Starting phenix.real_space_refine on Wed Feb 21 08:03:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o8w_0656/02_2024/6o8w_0656.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o8w_0656/02_2024/6o8w_0656.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o8w_0656/02_2024/6o8w_0656.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o8w_0656/02_2024/6o8w_0656.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o8w_0656/02_2024/6o8w_0656.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o8w_0656/02_2024/6o8w_0656.pdb" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.092 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 4623 5.49 5 S 130 5.16 5 C 69782 2.51 5 N 25901 2.21 5 O 39513 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "d TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "p PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 16": "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 "N ARG 119": "NH1" <-> "NH2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "Q ARG 21": "NH1" <-> "NH2" Residue "Q TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 16": "NH1" <-> "NH2" Residue "V PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 15": "NH1" <-> "NH2" Residue "W ARG 53": "NH1" <-> "NH2" Residue "X ARG 80": "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-5238/modules/chem_data/mon_lib" Total number of atoms: 139953 Number of models: 1 Model: "" Number of chains: 55 Chain: "a" Number of atoms: 32646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1523, 32646 Classifications: {'RNA': 1523} Modifications used: {'rna2p_pur': 125, 'rna2p_pyr': 90, 'rna3p_pur': 732, 'rna3p_pyr': 576} Link IDs: {'rna2p': 215, 'rna3p': 1307} Chain breaks: 3 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: "u" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1623 Classifications: {'RNA': 76} Modifications used: {'p5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 32, 'rna3p_pyr': 32} Link IDs: {'rna2p': 11, 'rna3p': 64} Chain: "v" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "A" Number of atoms: 62301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62301 Classifications: {'RNA': 2903} Modifications used: {'rna2p_pur': 309, 'rna2p_pyr': 157, 'rna3p_pur': 1375, 'rna3p_pyr': 1058} Link IDs: {'rna2p': 466, 'rna3p': 2436} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Unresolved non-hydrogen planarities: 7 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': 7, 'rna2p_pyr': 7, 'rna3p_pur': 55, 'rna3p_pyr': 47} Link IDs: {'rna2p': 14, 'rna3p': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2113 Classifications: {'peptide': 275} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 257} Unresolved chain links: 2 Unresolved chain link angles: 6 Unresolved chain link dihedrals: 8 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen chiralities: 2 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: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1573 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 8, 'TRANS': 197} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 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: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1344 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1129 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 7, 'TRANS': 137} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 921 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1094 Classifications: {'peptide': 146} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 140} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1118 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "O" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 978 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "P" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 862 Classifications: {'peptide': 112} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 108} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 923 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} 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: "R" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 950 Classifications: {'peptide': 118} Link IDs: {'TRANS': 117} Chain: "S" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 783 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "T" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 848 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "U" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 720 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "V" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 762 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 758 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "X" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 571 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 425 Classifications: {'peptide': 54} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 434 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} 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: "1" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 472 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "2" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 428 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 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: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 374 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "5" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 521 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 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 44928 SG CYS n 24 56.902 132.509 121.225 1.00 98.96 S ATOM 44954 SG CYS n 27 60.472 132.828 121.035 1.00 98.32 S ATOM 45066 SG CYS n 40 59.999 132.099 124.520 1.00 97.98 S ATOM 45091 SG CYS n 43 59.937 135.481 123.377 1.00 96.80 S ATOM A0TF7 SG CYS 2 30 249.238 136.986 87.107 1.00 30.00 S ATOM A0TIF SG CYS 2 46 251.539 137.518 89.854 1.00 30.00 S ATOM A0TMR SG CYS 3 9 137.262 42.895 135.641 1.00170.00 S ATOM A0TNA SG CYS 3 12 140.419 41.676 136.694 1.00172.16 S ATOM A0TT7 SG CYS 3 36 139.827 41.684 132.742 1.00166.07 S ATOM A0UNM SG CYS 6 11 140.978 124.113 50.296 1.00 30.00 S ATOM A0UR9 SG CYS 6 27 144.977 124.262 47.488 1.00 30.00 S Time building chain proxies: 52.79, per 1000 atoms: 0.38 Number of scatterers: 139953 At special