: L 1 MET cc_start: 0.7791 (mmt) cc_final: 0.7519 (mmm) REVERT: L 81 GLU cc_start: 0.8938 (mp0) cc_final: 0.8700 (mp0) REVERT: L 110 ASN cc_start: 0.9375 (OUTLIER) cc_final: 0.9152 (t0) REVERT: L 120 GLU cc_start: 0.8528 (tt0) cc_final: 0.7532 (mp0) REVERT: N 1 MET cc_start: -0.0975 (mmm) cc_final: -0.2304 (mmm) REVERT: N 58 MET cc_start: 0.9018 (tpt) cc_final: 0.8448 (tpt) REVERT: N 63 LYS cc_start: 0.9063 (mttt) cc_final: 0.8745 (tppp) REVERT: N 64 VAL cc_start: 0.8934 (t) cc_final: 0.8403 (m) REVERT: O 80 ILE cc_start: 0.8312 (mt) cc_final: 0.7825 (tp) REVERT: O 120 MET cc_start: 0.8239 (tpp) cc_final: 0.7757 (tpp) REVERT: P 16 ARG cc_start: 0.9496 (mtt180) cc_final: 0.9293 (tmm-80) REVERT: Q 4 LEU cc_start: 0.9297 (mt) cc_final: 0.8809 (tt) REVERT: R 71 MET cc_start: 0.9479 (mmm) cc_final: 0.9163 (mmm) REVERT: S 75 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8386 (tt0) REVERT: T 114 GLU cc_start: 0.6713 (mt-10) cc_final: 0.6113 (mt-10) REVERT: U 59 ARG cc_start: 0.7576 (mtt180) cc_final: 0.7344 (mtt180) REVERT: V 8 LYS cc_start: 0.9482 (mttt) cc_final: 0.9276 (mmmm) REVERT: W 80 ASP cc_start: 0.8664 (t0) cc_final: 0.7939 (p0) REVERT: W 89 VAL cc_start: 0.7446 (t) cc_final: 0.7209 (t) REVERT: X 53 LYS cc_start: 0.9376 (mttt) cc_final: 0.9037 (mmmm) REVERT: 0 15 ARG cc_start: 0.8605 (tpp80) cc_final: 0.7878 (mmt90) REVERT: 0 20 ARG cc_start: 0.9337 (ptp-110) cc_final: 0.8919 (ptp90) REVERT: 0 46 MET cc_start: 0.8507 (mmt) cc_final: 0.8263 (mmt) REVERT: 3 46 ARG cc_start: 0.9127 (ptm160) cc_final: 0.8699 (ptm160) REVERT: 4 20 LYS cc_start: 0.9448 (mmmt) cc_final: 0.9059 (tppp) REVERT: 4 25 LYS cc_start: 0.8898 (mttt) cc_final: 0.8456 (mtmt) REVERT: 5 10 LEU cc_start: 0.9505 (mm) cc_final: 0.9291 (mm) REVERT: 5 64 ARG cc_start: 0.8781 (mtt180) cc_final: 0.8328 (mmt180) REVERT: 5 65 MET cc_start: 0.7911 (mmm) cc_final: 0.7704 (mmm) outliers start: 4 outliers final: 1 residues processed: 751 average time/residue: 1.2650 time to fit residues: 1656.2611 Evaluate side-chains 583 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 581 time to evaluate : 5.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 765 optimal weight: 10.0000 chunk 521 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 684 optimal weight: 10.0000 chunk 379 optimal weight: 30.0000 chunk 784 optimal weight: 2.9990 chunk 635 optimal weight: 10.0000 chunk 1 optimal weight: 30.0000 chunk 469 optimal weight: 10.0000 chunk 825 optimal weight: 0.0980 chunk 231 optimal weight: 30.0000 overall best weight: 6.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 6 HIS c 64 ASN ** d 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 36 ASN ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 45 ASN ** i 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 31 ASN i 66 ASN ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 HIS D 184 ASN E 14 ASN E 145 ASN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 GLN G 6 ASN ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 150413 Z= 0.235 Angle : 0.665 15.120 225543 Z= 0.340 Chirality : 0.038 0.371 28923 Planarity : 0.005 0.100 11684 Dihedral : 24.301 179.956 76255 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.45 % Favored : 87.45 % Rotamer: Outliers : 0.02 % Allowed : 2.55 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.28 % Twisted Proline : 0.52 % Twisted General : 0.24 % 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: -3.04 (0.11), residues: 5101 helix: -0.41 (0.14), residues: 1363 sheet: -1.81 (0.17), residues: 861 loop : -3.04 (0.10), residues: 2877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 93 HIS 0.010 0.002 HIS p 84 PHE 0.026 0.002 PHE S 74 TYR 0.023 0.002 TYR h 88 ARG 0.009 0.001 ARG Q 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10202 Ramachandran restraints generated. 5101 Oldfield, 0 Emsley, 5101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10202 Ramachandran restraints generated. 5101 Oldfield, 0 Emsley, 5101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 759 time to evaluate : 5.942 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: "LYS K 118 " (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 TARDY: cannot create tardy model for: "TYR R 43 " (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: c 22 TRP cc_start: 0.6494 (m-10) cc_final: 0.6138 (m-10) REVERT: c 74 MET cc_start: 0.8702 (mtp) cc_final: 0.8108 (ttm) REVERT: c 123 LEU cc_start: 0.8698 (tp) cc_final: 0.8293 (pp) REVERT: c 183 TYR cc_start: 0.6412 (t80) cc_final: 0.6154 (t80) REVERT: d 47 TYR cc_start: 0.7569 (t80) cc_final: 0.7223 (t80) REVERT: e 76 MET cc_start: 0.8709 (tpp) cc_final: 0.8313 (tpp) REVERT: f 10 MET cc_start: 0.8022 (tmm) cc_final: 0.7770 (tmm) REVERT: f 48 LYS cc_start: 0.8962 (tptt) cc_final: 0.8741 (tptt) REVERT: g 33 ASP cc_start: 0.8874 (m-30) cc_final: 0.8419 (t70) REVERT: g 110 LEU cc_start: 0.7532 (mt) cc_final: 0.7090 (pp) REVERT: h 5 ASP cc_start: 0.8582 (t0) cc_final: 0.8152 (t0) REVERT: h 76 ASN cc_start: 0.8620 (t0) cc_final: 0.8205 (t0) REVERT: h 98 LEU cc_start: 0.8501 (tp) cc_final: 0.8234 (tp) REVERT: i 103 LEU cc_start: 0.8021 (mt) cc_final: 0.7723 (tt) REVERT: i 107 ASP cc_start: 0.9093 (m-30) cc_final: 0.8518 (t0) REVERT: j 85 ASP cc_start: 0.8169 (m-30) cc_final: 0.7901 (m-30) REVERT: j 89 LYS cc_start: 0.8428 (tptp) cc_final: 0.7812 (mmtm) REVERT: k 33 MET cc_start: 0.8776 (tpp) cc_final: 0.8488 (tpp) REVERT: k 65 MET cc_start: 0.8243 (mtm) cc_final: 0.8002 (mtm) REVERT: k 79 LEU cc_start: 0.9579 (mt) cc_final: 0.9370 (mt) REVERT: k 122 ARG cc_start: 0.9140 (mtp180) cc_final: 0.8544 (mtp-110) REVERT: l 42 GLN cc_start: 0.8394 (pm20) cc_final: 0.8103 (pm20) REVERT: l 116 ASP cc_start: 0.8115 (t70) cc_final: 0.7787 (t0) REVERT: l 122 ASP cc_start: 0.7890 (t0) cc_final: 0.7282 (m-30) REVERT: m 9 ILE cc_start: 0.3237 (mm) cc_final: 0.2732 (mm) REVERT: n 46 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6830 (mm-30) REVERT: o 10 GLU cc_start: 0.9418 (tp30) cc_final: 0.8705 (tp30) REVERT: o 37 ASN cc_start: 0.9453 (t0) cc_final: 0.8915 (t0) REVERT: o 41 GLU cc_start: 0.9402 (tp30) cc_final: 