positions: 0 Unit cell: (285.22, 275.347, 225.982, 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 4623 15.00 O 39513 8.00 N 25901 7.00 C 69782 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: 58.42 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 2 101 " pdb="ZN ZN 2 101 " - pdb=" SG CYS 2 46 " pdb="ZN ZN 2 101 " - pdb=" SG CYS 2 30 " pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 12 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 9 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 36 " pdb=" ZN 6 101 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 27 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 11 " pdb="ZN ZN 6 101 " - pdb=" NE2 HIS 6 33 " pdb=" ZN n 101 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 43 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 40 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 24 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 27 " Number of angles added : 6 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9536 Finding SS restraints... Warning! N3 atom is missing from residue C B 88 Was trying to link: C B 88 N3 with U B 85 N3, Saenger class: 17 Warning! N3 atom is missing from residue C B 88 Was trying to link: C B 88 N3 with U B 85 N3, Saenger class: 18 Warning! N7 atom is missing from residue A B 27 Was trying to link: A B 27 N7 with U B 53 N3, Saenger class: 23 Warning! N7 atom is missing from residue A B 27 Was trying to link: A B 27 N7 with U B 53 N3, Saenger class: 24 Secondary structure from input PDB file: 145 helices and 65 sheets defined 28.7% alpha, 14.1% beta 1421 base pairs and 2325 stacking pairs defined. Time for finding SS restraints: 49.21 Creating SS restraints... Processing helix chain 'c' and resid 6 through 12 Processing helix chain 'c' and resid 28 through 41 Processing helix chain 'c' and resid 42 through 49 removed outlier: 4.591A pdb=" N ASP c 48 " --> pdb=" O THR c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 77 Processing helix chain 'c' and resid 80 through 95 removed outlier: 3.737A pdb=" N GLU c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS c 92 " --> pdb=" O LYS c 88 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU c 93 " --> pdb=" O GLU c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 112 through 123 Processing helix chain 'c' and resid 128 through 142 Processing helix chain 'd' and resid 9 through 16 Processing helix chain 'd' and resid 45 through 59 Processing helix chain 'd' and resid 64 through 75 Processing helix chain 'd' and resid 82 through 91 Processing helix chain 'd' and resid 94 through 103 removed outlier: 3.697A pdb=" N GLY d 103 " --> pdb=" O VAL d 99 " (cutoff:3.500A) Processing helix chain 'd' and resid 107 through 117 removed outlier: 4.068A pdb=" N HIS d 117 " --> pdb=" O GLN d 113 " (cutoff:3.500A) Processing helix chain 'd' and resid 149 through 158 removed outlier: 4.112A pdb=" N LYS d 153 " --> pdb=" O ILE d 149 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 68 removed outlier: 3.566A pdb=" N LYS e 68 " --> pdb=" O ILE e 64 " (cutoff:3.500A) Processing helix chain 'e' and resid 109 through 116 Processing helix chain 'e' and resid 132 through 146 removed outlier: 3.557A pdb=" N VAL e 137 " --> pdb=" O PRO e 133 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN e 146 " --> pdb=" O GLU e 142 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 157 Processing helix chain 'f' and resid 18 through 36 removed outlier: 4.304A pdb=" N ASN f 36 " --> pdb=" O ILE f 32 " (cutoff:3.500A) Processing helix chain 'f' and resid 77 through 85 removed outlier: 3.792A pdb=" N LEU f 83 " --> pdb=" O GLU f 79 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS f 85 " --> pdb=" O ASP f 81 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 Processing helix chain 'g' and resid 35 through 53 removed outlier: 4.044A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 69 Processing helix chain 'g' and resid 92 through 108 Processing helix chain 'g' and resid 117 through 129 Processing helix chain 'g' and resid 132 through 145 removed outlier: 3.820A pdb=" N LYS g 136 " --> pdb=" O GLY g 132 " (cutoff:3.500A) Processing helix chain 'g' and resid 149 through 153 removed outlier: 3.519A pdb=" N ALA g 152 " --> pdb=" O ARG g 149 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS g 153 " --> pdb=" O ALA g 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 149 through 153' Processing helix chain 'h' and resid 5 through 20 removed outlier: 3.825A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL h 20 " --> pdb=" O ASN h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 43 Processing helix chain 'h' and resid 115 through 120 removed outlier: 3.706A pdb=" N ARG h 119 " --> pdb=" O ASP h 115 " (cutoff:3.500A) Processing helix chain 'i' and resid 44 through 50 Processing helix chain 'i' and resid 71 through 78 Processing helix chain 'i' and resid 78 through 91 removed outlier: 3.684A pdb=" N GLY i 82 " --> pdb=" O ALA i 78 " (cutoff:3.500A) Processing helix chain 'i' and resid 94 through 102 removed outlier: 3.874A pdb=" N ALA i 101 " --> pdb=" O ALA i 97 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.751A pdb=" N LYS j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 58 removed outlier: 3.842A pdb=" N LYS k 57 " --> pdb=" O GLY k 54 " (cutoff:3.500A) Processing helix chain 'k' and resid 59 through 75 removed outlier: 3.576A pdb=" N ALA k 63 " --> pdb=" O THR k 59 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL k 73 " --> pdb=" O ALA k 69 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 101 removed outlier: 3.856A pdb=" N ILE k 97 " --> pdb=" O ARG k 93 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 9 Processing helix chain 'l' and resid 128 through 132 removed outlier: 4.153A pdb=" N THR l 132 " --> pdb=" O LYS l 129 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 19 Processing helix chain 'm' and resid 27 through 38 removed outlier: 3.561A pdb=" N VAL m 37 " --> pdb=" O VAL m 33 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 60 Processing helix chain 'm' and resid 61 through 63 No H-bonds generated for 'chain 'm' and resid 61 through 63' Processing helix chain 'm' and resid 66 through 81 removed outlier: 3.881A pdb=" N ARG m 70 " --> pdb=" O GLU m 66 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 93 Processing helix chain 'n' and resid 3 through 12 removed outlier: 3.692A pdb=" N ALA n 8 " --> pdb=" O LYS n 4 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN n 10 " --> pdb=" O MET n 6 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS n 11 " --> pdb=" O ILE n 7 " (cutoff:3.500A) Processing helix chain 'n' and resid 16 through 20 removed outlier: 4.026A pdb=" N GLN n 19 " --> pdb=" O HIS n 16 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA n 20 " --> pdb=" O SER n 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 16 through 20' Processing helix chain 'n' and resid 40 through 50 removed outlier: 3.727A pdb=" N PHE n 44 " --> pdb=" O CYS n 40 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 removed outlier: 3.805A pdb=" N ILE o 12 " --> pdb=" O LYS o 8 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS o 13 " --> pdb=" O ASN o 9 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU o 14 " --> pdb=" O GLU o 10 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR o 15 " --> pdb=" O ILE o 11 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 46 removed outlier: 3.924A pdb=" N GLN o 28 " --> pdb=" O SER o 24 " (cutoff:3.500A) Processing helix chain 'o' and resid 52 through 72 removed outlier: 3.776A pdb=" N LYS o 72 " --> pdb=" O ALA o 68 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 86 Processing helix chain 'p' and resid 54 through 63 removed outlier: 4.150A pdb=" N ASP p 58 " --> pdb=" O ASP p 54 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS p 62 " --> pdb=" O ASP p 58 " (cutoff:3.500A) Processing helix chain 'p' and resid 67 through 76 Processing helix chain 'p' and resid 78 through 87 Processing helix chain 'r' and resid 33 through 37 removed outlier: 3.502A pdb=" N PHE r 36 " --> pdb=" O LEU r 33 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE r 37 " --> pdb=" O LYS r 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 33 through 37' Processing helix chain 'r' and resid 45 through 50 Processing helix chain 'r' and resid 52 through 67 Processing helix chain 's' and resid 12 through 24 removed outlier: 4.718A pdb=" N GLY s 24 " --> pdb=" O GLU s 20 " (cutoff:3.500A) Processing helix chain 't' and resid 7 through 42 removed outlier: 4.008A pdb=" N ALA t 38 " --> pdb=" O LYS t 34 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL t 39 " --> pdb=" O PHE t 35 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA t 40 " --> pdb=" O GLU t 36 " (cutoff:3.500A) Processing helix chain 't' and resid 47 through 63 Processing helix chain 't' and resid 68 through 80 Processing helix chain 'C' and resid 208 through 214 Processing helix chain 'C' and resid 221 through 225 removed outlier: 3.839A pdb=" N VAL C 224 " --> pdb=" O ARG C 221 " (cutoff:3.500A) 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: 3.859A pdb=" N VAL D 101 " --> pdb=" O LYS D 98 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE D 102 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN D 103 " --> pdb=" O ASP D 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 98 through 103' Processing helix chain 'D' and resid 121 through 127 removed outlier: 3.842A pdb=" N ARG D 125 " --> pdb=" O GLY D 121 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N HIS D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 43 Processing helix chain 'E' and resid 102 through 120 removed outlier: 3.757A pdb=" N ARG E 106 " --> pdb=" O PRO E 102 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG E 107 " --> pdb=" O LYS E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 146 removed outlier: 3.710A pdb=" N PHE E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 165 Processing helix chain 'E' and resid 182 through 188 removed outlier: 3.971A pdb=" N VAL E 186 " --> pdb=" O SER E 182 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.869A pdb=" N LEU E 199 " --> pdb=" O THR E 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 12 Processing helix chain 'F' and resid 12 through 19 removed outlier: 3.570A pdb=" N LEU F 16 " --> pdb=" O VAL F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 28 Processing helix chain 'F' and resid 48 through 61 removed outlier: 4.537A pdb=" N LYS F 52 " --> pdb=" O LYS F 48 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA F 53 " --> pdb=" O ASN F 49 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 106 removed outlier: 4.338A pdb=" N TYR F 97 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL F 106 " --> pdb=" O LYS F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 111 Processing helix chain 'F' and resid 163 through 173 Processing helix chain 'G' and resid 3 through 7 removed outlier: 3.859A pdb=" N LYS G 7 " --> pdb=" O ILE G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 69 removed outlier: 3.977A pdb=" N GLY G 66 " --> pdb=" O LYS G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 81 Processing helix chain 'G' and resid 138 through 150 Processing helix chain 'K' and resid 25 through 38 removed outlier: 3.673A pdb=" N LEU K 29 " --> pdb=" O PRO K 25 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG K 38 " --> pdb=" O ALA K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 95 removed outlier: 3.949A pdb=" N LEU K 93 " --> pdb=" O ALA K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 106 removed outlier: 3.645A pdb=" N LEU K 101 " --> pdb=" O ASN K 97 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE K 102 " --> pdb=" O SER K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 110 removed outlier: 3.517A 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: 3.822A pdb=" N GLN K 137 " --> pdb=" O ALA K 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 110 removed outlier: 3.880A pdb=" N LEU L 106 " --> pdb=" O ALA L 103 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN L 110 " --> pdb=" O ARG L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 116 Processing helix chain 'M' and resid 2 through 6 removed outlier: 3.529A pdb=" N GLU M 5 " --> pdb=" O LYS M 2 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU M 6 " --> pdb=" O LEU M 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 2 through 6' Processing helix chain 'M' and resid 56 through 60 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'M' and resid 131 through 139 removed outlier: 3.856A pdb=" N ALA M 139 " --> pdb=" O ALA M 135 