0.9100 (tp30) REVERT: p 20 ILE cc_start: 0.8906 (mp) cc_final: 0.8692 (mp) REVERT: p 68 ASP cc_start: 0.9156 (p0) cc_final: 0.8863 (p0) REVERT: q 14 ARG cc_start: 0.8573 (ptm-80) cc_final: 0.8312 (ttp80) REVERT: q 20 MET cc_start: 0.8767 (mtm) cc_final: 0.8018 (mmp) REVERT: r 15 ASP cc_start: 0.8997 (m-30) cc_final: 0.8587 (p0) REVERT: r 36 PHE cc_start: 0.8238 (m-80) cc_final: 0.8003 (m-80) REVERT: s 66 MET cc_start: 0.6657 (ttt) cc_final: 0.6115 (ttt) REVERT: t 59 MET cc_start: 0.8386 (mmm) cc_final: 0.8045 (mmm) REVERT: t 75 LYS cc_start: 0.9423 (mtmm) cc_final: 0.9222 (mttm) REVERT: C 5 LYS cc_start: 0.9663 (mttt) cc_final: 0.9261 (tptt) REVERT: C 185 LEU cc_start: 0.9444 (mt) cc_final: 0.8906 (tp) REVERT: C 225 MET cc_start: 0.8676 (tpp) cc_final: 0.8192 (tpp) REVERT: D 152 ASN cc_start: 0.9231 (m-40) cc_final: 0.8843 (p0) REVERT: D 175 GLU cc_start: 0.8064 (tp30) cc_final: 0.7838 (tm-30) REVERT: E 83 TRP cc_start: 0.8071 (m100) cc_final: 0.7654 (m-10) REVERT: E 141 GLN cc_start: 0.9196 (tp-100) cc_final: 0.8871 (tp-100) REVERT: F 96 MET cc_start: 0.8855 (mmm) cc_final: 0.8616 (mmm) REVERT: F 99 PHE cc_start: 0.9269 (t80) cc_final: 0.9005 (t80) REVERT: K 77 ARG cc_start: 0.8366 (mtt180) cc_final: 0.7633 (mtm180) REVERT: L 81 GLU cc_start: 0.8900 (mp0) cc_final: 0.8616 (mp0) REVERT: L 104 ARG cc_start: 0.8951 (tmt170) cc_final: 0.8645 (tmt-80) REVERT: L 110 ASN cc_start: 0.9382 (t0) cc_final: 0.9181 (t0) REVERT: L 120 GLU cc_start: 0.8526 (tt0) cc_final: 0.7522 (mp0) REVERT: N 1 MET cc_start: -0.0938 (mmm) cc_final: -0.2379 (mmm) REVERT: N 58 MET cc_start: 0.8955 (tpt) cc_final: 0.8440 (tpt) REVERT: N 63 LYS cc_start: 0.9119 (mttt) cc_final: 0.8808 (tppp) REVERT: N 64 VAL cc_start: 0.8921 (t) cc_final: 0.8629 (m) REVERT: N 65 TRP cc_start: 0.8260 (m100) cc_final: 0.7932 (m100) REVERT: O 80 ILE cc_start: 0.8322 (mt) cc_final: 0.7882 (tp) REVERT: O 120 MET cc_start: 0.8060 (tpp) cc_final: 0.7685 (tpp) REVERT: P 17 ARG cc_start: 0.8710 (ptp90) cc_final: 0.8255 (ptp-170) REVERT: P 45 ILE cc_start: 0.8965 (mm) cc_final: 0.8723 (mm) REVERT: Q 4 LEU cc_start: 0.9219 (mt) cc_final: 0.8864 (tt) REVERT: R 32 PHE cc_start: 0.6664 (m-80) cc_final: 0.6137 (m-80) REVERT: R 71 MET cc_start: 0.9437 (mmm) cc_final: 0.9073 (mmm) REVERT: T 114 GLU cc_start: 0.6728 (mt-10) cc_final: 0.6073 (mt-10) REVERT: U 65 MET cc_start: 0.7457 (ppp) cc_final: 0.6955 (ptp) REVERT: V 8 LYS cc_start: 0.9534 (mttt) cc_final: 0.9322 (mmmm) REVERT: W 80 ASP cc_start: 0.8710 (t0) cc_final: 0.7938 (p0) REVERT: X 53 LYS cc_start: 0.9341 (mttt) cc_final: 0.9010 (mttp) REVERT: Z 14 MET cc_start: 0.6423 (mtp) cc_final: 0.6148 (mtp) REVERT: 0 15 ARG cc_start: 0.8568 (tpp80) cc_final: 0.7979 (mmt90) REVERT: 0 20 ARG cc_start: 0.9333 (ptp-110) cc_final: 0.8966 (ptp90) REVERT: 0 46 MET cc_start: 0.8532 (mmt) cc_final: 0.8238 (mmt) REVERT: 3 46 ARG cc_start: 0.9104 (ptm160) cc_final: 0.8638 (ptm160) REVERT: 4 20 LYS cc_start: 0.9411 (mmmt) cc_final: 0.9025 (tppp) REVERT: 4 25 LYS cc_start: 0.8896 (mttt) cc_final: 0.8511 (mmtm) REVERT: 4 28 ARG cc_start: 0.8300 (mtt180) cc_final: 0.7757 (mmt90) REVERT: 5 10 LEU cc_start: 0.9472 (mm) cc_final: 0.9236 (mm) REVERT: 5 65 MET cc_start: 0.7882 (mmm) cc_final: 0.7646 (mmm) REVERT: 6 35 GLN cc_start: 0.8858 (mm110) cc_final: 0.8569 (mm110) outliers start: 1 outliers final: 0 residues processed: 759 average time/residue: 1.1749 time to fit residues: 1541.8848 Evaluate side-chains 593 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 593 time to evaluate : 5.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 309 optimal weight: 8.9990 chunk 827 optimal weight: 10.0000 chunk 181 optimal weight: 5.9990 chunk 539 optimal weight: 20.0000 chunk 226 optimal weight: 8.9990 chunk 920 optimal weight: 9.9990 chunk 763 optimal weight: 0.9990 chunk 426 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 304 optimal weight: 20.0000 chunk 483 optimal weight: 20.0000 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 6 HIS c 64 ASN ** d 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 28 GLN ** p 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 HIS ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 HIS D 184 ASN E 145 ASN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 131 HIS M 27 ASN ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 87 GLN ** Y 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 150413 Z= 0.245 Angle : 0.675 15.890 225543 Z= 0.344 Chirality : 0.038 0.371 28923 Planarity : 0.005 0.105 11684 Dihedral : 24.309 179.453 76255 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 23.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.62 % Favored : 86.30 % Rotamer: Outliers : 0.02 % Allowed : 2.16 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.28 % Twisted Proline : 0.52 % Twisted General : 0.24 % 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: -2.94 (0.11), residues: 5101 helix: -0.31 (0.14), residues: 1356 sheet: -1.81 (0.17), residues: 859 loop : -2.96 (0.11), residues: 2886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP N 93 HIS 0.010 0.002 HIS C 53 PHE 0.023 0.002 PHE U 62 TYR 0.022 0.002 TYR r 27 ARG 0.009 0.001 ARG Q 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10202 Ramachandran restraints generated. 5101 Oldfield, 0 Emsley, 5101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10202 Ramachandran restraints generated. 