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 56 Processing helix chain 'N' and resid 110 through 120 Processing helix chain 'O' and resid 9 through 23 removed outlier: 3.643A pdb=" N ARG O 13 " --> pdb=" O THR O 9 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS O 14 " --> pdb=" O SER O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 47 Processing helix chain 'O' and resid 48 through 54 removed outlier: 3.955A pdb=" N ARG O 53 " --> pdb=" O THR O 49 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY O 54 " --> pdb=" O LEU O 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 60 removed outlier: 3.620A pdb=" N ARG O 59 " --> pdb=" O ASP O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 97 Processing helix chain 'P' and resid 6 through 20 removed outlier: 4.540A pdb=" N THR P 10 " --> pdb=" O ASP P 6 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG P 11 " --> pdb=" O LYS P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 85 removed outlier: 3.730A pdb=" N ALA P 80 " --> pdb=" O GLY P 76 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU P 85 " --> pdb=" O GLU P 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 113 removed outlier: 3.600A 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: 3.673A pdb=" N LEU Q 100 " --> pdb=" O LEU Q 97 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG Q 101 " --> pdb=" O TYR Q 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 97 through 101' Processing helix chain 'Q' and resid 104 through 108 removed outlier: 3.780A pdb=" N ALA Q 107 " --> pdb=" O HIS Q 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 8 through 19 removed outlier: 3.950A pdb=" N LYS R 12 " --> pdb=" O THR R 8 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 50 removed outlier: 4.612A pdb=" N GLU R 37 " --> pdb=" O LYS R 33 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN R 38 " --> pdb=" O SER R 34 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL R 39 " --> pdb=" O ALA R 35 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N MET R 40 " --> pdb=" O LYS R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 72 removed outlier: 3.789A pdb=" N ARG R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS R 59 " --> pdb=" O ARG R 55 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN R 72 " --> pdb=" O ALA R 68 " (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 removed outlier: 3.751A pdb=" N LEU R 117 " --> pdb=" O ALA R 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 21 through 26 removed outlier: 4.127A pdb=" N VAL T 25 " --> pdb=" O LYS T 21 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE T 26 " --> pdb=" O ALA T 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 21 through 26' Processing helix chain 'T' and resid 27 through 29 No H-bonds generated for 'chain 'T' and resid 27 through 29' Processing helix chain 'T' and resid 33 through 42 removed outlier: 4.552A pdb=" N SER T 39 " --> pdb=" O ALA T 35 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 66 removed outlier: 4.188A pdb=" N ILE T 52 " --> pdb=" O SER T 48 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU T 53 " --> pdb=" O ALA T 49 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LYS T 54 " --> pdb=" O GLY T 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 70 through 74 removed outlier: 3.714A pdb=" N LEU T 74 " --> pdb=" O VAL T 71 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 20 removed outlier: 3.838A pdb=" N LEU U 18 " --> pdb=" O GLU U 14 " (cutoff:3.500A) Processing helix chain 'U' and resid 34 through 47 removed outlier: 3.738A pdb=" N VAL U 38 " --> pdb=" O ASN U 34 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP U 47 " --> pdb=" O GLU U 43 " (cutoff:3.500A) Processing helix chain 'V' and resid 66 through 68 No H-bonds generated for 'chain 'V' and resid 66 through 68' Processing helix chain 'W' and resid 15 through 17 No H-bonds generated for 'chain 'W' and resid 15 through 17' Processing helix chain 'W' and resid 18 through 24 Processing helix chain 'W' and resid 44 through 47 Processing helix chain 'W' and resid 48 through 56 removed outlier: 4.425A pdb=" N GLU W 54 " --> pdb=" O LYS W 50 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 54 removed outlier: 3.731A pdb=" N LEU Y 54 " --> pdb=" O ALA Y 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3 through 7 Processing helix chain 'Z' and resid 10 through 34 removed outlier: 3.540A pdb=" N LEU Z 15 " --> pdb=" O THR Z 11 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 60 removed outlier: 3.594A pdb=" N VAL Z 46 " --> pdb=" O ARG Z 42 " (cutoff:3.500A) Processing helix chain '0' and resid 16 through 27 removed outlier: 3.595A 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 10 through 15 removed outlier: 3.617A pdb=" N ALA 2 14 " --> pdb=" O LYS 2 10 " (cutoff:3.500A) Processing helix chain '2' and resid 16 through 20 removed outlier: 3.635A pdb=" N HIS 2 19 " --> pdb=" O ARG 2 16 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 14 removed outlier: 3.868A pdb=" N GLN 4 13 " --> pdb=" O LYS 4 9 " (cutoff:3.500A) Processing helix chain '4' and resid 18 through 22 Processing helix chain '4' and resid 26 through 38 removed outlier: 3.913A pdb=" N ARG 4 36 " --> pdb=" O ALA 4 32 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS 4 37 " --> pdb=" O SER 4 33 " (cutoff:3.500A) Processing helix chain '5' and resid 38 through 43 Processing helix chain '5' and resid 44 through 46 No H-bonds generated for 'chain '5' and resid 44 through 46' Processing helix chain '5' and resid 51 through 56 removed outlier: 3.530A pdb=" N TYR 5 55 " --> pdb=" O LYS 5 52 " (cutoff:3.500A) Processing helix chain '6' and resid 30 through 33 removed outlier: 3.786A pdb=" N HIS 6 33 " --> pdb=" O ASN 6 30 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 30 through 33' Processing sheet with id=AA1, first strand: chain 'c' and resid 51 through 58 removed outlier: 6.661A pdb=" N HIS c 68 " --> pdb=" O SER c 52 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE c 54 " --> pdb=" O SER c 66 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N SER c 66 " --> pdb=" O ILE c 54 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ILE c 56 " --> pdb=" O ASN c 64 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASN c 64 " --> pdb=" O ILE c 56 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ARG c 58 " --> pdb=" O ARG c 62 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ARG c 62 " --> pdb=" O ARG c 58 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE c 65 " --> pdb=" O HIS c 99 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'c' and resid 163 through 165 Processing sheet with id=AA3, first strand: chain 'c' and resid 163 through 165 removed outlier: 3.585A pdb=" N VAL c 199 " --> pdb=" O ALA c 184 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA c 184 " --> pdb=" O VAL c 199 " (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 167 through 169 removed outlier: 3.812A pdb=" N SER d 167 " --> pdb=" O SER d 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'e' and resid 12 through 24 removed outlier: 6.866A pdb=" N LEU e 36 " --> pdb=" O VAL e 16 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE e 18 " --> pdb=" O ALA e 34 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA e 34 " --> pdb=" O ILE e 18 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ARG e 20 " --> pdb=" O ARG e 32 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ARG e 32 " --> pdb=" O ARG e 20 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR e 22 " --> pdb=" O ARG e 30 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ARG e 30 " --> pdb=" O THR e 22 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY e 51 " --> pdb=" O ALA e 35 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'e' and resid 85 through 88 removed outlier: 3.735A pdb=" N LEU e 95 " --> pdb=" O LYS e 126 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS e 126 " --> pdb=" O LEU e 95 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA e 106 " --> pdb=" O SER e 125 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N SER e 127 " --> pdb=" O ALA e 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'f' and resid 39 through 50 removed outlier: 5.074A pdb=" N VAL f 40 " --> pdb=" O THR f 69 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR f 69 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU f 42 " --> pdb=" O ASN f 67 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TYR f 63 " --> pdb=" O TRP f 46 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS f 48 " --> pdb=" O GLY f 61 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY f 61 " --> pdb=" O LYS f 48 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS f 64 " --> pdb=" O TYR f 11 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR f 11 " --> pdb=" O HIS f 64 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL f 68 " --> pdb=" O TYR f 7 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER f 70 " --> pdb=" O THR f 5 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LYS f 6 " --> pdb=" O LYS f 97 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS f 97 " --> pdb=" O LYS f 6 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLU f 8 " --> pdb=" O ILE f 95 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE f 95 " --> pdb=" O GLU f 8 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N MET f 10 " --> pdb=" O HIS f 93 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N HIS f 93 " --> pdb=" O MET f 10 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE f 12 " --> pdb=" O ILE f 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'g' and resid 74 through 76 Processing sheet with id=AB1, first strand: chain 'h' and resid 25 through 27 removed outlier: 3.635A pdb=" N VAL h 27 " --> pdb=" O ILE h 60 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG h 61 " --> pdb=" O VAL h 49 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL h 49 " --> pdb=" O ARG h 61 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N PHE h 63 " --> pdb=" O ARG h 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'h' and resid 76 through 79 removed outlier: 3.545A pdb=" N ASN h 76 " --> pdb=" O TRP h 132 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP h 132 " --> pdb=" O ASN h 76 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'h' and resid 76 through 79 removed outlier: 3.545A pdb=" N ASN h 76 " --> pdb=" O TRP h 132 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP h 132 " --> pdb=" O ASN h 76 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE h 105 " --> pdb=" O ILE h 128 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N TYR h 130 " --> pdb=" O ILE h 103 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE h 103 " --> pdb=" O TYR h 130 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY h 111 " --> pdb=" O THR h 108 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'i' and resid 6 through 10 removed outlier: 6.629A pdb=" N THR i 29 " --> pdb=" O VAL i 65 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N VAL i 67 " --> pdb=" O THR i 29 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'j' and resid 36 through 41 removed outlier: 5.032A pdb=" N GLY j 38 " --> pdb=" O ASP j 75 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASP j 75 " --> pdb=" O GLY j 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'j' and resid 45 through 52 removed outlier: 3.590A pdb=" N GLU j 45 " --> pdb=" O THR j 69 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N MET j 67 " --> pdb=" O SER j 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'k' and resid 41 through 46 removed outlier: 3.725A pdb=" N ALA k 43 " --> pdb=" O ILE k 34 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL k 20 " --> pdb=" O THR k 35 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA k 21 " --> pdb=" O THR k 85 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LYS k 87 " --> pdb=" O ALA k 21 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ILE k 23 " --> pdb=" O LYS k 87 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N VAL k 84 " --> pdb=" O ARG k 111 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'l' and resid 52 through 53 removed outlier: 4.148A pdb=" N TYR l 108 " --> pdb=" O THR l 77 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR l 48 " --> pdb=" O ARG l 67 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ARG l 67 " --> pdb=" O THR l 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'p' and resid 3 through 9 removed outlier: 3.717A pdb=" N TYR p 18 " --> pdb=" O TYR p 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'q' and resid 14 through 15 Processing sheet with id=AC2, first strand: chain 