5101 Oldfield, 0 Emsley, 5101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 747 time to evaluate : 7.563 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 TARDY: cannot create tardy model for: "LYS K 118 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR R 43 " (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: c 18 TRP cc_start: 0.7968 (m-90) cc_final: 0.7555 (m-90) REVERT: c 22 TRP cc_start: 0.6055 (m-10) cc_final: 0.5739 (m-10) REVERT: c 123 LEU cc_start: 0.8716 (tp) cc_final: 0.8326 (pp) REVERT: d 47 TYR cc_start: 0.7578 (t80) cc_final: 0.7239 (t80) REVERT: e 76 MET cc_start: 0.8632 (tpp) cc_final: 0.8192 (tpp) REVERT: f 10 MET cc_start: 0.8122 (tmm) cc_final: 0.7811 (tmm) REVERT: f 48 LYS cc_start: 0.8966 (tptt) cc_final: 0.8690 (tptp) REVERT: g 33 ASP cc_start: 0.8771 (m-30) cc_final: 0.8281 (t70) REVERT: g 110 LEU cc_start: 0.7531 (mt) cc_final: 0.7090 (pp) REVERT: h 76 ASN cc_start: 0.8651 (t0) cc_final: 0.8238 (t0) REVERT: i 103 LEU cc_start: 0.7995 (mt) cc_final: 0.7692 (tt) REVERT: i 107 ASP cc_start: 0.9106 (m-30) cc_final: 0.8561 (t0) REVERT: j 85 ASP cc_start: 0.8359 (m-30) cc_final: 0.8099 (m-30) REVERT: j 89 LYS cc_start: 0.8343 (tptp) cc_final: 0.7715 (mmtm) REVERT: k 33 MET cc_start: 0.8727 (tpp) cc_final: 0.8465 (tpp) REVERT: k 75 MET cc_start: 0.9260 (tpt) cc_final: 0.8903 (tpt) REVERT: k 79 LEU cc_start: 0.9512 (mt) cc_final: 0.9024 (mt) REVERT: k 122 ARG cc_start: 0.9135 (mtp180) cc_final: 0.8533 (mtp-110) REVERT: l 77 THR cc_start: 0.9234 (p) cc_final: 0.8970 (t) REVERT: l 116 ASP cc_start: 0.8120 (t70) cc_final: 0.7797 (t0) REVERT: l 122 ASP cc_start: 0.8022 (t0) cc_final: 0.7451 (m-30) REVERT: m 9 ILE cc_start: 0.3417 (mm) cc_final: 0.2945 (mm) REVERT: n 46 GLU cc_start: 0.7101 (mm-30) cc_final: 0.6830 (mm-30) REVERT: n 57 LYS cc_start: 0.7389 (mmtm) cc_final: 0.7090 (ttmt) REVERT: o 37 ASN cc_start: 0.9427 (t0) cc_final: 0.8905 (t0) REVERT: o 41 GLU cc_start: 0.9398 (tp30) cc_final: 0.9122 (tp30) REVERT: p 7 LEU cc_start: 0.8350 (mp) cc_final: 0.7514 (mt) REVERT: p 35 GLU cc_start: 0.7453 (pm20) cc_final: 0.7220 (pm20) REVERT: p 68 ASP cc_start: 0.9192 (p0) cc_final: 0.8919 (p0) REVERT: q 14 ARG cc_start: 0.8530 (ptm-80) cc_final: 0.8247 (ttp80) REVERT: q 20 MET cc_start: 0.8745 (mtm) cc_final: 0.8018 (mmp) REVERT: r 15 ASP cc_start: 0.9011 (m-30) cc_final: 0.8623 (p0) REVERT: r 27 TYR cc_start: 0.7837 (t80) cc_final: 0.7619 (t80) REVERT: r 36 PHE cc_start: 0.8299 (m-80) cc_final: 0.8034 (m-80) REVERT: r 68 ILE cc_start: 0.9052 (tp) cc_final: 0.8730 (tp) REVERT: s 66 MET cc_start: 0.6846 (ttt) cc_final: 0.6313 (ttt) REVERT: t 59 MET cc_start: 0.8391 (mmm) cc_final: 0.8046 (mmm) REVERT: C 5 LYS cc_start: 0.9664 (mttt) cc_final: 0.9384 (mmmt) REVERT: C 62 TYR cc_start: 0.5444 (m-10) cc_final: 0.4755 (m-80) REVERT: C 185 LEU cc_start: 0.9475 (mt) cc_final: 0.9247 (tp) REVERT: C 225 MET cc_start: 0.8777 (tpp) cc_final: 0.8264 (tpp) REVERT: D 152 ASN cc_start: 0.9195 (m-40) cc_final: 0.8849 (p0) REVERT: D 175 GLU cc_start: 0.8018 (tp30) cc_final: 0.7794 (tm-30) REVERT: D 184 ASN cc_start: 0.9063 (m-40) cc_final: 0.8853 (m-40) REVERT: E 83 TRP cc_start: 0.8163 (m100) cc_final: 0.7849 (m-10) REVERT: E 141 GLN cc_start: 0.9239 (tp-100) cc_final: 0.8914 (tp-100) REVERT: F 26 MET cc_start: 0.8017 (mmm) cc_final: 0.7807 (mmm) REVERT: F 96 MET cc_start: 0.8842 (mmm) cc_final: 0.8635 (mmm) REVERT: F 99 PHE cc_start: 0.9259 (t80) cc_final: 0.9015 (t80) REVERT: G 84 GLN cc_start: 0.8830 (mt0) cc_final: 0.8139 (mm-40) REVERT: K 77 ARG cc_start: 0.8396 (mtt180) cc_final: 0.7642 (mtm180) REVERT: L 81 GLU cc_start: 0.8950 (mp0) cc_final: 0.8659 (mp0) REVERT: L 104 ARG cc_start: 0.8962 (tmt170) cc_final: 0.8380 (tmt-80) REVERT: L 110 ASN cc_start: 0.9392 (t0) cc_final: 0.9188 (t0) REVERT: L 120 GLU cc_start: 0.8533 (tt0) cc_final: 0.7534 (mp0) REVERT: N 1 MET cc_start: -0.0621 (mmm) cc_final: -0.2133 (mmm) REVERT: N 58 MET cc_start: 0.8949 (tpt) cc_final: 0.8411 (tpt) REVERT: N 63 LYS cc_start: 0.9109 (mttt) cc_final: 0.8758 (tppp) REVERT: N 64 VAL cc_start: 0.8896 (t) cc_final: 0.8566 (m) REVERT: O 80 ILE cc_start: 0.8307 (mt) cc_final: 0.7843 (tp) REVERT: O 120 MET cc_start: 0.8009 (tpp) cc_final: 0.7612 (tpp) REVERT: P 17 ARG cc_start: 0.8685 (ptp90) cc_final: 0.8329 (ptp-170) REVERT: P 45 ILE cc_start: 0.8900 (mm) cc_final: 0.8695 (mm) REVERT: P 46 ASP cc_start: 0.8452 (m-30) cc_final: 0.8180 (m-30) REVERT: Q 4 LEU cc_start: 0.9264 (mt) cc_final: 0.8895 (tt) REVERT: R 71 MET cc_start: 0.9483 (mmm) cc_final: 0.9004 (mmm) REVERT: T 114 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6358 (mt-10) REVERT: U 5 ASP cc_start: 0.8430 (m-30) cc_final: 0.8002 (t0) REVERT: V 8 LYS cc_start: 0.9519 (mttt) cc_final: 0.9312 (mmmm) REVERT: W 80 ASP cc_start: 0.8685 (t0) cc_final: 0.7905 (p0) REVERT: W 89 VAL cc_start: 0.7149 (t) cc_final: 0.6822 (t) REVERT: X 53 LYS cc_start: 0.9382 (mttt) cc_final: 0.9019 (mttp) REVERT: Z 14 MET cc_start: 0.6604 (mtp) cc_final: 0.6295 (mtp) REVERT: 0 15 ARG cc_start: 0.8573 (tpp80) cc_final: 0.7923 (mmt90) REVERT: 0 20 ARG cc_start: 0.9344 (ptp-110) cc_final: 0.8999 (ptp90) REVERT: 0 46 MET cc_start: 0.8567 (mmt) cc_final: 0.8258 (mmt) REVERT: 3 46 ARG cc_start: 0.9107 (ptm160) cc_final: 0.8659 (ptm160) REVERT: 4 25 LYS cc_start: 0.8931 (mttt) cc_final: 0.8464 (mmtm) REVERT: 4 28 ARG cc_start: 0.8259 (mtt180) cc_final: 0.7605 (mtt90) REVERT: 5 10 LEU cc_start: 0.9455 (mm) cc_final: 0.9242 (mm) REVERT: 5 65 MET cc_start: 0.7943 (mmm) cc_final: 0.7739 (mmm) REVERT: 6 35 GLN cc_start: 0.8770 (mm110) cc_final: 0.8547 (mm110) outliers start: 1 outliers final: 0 residues processed: 747 average time/residue: 1.2329 time to fit residues: 1598.9953 Evaluate side-chains 596 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 596 time to evaluate : 5.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 887 optimal weight: 40.0000 chunk 103 optimal weight: 50.0000 chunk 524 optimal weight: 20.0000 chunk 671 optimal weight: 20.0000 chunk 520 optimal weight: 20.0000 chunk 774 optimal weight: 10.0000 chunk 513 optimal weight: 20.0000 chunk 916 optimal weight: 2.9990 chunk 573 optimal weight: 20.0000 chunk 558 optimal weight: 20.0000 chunk 423 optimal weight: 10.0000 overall best weight: 12.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 6 HIS c 64 ASN ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 147 GLN ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 36 ASN o 28 GLN ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 24 GLN ** t 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN ** E 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 101 ASN ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 40 HIS ** 3 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 150413 Z= 0.411 Angle : 0.876 16.192 225543 Z= 0.443 Chirality : 0.046 0.418 28923 Planarity : 0.007 0.108 11684 Dihedral : 24.706 179.499 76255 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 35.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 16.09 % Favored : 83.77 % Rotamer: Outliers : 0.02 % Allowed : 2.09 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.28 % Twisted Proline : 0.52 % Twisted General : 0.36 % 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: -3.41 (0.11), residues: 5101 helix: -0.91 (0.13), residues: 1346 sheet: -2.09 (0.17), residues: 857 loop : -3.12 (0.10), residues: 2898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP N 93 HIS 0.015 0.003 HIS k 24 PHE 0.051 0.003 PHE U 62 TYR 0.039 0.003 TYR C 257 ARG 0.014 0.001 ARG Z 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10202 Ramachandran restraints generated. 5101 Oldfield, 0 Emsley, 5101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10202 Ramachandran restraints generated. 5101 Oldfield, 0 Emsley, 5101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 691 time to evaluate : 5.917 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: "LYS K 118 " (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 TARDY: cannot create tardy model for: "TYR R 43 " (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: c 22 TRP cc_start: 0.6498 (m-10) cc_final: 0.6061 (m-10) REVERT: c 123 LEU cc_start: 0.8695 (tp) cc_final: 0.8286 (pp) REVERT: c 183 TYR cc_start: 0.6384 (t80) cc_final: 0.6141 (t80) REVERT: d 47 TYR cc_start: 0.7682 (t80) cc_final: 0.7367 (t80) REVERT: f 10 MET cc_start: 0.8040 (tmm) cc_final: 0.7692 (tmm) REVERT: f 51 LEU cc_start: 0.8177 (tp) cc_final: 0.7936 (tp) REVERT: f 94 MET cc_start: 0.8124 (mmt) cc_final: 0.7812 (mmp) REVERT: g 31 MET cc_start: 0.8246 (ttp) cc_final: 0.6745 (tpp) REVERT: g 33 ASP cc_start: 0.8742 (m-30) cc_final: 0.8355 (t70) REVERT: g 110 LEU cc_start: 0.7302 (mt) cc_final: 0.6895 (pp) REVERT: h 35 ASP cc_start: 0.9200 (m-30) cc_final: 0.8994 (m-30) REVERT: h 61 ARG cc_start: 0.8560 (mtt180) cc_final: 0.8258 (mtt90) REVERT: h 76 ASN cc_start: 0.8665 (t0) cc_final: 0.8346 (t0) REVERT: i 103 LEU cc_start: 0.7828 (mt) cc_final: 0.7490 (tt) REVERT: i 107 ASP cc_start: 0.9170 (m-30) cc_final: 0.8557 (t0) REVERT: j 85 ASP cc_start: 0.7747 (m-30) cc_final: 0.7488 (m-30) REVERT: j 88 MET cc_start: 0.7019 (ptm) cc_final: 0.6655 (ppp) REVERT: k 17 GLU cc_start: 0.8903 (tp30) cc_final: 0.8606 (tp30) REVERT: k 33 MET cc_start: 0.8655 (tpp) cc_final: 0.8433 (tpp) REVERT: k 79 LEU cc_start: 0.9484 (mt) cc_final: 0.9204 (mt) REVERT: k 122 ARG cc_start: 0.9204 (mtp180) cc_final: 0.8607 (mtp-110) REVERT: l 77 THR cc_start: 0.9269 (p) cc_final: 0.8997 (t) REVERT: l 116 ASP cc_start: 0.7963 (t70) cc_final: 0.7632 (t0) REVERT: l 122 ASP cc_start: 0.8158 (t0) cc_final: 0.7500 (m-30) REVERT: n 46 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6982 (mm-30) REVERT: o 10 GLU cc_start: 0.9472 (tp30) cc_final: 0.8848 (tp30) REVERT: o 15 TYR cc_start: 0.8451 (m-80) cc_final: 0.8051 (m-10) REVERT: o 34 GLU cc_start: 0.8599 (mp0) cc_final: 0.8374 (mp0) REVERT: o 37 ASN cc_start: 0.9429 (t0) cc_final: 0.8963 (t0) REVERT: o 38 GLN cc_start: 0.8992 (mp10) cc_final: 0.8681 (mp10) REVERT: o 41 GLU cc_start: 0.9510 (tp30) cc_final: 0.9268 (tp30) REVERT: p 68 ASP cc_start: 0.9164 (p0) cc_final: 0.8962 (p0) REVERT: q 20 MET cc_start: 0.8792 (mtm) cc_final: 0.8089 (mmt) REVERT: r 15 ASP cc_start: 0.9029 (m-30) cc_final: 0.8642 (p0) REVERT: r 27 TYR cc_start: 0.7417 (t80) cc_final: 0.7098 (t80) REVERT: r 36 PHE cc_start: 0.8461 (m-80) cc_final: 0.8143 (m-80) REVERT: r 68 ILE cc_start: 0.8947 (tp) cc_final: 0.8729 (tp) REVERT: s 66 MET cc_start: 0.6796 (ttt) cc_final: 0.6479 (ttt) REVERT: t 3 ASN cc_start: 0.9167 (p0) cc_final: 0.8707 (p0) REVERT: t 59 MET cc_start: 0.8365 (mmm) cc_final: 0.7922 (mmm) REVERT: C 5 LYS cc_start: 0.9668 (mttt) cc_final: 0.9359 (mmmt) REVERT: C 185 LEU cc_start: 0.9446 (mt) cc_final: 0.9108 (tp) REVERT: D 85 ASN cc_start: 0.9324 (t0) cc_final: 0.9062 (t0) REVERT: D 175 GLU cc_start: 0.8046 (tp30) cc_final: 0.7761 (tp30) REVERT: E 83 TRP cc_start: 0.8267 (m100) cc_final: 0.7941 (m-10) REVERT: E 141 GLN cc_start: 0.9284 (tp-100) cc_final: 0.9005 (tp-100) REVERT: F 96 MET cc_start: 0.8898 (mmm) cc_final: 0.8614 (mmm) REVERT: F 97 TYR cc_start: 0.9176 (m-10) cc_final: 0.8958 (m-10) REVERT: F 99 PHE cc_start: 0.9240 (t80) cc_final: 0.8972 (t80) REVERT: G 19 GLN cc_start: 0.9261 (pp30) cc_final: 0.9057 (pp30) REVERT: G 84 GLN cc_start: 0.8730 (mt0) cc_final: 0.8403 (mp10) REVERT: K 77 ARG cc_start: 0.8133 (mtt180) cc_final: 0.7145 (mtm180) REVERT: K 103 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8136 (mt-10) REVERT: L 81 GLU cc_start: 0.9141 (mp0) cc_final: 0.8941 (mp0) REVERT: N 1 MET cc_start: 0.0222 (mmm) cc_final: -0.1211 (mmm) REVERT: N 58 MET cc_start: 0.9073 (tpt) cc_final: 0.8576 (tpt) REVERT: N 63 LYS cc_start: 0.9092 (mttt) cc_final: 0.8646 (tppp) REVERT: N 64 VAL cc_start: 0.9048 (t) cc_final: 0.8462 (m) REVERT: O 80 ILE cc_start: 0.8367 (mt) cc_final: 0.7939 (tp) REVERT: O 120 MET cc_start: 0.8104 (tpp) cc_final: 0.7773 (tpp) REVERT: P 45 ILE cc_start: 0.8965 (mm) cc_final: 0.8756 (mm) REVERT: Q 4 LEU cc_start: 0.9264 (mt) cc_final: 0.8771 (tt) REVERT: Q 78 THR cc_start: 0.9572 (p) cc_final: 0.9356 (t) REVERT: Q 100 LEU cc_start: 0.9316 (mt) cc_final: 0.9011 (mt) REVERT: R 71 MET cc_start: 0.9595 (mmm) cc_final: 0.9199 (mmm) REVERT: R 106 PHE cc_start: 0.9438 (t80) cc_final: 0.9107 (t80) REVERT: T 114 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6395 (mt-10) REVERT: U 5 ASP cc_start: 0.8557 (m-30) cc_final: 0.8253 (t0) REVERT: U 59 ARG cc_start: 0.7646 (mtt180) cc_final: 0.7424 (mtt180) REVERT: U 65 MET cc_start: 0.7535 (ppp) cc_final: 0.6919 (ptp) REVERT: V 1 MET cc_start: 0.7814 (ttp) cc_final: 0.6458 (tpt) REVERT: V 8 LYS cc_start: 0.9499 (mttt) cc_final: 0.9266 (mmmm) REVERT: W 80 ASP cc_start: 0.8817 (t0) cc_final: 0.7984 (p0) REVERT: X 53 LYS cc_start: 0.9390 (mttt) cc_final: 0.9119 (mmmm) REVERT: Y 23 ASN cc_start: 0.7372 (m110) cc_final: 0.7033 (m110) REVERT: Z 14 MET cc_start: 0.7041 (mtp) cc_final: 0.6544 (mtp) REVERT: 0 15 ARG cc_start: 0.8751 (tpp80) cc_final: 0.8521 (mmt90) REVERT: 0 20 ARG cc_start: 0.9393 (ptp-110) cc_final: 0.9079 (ptp90) REVERT: 0 46 MET cc_start: 0.8600 (mmt) cc_final: 0.8263 (mmm) REVERT: 4 25 LYS cc_start: 0.9025 (mttt) cc_final: 0.8655 (mmtm) REVERT: 5 10 LEU cc_start: 0.9455 (mm) cc_final: 0.9215 (mm) REVERT: 6 24 MET cc_start: 0.8295 (mmp) cc_final: 0.7950 (mmm) outliers start: 1 outliers final: 0 residues processed: 691 average time/residue: 1.2002 time to fit residues: 1440.9618 Evaluate side-chains 557 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 557 time to evaluate : 5.