'q' and resid 61 through 65 removed outlier: 6.714A pdb=" N ILE q 61 " --> pdb=" O VAL q 82 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS q 63 " --> pdb=" O GLU q 80 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU q 80 " --> pdb=" O LYS q 63 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N MET q 65 " --> pdb=" O LEU q 78 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LEU q 78 " --> pdb=" O MET q 65 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 's' and resid 49 through 52 Processing sheet with id=AC4, first strand: chain 'C' and resid 3 through 5 removed outlier: 3.608A 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 76 through 78 removed outlier: 3.693A pdb=" N ALA C 102 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AC8, first strand: chain 'C' and resid 163 through 167 removed outlier: 5.655A pdb=" N VAL C 164 " --> pdb=" O ARG C 175 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ARG C 175 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY C 166 " --> pdb=" O LEU C 173 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 247 through 248 removed outlier: 3.529A pdb=" N SER C 248 " --> pdb=" O GLY C 251 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 4 through 5 removed outlier: 5.728A pdb=" N VAL D 108 " --> pdb=" O ASN D 173 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 12 through 16 removed outlier: 3.525A pdb=" N ILE D 188 " --> pdb=" O THR D 26 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL D 185 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL D 179 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU D 187 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 34 through 39 removed outlier: 3.964A pdb=" N VAL D 34 " --> pdb=" O GLY D 52 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLN D 50 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL D 38 " --> pdb=" O ALA D 48 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA D 48 " --> pdb=" O VAL D 38 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 14 through 18 removed outlier: 4.249A pdb=" N LEU E 6 " --> pdb=" O ASN E 14 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLU E 16 " --> pdb=" O VAL E 4 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL E 4 " --> pdb=" O GLU E 16 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N LEU E 123 " --> pdb=" O ASN E 3 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA E 5 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA E 125 " --> pdb=" O ALA E 5 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU E 153 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N VAL E 176 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL E 154 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 86 through 91 removed outlier: 3.727A pdb=" N ILE F 34 " --> pdb=" O LEU F 91 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS F 33 " --> pdb=" O VAL F 157 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP F 153 " --> pdb=" O ASN F 37 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 18 through 20 removed outlier: 3.628A pdb=" N LYS G 18 " --> pdb=" O THR G 25 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE G 24 " --> pdb=" O ARG G 35 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG G 35 " --> pdb=" O ILE G 24 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 83 through 86 Processing sheet with id=AD8, first strand: chain 'G' and resid 95 through 98 removed outlier: 3.574A pdb=" N MET G 115 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 123 through 125 removed outlier: 6.646A pdb=" N TRP K 16 " --> pdb=" O GLU K 139 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 19 through 23 removed outlier: 3.615A pdb=" N LEU L 20 " --> pdb=" O THR L 42 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL L 40 " --> pdb=" O ILE L 22 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 76 through 78 removed outlier: 3.622A pdb=" N VAL Q 68 " --> pdb=" O SER Q 65 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 110 through 111 Processing sheet with id=AE4, first strand: chain 'M' and resid 122 through 125 Processing sheet with id=AE5, first strand: chain 'N' and resid 32 through 33 Processing sheet with id=AE6, first strand: chain 'N' and resid 39 through 42 Processing sheet with id=AE7, first strand: chain 'O' and resid 30 through 32 removed outlier: 4.064A pdb=" N GLU O 111 " --> pdb=" O MET O 120 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL O 122 " --> pdb=" O LYS O 109 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LYS O 109 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N GLU O 124 " --> pdb=" O ILE O 107 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ILE O 107 " --> pdb=" O GLU O 124 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'P' and resid 42 through 46 removed outlier: 7.062A pdb=" N ALA P 42 " --> pdb=" O SER P 55 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N SER P 55 " --> pdb=" O ALA P 42 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL P 44 " --> pdb=" O LEU P 53 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL P 51 " --> pdb=" O ASP P 46 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 43 through 46 removed outlier: 3.642A pdb=" N GLY Q 45 " --> pdb=" O VAL Q 26 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL Q 26 " --> pdb=" O GLY Q 45 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Q' and resid 32 through 34 removed outlier: 3.744A pdb=" N GLU Q 34 " --> pdb=" O ARG Q 37 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG Q 37 " --> pdb=" O GLU Q 34 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'S' and resid 10 through 14 removed outlier: 6.221A pdb=" N ILE S 4 " --> pdb=" O ILE S 39 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'S' and resid 19 through 22 Processing sheet with id=AF4, first strand: chain 'S' and resid 32 through 35 Processing sheet with id=AF5, first strand: chain 'T' and resid 11 through 15 removed outlier: 5.845A pdb=" N THR T 11 " --> pdb=" O VAL T 110 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL T 110 " --> pdb=" O THR T 11 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LYS T 13 " --> pdb=" O ILE T 108 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE T 108 " --> pdb=" O LYS T 13 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR T 109 " --> pdb=" O