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 567 optimal weight: 40.0000 chunk 366 optimal weight: 20.0000 chunk 547 optimal weight: 20.0000 chunk 276 optimal weight: 30.0000 chunk 180 optimal weight: 7.9990 chunk 177 optimal weight: 10.0000 chunk 582 optimal weight: 20.0000 chunk 624 optimal weight: 10.0000 chunk 453 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 720 optimal weight: 5.9990 overall best weight: 8.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 6 HIS c 64 ASN ** d 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 87 ASN ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 106 ASN ** i 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 28 GLN ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 23 GLN ** s 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 2 ASN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 101 ASN ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 150413 Z= 0.298 Angle : 0.742 15.950 225543 Z= 0.377 Chirality : 0.041 0.401 28923 Planarity : 0.006 0.103 11684 Dihedral : 24.491 179.866 76255 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 27.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 14.13 % Favored : 85.75 % Rotamer: Outliers : 0.02 % Allowed : 1.19 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.28 % Twisted Proline : 0.52 % Twisted General : 0.30 % 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: -3.23 (0.11), residues: 5101 helix: -0.71 (0.13), residues: 1357 sheet: -2.03 (0.16), residues: 875 loop : -3.04 (0.11), residues: 2869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 93 HIS 0.013 0.002 HIS t 67 PHE 0.032 0.002 PHE O 125 TYR 0.026 0.002 TYR l 65 ARG 0.010 0.001 ARG O 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10202 Ramachandran restraints generated. 5101 Oldfield, 0 Emsley, 5101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10202 Ramachandran restraints generated. 5101 Oldfield, 0 Emsley, 5101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 715 time to evaluate : 5.882 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 TARDY: cannot create tardy model for: "LYS K 118 " (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 TARDY: cannot create tardy model for: "TYR R 43 " (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: c 18 TRP cc_start: 0.8023 (m-90) cc_final: 0.7603 (m-90) REVERT: c 22 TRP cc_start: 0.6369 (m-10) cc_final: 0.5972 (m-10) REVERT: d 47 TYR cc_start: 0.7636 (t80) cc_final: 0.7287 (t80) REVERT: d 201 GLN cc_start: 0.8583 (pm20) cc_final: 0.8139 (pm20) REVERT: f 10 MET cc_start: 0.8209 (tmm) cc_final: 0.7862 (tmm) REVERT: f 94 MET cc_start: 0.8257 (mmt) cc_final: 0.7632 (mmp) REVERT: g 33 ASP cc_start: 0.8729 (m-30) cc_final: 0.8149 (t70) REVERT: g 110 LEU cc_start: 0.7277 (mt) cc_final: 0.6808 (pp) REVERT: h 76 ASN cc_start: 0.8618 (t0) cc_final: 0.8319 (t0) REVERT: i 103 LEU cc_start: 0.7867 (mt) cc_final: 0.7565 (tt) REVERT: i 107 ASP cc_start: 0.9156 (m-30) cc_final: 0.8543 (t0) REVERT: j 85 ASP cc_start: 0.8086 (m-30) cc_final: 0.7404 (m-30) REVERT: j 88 MET cc_start: 0.7022 (ptm) cc_final: 0.6769 (ppp) REVERT: j 89 LYS cc_start: 0.8335 (tptp) cc_final: 0.7487 (pptt) REVERT: k 75 MET cc_start: 0.9310 (tpt) cc_final: 0.8771 (tpt) REVERT: k 79 LEU cc_start: 0.9429 (mt) cc_final: 0.8855 (mt) REVERT: k 122 ARG cc_start: 0.9196 (mtp180) cc_final: 0.8609 (mtp-110) REVERT: l 77 THR cc_start: 0.9269 (p) cc_final: 0.9038 (t) REVERT: l 116 ASP cc_start: 0.8025 (t70) cc_final: 0.7724 (t0) REVERT: l 122 ASP cc_start: 0.8149 (t0) cc_final: 0.7487 (m-30) REVERT: m 13 LYS cc_start: 0.8835 (tppt) cc_final: 0.8626 (tppt) REVERT: n 46 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6926 (mm-30) REVERT: o 10 GLU cc_start: 0.9425 (tp30) cc_final: 0.8843 (tp30) REVERT: o 37 ASN cc_start: 0.9428 (t0) cc_final: 0.8962 (t0) REVERT: o 38 GLN cc_start: 0.8904 (mp10) cc_final: 0.8676 (mp10) REVERT: p 68 ASP cc_start: 0.9123 (p0) cc_final: 0.8870 (p0) REVERT: q 20 MET cc_start: 0.8763 (mtm) cc_final: 0.8000 (mmp) REVERT: r 15 ASP cc_start: 0.9009 (m-30) cc_final: 0.8603 (p0) REVERT: r 27 TYR cc_start: 0.7393 (t80) cc_final: 0.7106 (t80) REVERT: r 36 PHE cc_start: 0.8406 (m-80) cc_final: 0.8095 (m-80) REVERT: r 68 ILE cc_start: 0.8970 (tp) cc_final: 0.8301 (tt) REVERT: s 66 MET cc_start: 0.6786 (ttt) cc_final: 0.6437 (ttt) REVERT: t 59 MET cc_start: 0.8324 (mmm) cc_final: 0.7839 (mmt) REVERT: C 5 LYS cc_start: 0.9656 (mttt) cc_final: 0.9343 (mmmt) REVERT: C 185 LEU cc_start: 0.9502 (mt) cc_final: 0.9209 (tp) REVERT: C 199 GLN cc_start: 0.8972 (mp10) cc_final: 0.8741 (mp10) REVERT: C 274 ARG cc_start: 0.9229 (tpm170) cc_final: 0.8817 (tpm170) REVERT: D 175 GLU cc_start: 0.8052 (tp30) cc_final: 0.7738 (tp30) REVERT: E 83 TRP cc_start: 0.8233 (m100) cc_final: 0.7802 (m-10) REVERT: E 141 GLN cc_start: 0.9256 (tp-100) cc_final: 0.8958 (tp-100) REVERT: F 96 MET cc_start: 0.8867 (mmm) cc_final: 0.8597 (mmm) REVERT: F 97 TYR cc_start: 0.9139 (m-10) cc_final: 0.8903 (m-10) REVERT: F 99 PHE cc_start: 0.9233 (t80) cc_final: 0.8979 (t80) REVERT: F 152 MET cc_start: 0.8912 (mmm) cc_final: 0.8539 (mmm) REVERT: G 19 GLN cc_start: 0.9277 (pp30) cc_final: 0.9064 (pp30) REVERT: G 84 GLN cc_start: 0.8865 (mt0) cc_final: 0.8558 (mp10) REVERT: K 77 ARG cc_start: 0.8361 (mtt180) cc_final: 0.7652 (mtm180) REVERT: L 120 GLU cc_start: 0.8614 (tt0) cc_final: 0.7816 (mp0) REVERT: N 1 MET cc_start: 0.0378 (mmm) cc_final: -0.1091 (mmm) REVERT: N 58 MET cc_start: 0.9034 (tpt) cc_final: 0.8494 (tpt) REVERT: N 63 LYS cc_start: 0.9042 (mttt) cc_final: 0.8598 (tppp) REVERT: N 64 VAL cc_start: 0.8993 (t) cc_final: 0.8286 (m) REVERT: O 16 MET cc_start: 0.8596 (mtm) cc_final: 0.8177 (mtm) REVERT: O 20 ILE cc_start: 0.8868 (tt) cc_final: 0.8620 (tt) REVERT: O 80 ILE cc_start: 0.8382 (mt) cc_final: 0.7949 (tp) REVERT: P 45 ILE cc_start: 0.8925 (mm) cc_final: 0.8722 (mm) REVERT: Q 4 LEU cc_start: 0.9176 (mt) cc_final: 0.8781 (tt) REVERT: Q 100 LEU cc_start: 0.9291 (mt) cc_final: 0.8969 (mt) REVERT: R 71 MET cc_start: 0.9550 (mmm) cc_final: 0.9062 (mmm) REVERT: R 106 PHE cc_start: 0.9414 (t80) cc_final: 0.9154 (t80) REVERT: T 114 GLU cc_start: 0.6876 (mt-10) cc_final: 0.6316 (mt-10) REVERT: U 5 ASP cc_start: 0.8594 (m-30) cc_final: 0.8261 (t0) REVERT: U 65 MET cc_start: 0.7542 (ppp) cc_final: 0.6894 (ptp) REVERT: V 1 MET cc_start: 0.7837 (ttp) cc_final: 0.6405 (tpt) REVERT: V 8 LYS cc_start: 0.9508 (mttt) cc_final: 0.9282 (mmmm) REVERT: W 80 ASP cc_start: 0.8692 (t0) cc_final: 0.8048 (p0) REVERT: W 89 VAL cc_start: 0.6761 (t) cc_final: 0.6465 (t) REVERT: X 53 LYS cc_start: 0.9374 (mttt) cc_final: 0.9143 (mmmm) REVERT: Z 14 MET cc_start: 0.7082 (mtp) cc_final: 0.6661 (mtp) REVERT: 0 20 ARG cc_start: 0.9353 (ptp-110) cc_final: 0.9025 (ptp90) REVERT: 0 46 MET cc_start: 0.8616 (mmt) cc_final: 0.8316 (mmt) REVERT: 4 25 LYS cc_start: 0.9029 (mttt) cc_final: 0.8691 (mmtm) REVERT: 5 10 LEU cc_start: 0.9428 (mm) cc_final: 0.9184 (mm) outliers start: 1 outliers final: 0 residues processed: 715 average time/residue: 1.1907 time to fit residues: 1483.0736 Evaluate side-chains 571 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 571 time to evaluate : 5.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 833 optimal weight: 3.9990 chunk 878 optimal weight: 3.9990 chunk 801 optimal weight: 30.0000 chunk 854 optimal weight: 7.9990 chunk 877 optimal weight: 2.9990 chunk 514 optimal weight: 30.0000 chunk 372 optimal weight: 10.0000 chunk 670 optimal weight: 20.0000 chunk 262 optimal weight: 40.0000 chunk 771 optimal weight: 8.9990 chunk 807 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 6 HIS ** d 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 64 HIS f 87 ASN ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 20 ASN ** s 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 ASN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 ASN N 9 HIS ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 44 ASN ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 23 ASN ** 0 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 26 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 150413 Z= 0.210 Angle : 0.652 15.953 225543 Z= 0.333 Chirality : 0.037 0.417 28923 Planarity : 0.005 0.100 11684 Dihedral : 24.282 179.874 76255 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 21.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.98 % Favored : 86.92 % Rotamer: Outliers : 0.07 % Allowed : 0.60 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.28 % Twisted Proline : 0.52 % Twisted General : 0.22 % 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: -2.92 (0.11), residues: 5101 helix: -0.32 (0.14), residues: 1367 sheet: -1.95 (0.17), residues: 875 loop : -2.88 (0.11), residues: 2859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP c 18 HIS 0.015 0.002 HIS K 131 PHE 0.023 0.002 PHE Z 30 TYR 0.024 0.002 TYR C 257 ARG 0.017 0.001 ARG k 111 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10202 Ramachandran restraints generated. 5101 Oldfield, 0 Emsley, 5101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10202 Ramachandran restraints generated. 5101 Oldfield, 0 Emsley, 5101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 734 time to evaluate : 5.293 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 TARDY: cannot create tardy model for: "LYS K 118 " (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 TARDY: cannot create tardy model for: "TYR R 43 " (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: c 180 ASP cc_start: 0.7725 (t0) cc_final: 0.7228 (t70) REVERT: c 182 ASP cc_start: 0.7030 (m-30) cc_final: 0.6727 (m-30) REVERT: d 47 TYR cc_start: 0.7540 (t80) cc_final: 0.7194 (t80) REVERT: d 88 MET cc_start: 0.9033 (mmp) cc_final: 0.8712 (mmm) REVERT: d 201 GLN cc_start: 0.8638 (pm20) cc_final: 0.8198 (pm20) REVERT: e 76 MET cc_start: 0.8424 (tpp) cc_final: 0.8052 (tpp) REVERT: f 10 MET cc_start: 0.8196 (tmm) cc_final: 0.7837 (tmm) REVERT: f 51 LEU cc_start: 0.8382 (tp) cc_final: 0.8168 (tp) REVERT: f 94 MET cc_start: 0.8196 (mmt) cc_final: 0.7069 (tmm) REVERT: g 33 ASP cc_start: 0.8949 (m-30) cc_final: 0.8467 (t70) REVERT: g 110 LEU cc_start: 0.7215 (mt) cc_final: 0.6770 (pp) REVERT: h 76 ASN cc_start: 0.8577 (t0) cc_final: 0.8156 (t0) REVERT: i 103 LEU cc_start: 0.7875 (mt) cc_final: 0.7571 (tt) REVERT: i 107 ASP cc_start: 0.9117 (m-30) cc_final: 0.8460 (t0) REVERT: j 85 ASP cc_start: 0.8345 (m-30) cc_final: 0.8097 (t0) REVERT: j 89 LYS cc_start: 0.8365 (tptp) cc_final: 0.7698 (mmtm) REVERT: l 116 ASP cc_start: 0.8136 (t70) cc_final: 0.7860 (t0) REVERT: l 122 ASP cc_start: 0.8111 (t0) cc_final: 0.7458 (m-30) REVERT: n 46 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6917 (mm-30) REVERT: o 10 GLU cc_start: 0.9209 (tp30) cc_final: 0.8611 (tp30) REVERT: o 34 GLU cc_start: 0.8640 (mp0) cc_final: 0.8377 (mp0) REVERT: o 37 ASN cc_start: 0.9377 (t0) cc_final: 0.9004 (t0) REVERT: o 47 LYS cc_start: 0.9666 (mmmm) cc_final: 0.9272 (mmmt) REVERT: p 68 ASP cc_start: 0.9119 (p0) cc_final: 0.8892 (p0) REVERT: q 20 MET cc_start: 0.8682 (mtm) cc_final: 0.7933 (mmp) REVERT: r 15 ASP cc_start: 0.8985 (m-30) cc_final: 0.8585 (p0) REVERT: r 27 TYR cc_start: 0.7515 (t80) cc_final: 0.7290 (t80) REVERT: r 36 PHE cc_start: 0.8356 (m-80) cc_final: 0.8043 (m-80) REVERT: r 68 ILE cc_start: 0.8971 (tp) cc_final: 0.8510 (tt) REVERT: s 66 MET cc_start: 0.6516 (ttt) cc_final: 0.6202 (ttt) REVERT: t 59 MET cc_start: 0.8394 (mmm) cc_final: 0.7879 (mmt) REVERT: C 5 LYS cc_start: 0.9655 (mttt) cc_final: 0.9367 (mmmt) REVERT: C 185 LEU cc_start: 0.9494 (mt) cc_final: 0.9204 (tp) REVERT: C 199 GLN cc_start: 0.8910 (mp10) cc_final: 0.8695 (mp10) REVERT: D 128 GLN cc_start: 0.8627 (mt0) cc_final: 0.8398 (mt0) REVERT: D 175 GLU cc_start: 0.8000 (tp30) cc_final: 0.7690 (tp30) REVERT: E 83 TRP cc_start: 0.8111 (m100) cc_final: 0.7701 (m-10) REVERT: E 141 GLN cc_start: 0.9229 (tp-100) cc_final: 0.8905 (tp-100) REVERT: F 96 MET cc_start: 0.8825 (mmm) cc_final: 0.8616 (mmm) REVERT: F 97 TYR cc_start: 0.9053 (m-10) cc_final: 0.8834 (m-10) REVERT: G 57 ASP cc_start: 0.8288 (m-30) cc_final: 0.7959 (m-30) REVERT: G 61 MET cc_start: 0.8784 (tpt) cc_final: 0.8279 (tpt) REVERT: G 84 GLN cc_start: 0.8885 (mt0) cc_final: 0.7970 (pp30) REVERT: K 77 ARG cc_start: 0.8375 (mtt180) cc_final: 0.7554 (mtm180) REVERT: L 42 THR cc_start: 0.8850 (t) cc_final: 0.8586 (m) REVERT: L 81 GLU cc_start: 0.9048 (mp0) cc_final: 0.8823 (mp0) REVERT: L 120 GLU cc_start: 0.8754 (tt0) cc_final: 0.8061 (mp0) REVERT: N 1 MET cc_start: 0.0196 (mmm) cc_final: -0.1270 (mmm) REVERT: N 58 MET cc_start: 0.8954 (tpt) cc_final: 0.8616 (tpt) REVERT: N 63 LYS cc_start: 0.8971 (mttt) cc_final: 0.8523 (tppp) REVERT: N 64 VAL cc_start: 0.8987 (t) cc_final: 0.8136 (m) REVERT: O 80 ILE cc_start: 0.8428 (mt) cc_final: 0.7961 (tp) REVERT: P 45 ILE cc_start: 0.8886 (mm) cc_final: 0.8674 (mm) REVERT: P 46 ASP cc_start: 0.8397 (m-30) cc_final: 0.8194 (m-30) REVERT: Q 4 LEU cc_start: 0.9175 (mt) cc_final: 0.8799 (tt) REVERT: Q 100 LEU cc_start: 0.9249 (mt) cc_final: 0.9035 (mt) REVERT: R 71 MET cc_start: 0.9490 (mmm) cc_final: 0.8989 (mmm) REVERT: R 106 PHE cc_start: 0.9376 (t80) cc_final: 0.9168 (t80) REVERT: U 5 ASP cc_start: 0.8549 (m-30) cc_final: 0.8146 (t0) REVERT: U 20 MET cc_start: 0.9020 (mmm) cc_final: 0.8794 (mmm) REVERT: U 59 ARG cc_start: 0.7199 (ttm170) cc_final: 0.6645 (ttm170) REVERT: V 1 MET cc_start: 0.7833 (ttp) cc_final: 0.6352 (tpt) REVERT: V 8 LYS cc_start: 0.9513 (mttt) cc_final: 0.9301 (mmmm) REVERT: W 80 ASP cc_start: 0.8647 (t0) cc_final: 0.8105 (p0) REVERT: X 53 LYS cc_start: 0.9356 (mttt) cc_final: 0.9041 (mttp) REVERT: Z 14 MET cc_start: 0.7117 (mtp) cc_final: 0.6813 (mtp) REVERT: 0 20 ARG cc_start: 0.9289 (ptp-110) cc_final: 0.8959 (ptp90) REVERT: 0 46 MET cc_start: 0.8694 (mmt) cc_final: 0.8348 (mmt) REVERT: 0 55 ASP cc_start: 0.9057 (m-30) cc_final: 0.8722 (m-30) REVERT: 3 20 ASN cc_start: 0.8595 (m-40) cc_final: 0.8392 (p0) REVERT: 4 25 LYS cc_start: 0.8944 (mttt) cc_final: 0.8653 (mmtm) REVERT: 5 10 LEU cc_start: 0.9470 (mm) cc_final: 0.9239 (mm) REVERT: 6 24 MET cc_start: 0.7836 (mmp) cc_final: 0.7408 (mmp) outliers start: 3 outliers final: 1 residues processed: 735 average time/residue: 1.1944 time to fit residues: 1531.4058 Evaluate side-chains 581 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 580 time to evaluate : 5.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 851 optimal weight: 5.9990 chunk 560 optimal weight: 20.0000 chunk 903 optimal weight: 7.9990 chunk 551 optimal weight: 20.0000 chunk 428 optimal weight: 20.0000 chunk 627 optimal weight: 20.0000 chunk 947 optimal weight: 9.9990 chunk 872 optimal weight: 5.9990 chunk 754 optimal weight: 30.0000 chunk 78 optimal weight: 20.0000 chunk 582 optimal weight: 30.0000 overall best weight: 9.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 6 HIS ** d 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 87 ASN ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 28 GLN ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 150413 Z= 0.327 Angle : 0.765 14.406 225543 Z= 0.388 Chirality : 0.042 0.432 28923 Planarity : 0.006 0.103 11684 Dihedral : 24.473 179.997 76255 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 29.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 15.21 % Favored : 84.67 % Rotamer: Outliers : 0.02 % Allowed : 0.34 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.28 % Twisted Proline : 0.52 % Twisted General : 0.24 % 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: -3.10 (0.11), residues: 5101 helix: -0.55 (0.14), residues: 1349 sheet: -2.07 (0.16), residues: 883 loop : -2.92 (0.11), residues: 2869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 1 37 HIS 0.012 0.002 HIS C 53 PHE 0.036 0.003 PHE U 62 TYR 0.031 0.002 TYR C 257 ARG 0.011 0.001 ARG 0 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10202 Ramachandran restraints generated. 5101 Oldfield, 0 Emsley, 5101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10202 Ramachandran restraints generated. 5101 Oldfield, 0 Emsley, 5101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 690 time to evaluate : 5.866 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 TARDY: cannot create tardy model for: "LYS K 118 " (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 TARDY: cannot create tardy model for: "TYR R 43 " (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: c 180 ASP cc_start: 0.7772 (t0) cc_final: 0.7303 (t70) REVERT: c 182 ASP cc_start: 0.7078 (m-30) cc_final: 0.6761 (m-30) REVERT: d 47 TYR cc_start: 0.7591 (t80) cc_final: 0.7245 (t80) REVERT: d 67 GLN cc_start: 0.9350 (mt0) cc_final: 0.9045 (mt0) REVERT: d 201 GLN cc_start: 0.8694 (pm20) cc_final: 0.8301 (pm20) REVERT: e 76 MET cc_start: 0.8456 (tpp) cc_final: 0.8051 (tpp) REVERT: f 6 LYS cc_start: 0.9027 (mppt) cc_final: 0.8754 (mppt) REVERT: f 10 MET cc_start: 0.8085 (tmm) cc_final: 0.7712 (tmm) REVERT: f 94 MET cc_start: 0.8247 (mmt) cc_final: 0.7235 (tmm) REVERT: g 33 ASP cc_start: 0.8726 (m-30) cc_final: 0.8158 (t70) REVERT: h 76 ASN cc_start: 0.8637 (t0) cc_final: 0.8329 (t0) REVERT: i 103 LEU cc_start: 0.7862 (mt) cc_final: 0.7547 (tt) REVERT: i 107 ASP cc_start: 0.9132 (m-30) cc_final: 0.8464 (t0) REVERT: j 85 ASP cc_start: 0.8411 (m-30) cc_final: 0.8184 (m-30) REVERT: j 88 MET cc_start: 0.7013 (ptm) cc_final: 0.6638 (ppp) REVERT: k 33 MET cc_start: 0.8949 (tpp) cc_final: 0.8741 (tpp) REVERT: k 79 LEU cc_start: 0.9523 (mt) cc_final: 0.9228 (mt) REVERT: k 122 ARG cc_start: 0.9176 (mtp180) cc_final: 0.8689 (mtp-110) REVERT: l 65 TYR cc_start: 0.8270 (p90) cc_final: 0.8062 (p90) REVERT: l 116 ASP cc_start: 0.8112 (t70) cc_final: 0.7839 (t0) REVERT: l 122 ASP cc_start: 0.8017 (t0) cc_final: 0.7377 (m-30) REVERT: n 46 GLU cc_start: 0.7102 (mm-30) cc_final: 0.6825 (mm-30) REVERT: o 10 GLU cc_start: 0.9408 (tp30) cc_final: 0.8978 (tp30) REVERT: o 13 LYS cc_start: 0.9616 (pttp) cc_final: 0.9248 (mtmm) REVERT: o 27 VAL cc_start: 0.8340 (t) cc_final: 0.8130 (t) REVERT: o 34 GLU cc_start: 0.8739 (mp0) cc_final: 0.8527 (mp0) REVERT: o 37 ASN cc_start: 0.9425 (t0) cc_final: 0.9003 (t0) REVERT: p 68 ASP cc_start: 0.9124 (p0) cc_final: 0.8883 (p0) REVERT: q 20 MET cc_start: 0.8758 (mtm) cc_final: 0.8068 (mmp) REVERT: r 15 ASP cc_start: 0.9017 (m-30) cc_final: 0.8603 (p0) REVERT: r 27 TYR cc_start: 0.7522 (t80) cc_final: 0.7280 (t80) REVERT: r 29 ASP cc_start: 0.9188 (t70) cc_final: 0.8903 (t0) REVERT: r 36 PHE cc_start: 0.8399 (m-80) cc_final: 0.8036 (m-80) REVERT: r 68 ILE cc_start: 0.8969 (tp) cc_final: 0.8542 (tt) REVERT: s 66 MET cc_start: 0.6769 (ttt) cc_final: 0.6413 (ttt) REVERT: t 59 MET cc_start: 0.8358 (mmm) cc_final: 0.7875 (mmt) REVERT: C 5 LYS cc_start: 0.9664 (mttt) cc_final: 0.9372 (mmmt) REVERT: C 185 LEU cc_start: 0.9397 (mt) cc_final: 0.9052 (tp) REVERT: C 199 GLN cc_start: 0.8916 (mp10) cc_final: 0.8618 (mp10) REVERT: C 273 ARG cc_start: 0.7663 (tmm160) cc_final: 0.7239 (ttp80) REVERT: D 53 TYR cc_start: 0.7283 (t80) cc_final: 0.6312 (t80) REVERT: D 175 GLU cc_start: 0.8036 (tp30) cc_final: 0.7758 (tp30) REVERT: E 83 TRP cc_start: 0.8227 (m100) cc_final: 0.7803 (m-10) REVERT: E 141 GLN cc_start: 0.9283 (tp-100) cc_final: 0.8991 (tp-100) REVERT: F 96 MET cc_start: 0.8836 (mmm) cc_final: 0.8560 (mmm) REVERT: F 152 MET cc_start: 0.8831 (mmm) cc_final: 0.8453 (mmm) REVERT: G 43 MET cc_start: 0.8543 (ppp) cc_final: 0.7904 (ppp) REVERT: G 84 GLN cc_start: 0.8798 (mt0) cc_final: 0.8110 (pp30) REVERT: K 77 ARG cc_start: 0.8290 (mtt180) cc_final: 0.7555 (mtm180) REVERT: L 81 GLU cc_start: 0.9083 (mp0) cc_final: 0.8811 (mp0) REVERT: L 120 GLU cc_start: 0.8807 (tt0) cc_final: 0.7978 (mp0) REVERT: N 42 ILE cc_start: 0.8625 (mt) cc_final: 0.8209 (mp) REVERT: N 58 MET cc_start: 0.9023 (tpt) cc_final: 0.8515 (tpt) REVERT: N 63 LYS cc_start: 0.9019 (mttt) cc_final: 0.8192 (tppp) REVERT: N 64 VAL cc_start: 0.9026 (t) cc_final: 0.7652 (m) REVERT: N 65 TRP cc_start: 0.8370 (m100) cc_final: 0.7891 (m100) REVERT: O 80 ILE cc_start: 0.8429 (mt) cc_final: 0.7993 (tp) REVERT: Q 4 LEU cc_start: 0.9174 (mt) cc_final: 0.8781 (tt) REVERT: Q 10 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8584 (mm-40) REVERT: Q 100 LEU cc_start: 0.9309 (mt) cc_final: 0.9086 (mt) REVERT: R 71 MET cc_start: 0.9538 (mmm) cc_final: 0.9062 (mmm) REVERT: R 106 PHE cc_start: 0.9438 (t80) cc_final: 0.9073 (t80) REVERT: T 23 ARG cc_start: 0.7967 (mtt180) cc_final: 0.7658 (mtt180) REVERT: T 114 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6387 (mt-10) REVERT: U 5 ASP cc_start: 0.8575 (m-30) cc_final: 0.8237 (t0) REVERT: U 59 ARG cc_start: 0.7203 (ttm170) cc_final: 0.6676 (ttm170) REVERT: U 65 MET cc_start: 0.7659 (ppp) cc_final: 0.6908 (ptp) REVERT: V 1 MET cc_start: 0.7864 (ttp) cc_final: 0.6411 (tpt) REVERT: V 8 LYS cc_start: 0.9514 (mttt) cc_final: 0.9294 (mmmm) REVERT: W 80 ASP cc_start: 0.8665 (t0) cc_final: 0.8062 (p0) REVERT: W 89 VAL cc_start: 0.6680 (t) cc_final: 0.6297 (t) REVERT: X 53 LYS cc_start: 0.9387 (mttt) cc_final: 0.9139 (mmmm) REVERT: X 77 ARG cc_start: 0.8630 (mpt90) cc_final: 0.8361 (mmt-90) REVERT: Z 14 MET cc_start: 0.7180 (mtp) cc_final: 0.6821 (mtp) REVERT: 0 20 ARG cc_start: 0.9338 (ptp-110) cc_final: 0.9014 (ptp90) REVERT: 0 46 MET cc_start: 0.8688 (mmt) cc_final: 0.8330 (mmt) REVERT: 2 55 MET cc_start: 0.8509 (pmm) cc_final: 0.8269 (pmm) REVERT: 4 25 LYS cc_start: 0.9063 (mttt) cc_final: 0.8686 (mmtm) REVERT: 5 10 LEU cc_start: 0.9412 (mm) cc_final: 0.9199 (mm) outliers start: 1 outliers final: 0 residues processed: 690 average time/residue: 1.1804 time to fit residues: 1426.6163 Evaluate side-chains 566 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 566 time to evaluate : 5.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 231 optimal weight: 30.0000 chunk 695 optimal weight: 7.9990 chunk 111 optimal weight: 40.0000 chunk 209 optimal weight: 1.9990 chunk 755 optimal weight: 5.9990 chunk 316 optimal weight: 9.9990 chunk 775 optimal weight: 20.0000 chunk 95 optimal weight: 50.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 6 HIS ** d 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 147 GLN f 87 ASN ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 28 GLN ** p 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 20 ASN ** s 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 ASN ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 11 GLN ** S 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 23 ASN ** 0 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 4 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.044519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.034752 restraints weight = 1337047.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.035840 restraints weight = 493902.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.036494 restraints weight = 266630.199| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 150413 Z= 0.229 Angle : 0.671 15.600 225543 Z= 0.342 Chirality : 0.038 0.446 28923 Planarity : 0.005 0.096 11684 Dihedral : 24.310 179.537 76255 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 23.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.90 % Favored : 87.00 % Rotamer: Outliers : 0.09 % Allowed : 0.41 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.28 % 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: -2.90 (0.11), residues: 5101 helix: -0.36 (0.14), residues: 1372 sheet: -1.94 (0.16), residues: 877 loop : -2.85 (0.11), residues: 2852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP c 18 HIS 0.010 0.002 HIS p 84 PHE 0.025 0.002 PHE k 61 TYR 0.023 0.002 TYR 3 17 ARG 0.010 0.001 ARG X 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26474.43 seconds wall clock time: 469 minutes 17.99 seconds (28157.99 seconds total)