PHE T 80 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU T 78 " --> pdb=" O VAL T 111 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR T 113 " --> pdb=" O VAL T 76 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL T 76 " --> pdb=" O THR T 113 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'T' and resid 87 through 92 Processing sheet with id=AF7, first strand: chain 'U' and resid 7 through 10 removed outlier: 6.513A pdb=" N GLU U 28 " --> pdb=" O LYS U 8 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N THR U 26 " --> pdb=" O PRO U 10 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'U' and resid 63 through 64 removed outlier: 3.623A pdb=" N GLY U 70 " --> pdb=" O LYS U 63 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 8 through 10 removed outlier: 3.630A pdb=" N GLY V 21 " --> pdb=" O VAL V 9 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA V 25 " --> pdb=" O ILE V 34 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'V' and resid 40 through 43 Processing sheet with id=AG2, first strand: chain 'V' and resid 70 through 71 removed outlier: 4.108A pdb=" N VAL V 70 " --> pdb=" O THR V 79 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'V' and resid 81 through 83 Processing sheet with id=AG4, first strand: chain 'X' and resid 31 through 32 removed outlier: 3.570A pdb=" N GLY X 31 " --> pdb=" O ARG X 48 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG X 48 " --> pdb=" O GLY X 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'X' and resid 39 through 40 removed outlier: 3.508A pdb=" N VAL X 88 " --> pdb=" O TYR X 55 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 34 through 40 Processing sheet with id=AG7, first strand: chain '0' and resid 3 through 5 Processing sheet with id=AG8, first strand: chain '2' and resid 27 through 29 Processing sheet with id=AG9, first strand: chain '3' and resid 15 through 21 removed outlier: 6.639A pdb=" N ARG 3 15 " --> pdb=" O CYS 3 9 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N CYS 3 9 " --> pdb=" O ARG 3 15 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS 3 21 " --> pdb=" O VAL 3 3 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain '5' and resid 14 through 16 removed outlier: 3.732A pdb=" N LYS 5 15 " --> pdb=" O LYS 5 23 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain '6' and resid 2 through 4 removed outlier: 5.205A pdb=" N VAL 6 23 " --> pdb=" O GLN 6 37 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS 6 15 " --> pdb=" O ILE 6 26 " (cutoff:3.500A) 1194 hydrogen bonds defined for protein. 3306 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3579 hydrogen bonds 5830 hydrogen bond angles 0 basepair planarities 1421 basepair parallelities 2325 stacking parallelities Total time for adding SS restraints: 214.12 Time building geometry restraints manager: 63.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.66: 152113 1.66 - 2.14: 242 2.14 - 2.61: 5 2.61 - 3.08: 0 3.08 - 3.55: 1 Bond restraints: 152361 Sorted by residual: bond pdb=" CA SER d 2 " pdb=" CB SER d 2 " ideal model delta sigma weight residual 1.530 3.550 -2.020 2.00e-02 2.50e+03 1.02e+04 bond pdb=" C6 A a 561 " pdb=" N1 A a 561 " ideal model delta sigma weight residual 1.351 2.186 -0.835 2.00e-02 2.50e+03 1.74e+03 bond pdb=" N3 A a 561 " pdb=" C4 A a 561 " ideal model delta sigma weight residual 1.344 2.153 -0.809 2.00e-02 2.50e+03 1.64e+03 bond pdb=" C2 A a 561 " pdb=" N3 A a 561 " ideal model delta sigma weight residual 1.331 2.136 -0.805 2.00e-02 2.50e+03 1.62e+03 bond pdb=" N1 A a 561 " pdb=" C2 A a 561 " ideal model delta sigma weight residual 1.339 2.142 -0.803 2.00e-02 2.50e+03 1.61e+03 ... (remaining 152356 not shown) Histogram of bond angle deviations from ideal: 80.87 - 93.22: 1 93.22 - 105.56: 23941 105.56 - 117.90: 120191 117.90 - 130.25: 82205 130.25 - 142.59: 2238 Bond angle restraints: 228576 Sorted by residual: angle pdb=" O3' U v 18 " pdb=" P C v 19 " pdb=" O5' C v 19 " ideal model delta sigma weight residual 104.00 80.87 23.13 1.50e+00 4.44e-01 2.38e+02 angle pdb=" C SER d 2 " pdb=" CA SER d 2 " pdb=" CB SER d 2 " ideal model delta sigma weight residual 110.10 129.71 -19.61 1.90e+00 2.77e-01 1.06e+02 angle pdb=" CA SER d 2 " pdb=" CB SER d 2 " pdb=" OG SER d 2 " ideal model delta sigma weight residual 111.10 127.14 -16.04 2.00e+00 2.50e-01 6.43e+01 angle pdb=" C LYS U 49 " pdb=" N VAL U 50 " pdb=" CA VAL U 50 " ideal model delta sigma weight residual 121.97 135.37 -13.40 1.80e+00 3.09e-01 5.54e+01 angle pdb=" CA ARG O 41 " pdb=" CB ARG O 41 " pdb=" CG ARG O 41 " ideal model delta sigma weight residual 114.10 127.81 -13.71 2.00e+00 2.50e-01 4.70e+01 ... (remaining 228571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 86248 35.91 - 71.81: 10021 71.81 - 107.72: 1172 107.72 - 143.63: 25 143.63 - 179.53: 29 Dihedral angle restraints: 97495 sinusoidal: 82675 harmonic: 14820 Sorted by residual: dihedral pdb=" CA GLY G 47 " pdb=" C GLY G 47 " pdb=" N ASN G 48 " pdb=" CA ASN G 48 " ideal model delta harmonic sigma weight residual -180.00 -112.08 -67.92 0 5.00e+00 4.00e-02 1.85e+02 dihedral pdb=" CA ASP V 72 " pdb=" C ASP V 72 " pdb=" N PRO V 73 " pdb=" CA PRO V 73 " ideal model delta harmonic sigma weight residual -180.00 -113.29 -66.71 0 5.00e+00 4.00e-02 1.78e+02 dihedral pdb=" CA TYR C 83 " pdb=" C TYR C 83 " pdb=" N ASP C 84 " pdb=" CA ASP C 84 " ideal model delta harmonic sigma weight residual 180.00 123.99 56.01 0 5.00e+00 4.00e-02 1.25e+02 ... (remaining 97492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.298: 29322 0.298 - 0.597: 14 0.597 - 0.895: 0 0.895 - 1.194: 0 1.194 - 1.492: 1 Chirality restraints: 29337 Sorted by residual: chirality pdb=" CA SER d 2 " pdb=" N SER d 2 " pdb=" C SER d 2 " pdb=" CB SER d 2 " both_signs ideal model delta sigma weight residual False 2.51 4.00 -1.49 2.00e-01 2.50e+01 5.56e+01 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 4.39e+00 chirality pdb=" C3' U A 949 " pdb=" C4' U A 949 " pdb=" O3' U A 949 " pdb=" C2' U A 949 " both_signs ideal model delta sigma weight residual False -2.48 -2.08 -0.40 2.00e-01 2.50e+01 3.99e+00 ... (remaining 29334 not shown) Planarity restraints: 11761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP V 72 " 0.082 5.00e-02 4.00e+02 1.25e-01 2.51e+01 pdb=" N PRO V 73 " -0.217 5.00e-02 4.00e+02 pdb=" CA PRO V 73 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO V 73 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G A1571 " -0.046 2.00e-02 2.50e+03 2.09e-02 1.31e+01 pdb=" N9 G A1571 " 0.054 2.00e-02 2.50e+03 pdb=" C8 G A1571 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G A1571 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G A1571 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G A1571 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G A1571 " -0.013 2.00e-02 2.50e+03 pdb=" N1 G A1571 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G A1571 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G A1571 " 0.005 2.00e-02 2.50e+03 pdb=" N3 G A1571 " 0.006 2.00e-02 2.50e+03 pdb=" C4 G A1571 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 83 " -0.010 2.00e-02 2.50e+03 2.49e-02 1.24e+01 pdb=" CG TYR C 83 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR C 83 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR C 83 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR C 83 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 83 " -0.024 2.00e-02 2.50e+03 pdb=" CZ TYR C 83 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 83 " 0.015 2.00e-02 2.50e+03 ... (remaining 11758 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 7831 2.66 - 3.22: 109575 3.22 - 3.78: 274147 3.78 - 4.34: 344182 4.34 - 4.90: 470025 Nonbonded interactions: 1205760 Sorted by model distance: nonbonded pdb=" C8 G A2637 " pdb=" C5 G A2637 " model vdw 2.100 2.784 nonbonded pdb=" C8 A B 27 " pdb=" C5 A B 27 " model vdw 2.121 2.784 nonbonded pdb=" C2 G A2818 " pdb=" C4 G A2818 " model vdw 2.201 3.480 nonbonded pdb=" O2 C A2697 " pdb=" N3 C A2697 " model vdw 2.208 3.120 nonbonded pdb=" OP1 U a 390 " pdb=" OG1 THR p 69 " model vdw 2.210 2.440 ... (remaining 1205755 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: 8.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.170 Extract box with map and model: 22.120 Check model and map are aligned: 1.510 Set scattering table: 0.970 Process input model: 494.900 Find NCS groups from input model: 2.580 Set up NCS constraints: 0.330 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: 0.020 Load rotamer database and sin/cos tables:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 533.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 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 : 0.011 2.020 152361 Z= 0.711 Angle : 1.070 23.128 228576 Z= 0.528 Chirality : 0.054 1.492 29337 Planarity : 0.007 0.125 11761 Dihedral : 22.947 179.532 87959 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.24 % Allowed : 14.58 % Favored : 85.18 % Rotamer: Outliers : 0.50 % Allowed : 2.68 % Favored : 96.81 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.24 % Twisted Proline : 2.07 % Twisted General : 0.61 % 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: -4.56 (0.09), residues: 5089 helix: -3.06 (0.10), residues: 1318 sheet: -2.30 (0.17), residues: 846 loop : -3.36 (0.09), residues: 2925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.004 TRP R 61 HIS 0.023 0.003 HIS C 232 PHE 0.054 0.004 PHE K 45 TYR 0.055 0.004 TYR C 83 ARG 0.018 0.001 ARG R 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1570 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 1548 time to evaluate : 5.785 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 TARDY: cannot create tardy model for: "ARG F 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARG G 69 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP K 61 " (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 TARDY: cannot create tardy model for: "ARG X 50 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS 2 57 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU 5 62 " (corrupted residue). Skipping it. REVERT: g 66 MET cc_start: 0.5827 (mmm) cc_final: 0.5578 (mmt) REVERT: h 25 LEU cc_start: 0.7645 (tp) cc_final: 0.7180 (tt) REVERT: h 69 ASN cc_start: 0.8126 (p0) cc_final: 0.7084 (p0) REVERT: i 130 ARG cc_start: 0.6341 (pmt100) cc_final: 0.6072 (ptt180) REVERT: l 39 ASN cc_start: 0.8315 (m-40) cc_final: 0.7852 (m-40) REVERT: n 47 LEU cc_start: 0.8651 (mt) cc_final: 0.8384 (mt) REVERT: o 15 TYR cc_start: 0.7004 (m-10) cc_final: 0.6746 (m-10) REVERT: p 34 ILE cc_start: 0.7955 (mt) cc_final: 0.7167 (mp) REVERT: s 6 LYS cc_start: 0.5920 (pmtt) cc_final: 0.5543 (tppt) REVERT: s 35 SER cc_start: 0.6980 (p) cc_final: 0.5789 (p) REVERT: C 103 TYR cc_start: 0.7205 (m-80) cc_final: 0.6927 (m-80) REVERT: C 171 TYR cc_start: 0.6099 (m-10) cc_final: 0.5883 (m-10) REVERT: C 229 ASP cc_start: 0.7020 (m-30) cc_final: 0.6793 (m-30) REVERT: D 119 PHE cc_start: 0.6799 (OUTLIER) cc_final: 0.5774 (m-10) REVERT: E 74 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7315 (ptt90) REVERT: F 105 THR cc_start: 0.4066 (p) cc_final: 0.3718 (p) REVERT: M 87 ASP cc_start: 0.6535 (m-30) cc_final: 0.5991 (m-30) REVERT: M 130 LYS cc_start: 0.8281 (ttpm) cc_final: 0.7020 (tppt) REVERT: N 1 MET cc_start: 0.4144 (mmm) cc_final: 0.3005 (mmm) REVERT: N 45 ARG cc_start: 0.7815 (mtt180) cc_final: 0.7183 (mtt180) REVERT: Q 8 LEU cc_start: 0.7368 (mt) cc_final: 0.6756 (mt) REVERT: S 1 MET cc_start: 0.6889 (mmm) cc_final: 0.6633 (mmm) REVERT: Z 28 LEU cc_start: 0.5677 (mt) cc_final: 0.4608 (mp) REVERT: 3 23 LYS cc_start: 0.9080 (pttt) cc_final: 0.8590 (pttm) REVERT: 5 22 LEU cc_start: 0.7506 (mt) cc_final: 0.7094 (mp) outliers start: 22 outliers final: 5 residues processed: 1560 average time/residue: 1.3040 time to fit residues: 3417.3968 Evaluate side-chains 868 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 861 time to evaluate : 5.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain D residue 119 PHE Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain N residue 74 TYR Chi-restraints excluded: chain N residue 94 VAL Chi-restraints excluded: chain U residue 48 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 958 random chunks: chunk 808 optimal weight: 10.0000 chunk 726 optimal weight: 0.9990 chunk 402 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 489 optimal weight: 9.9990 chunk 387 optimal weight: 30.0000 chunk 750 optimal weight: 0.7980 chunk 290 optimal weight: 0.9990 chunk 456 optimal weight: 10.0000 chunk 558 optimal weight: 10.0000 chunk 869 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 85 ASN c 175 HIS d 55 GLN f 36 ASN f 67 ASN f 87 ASN g 28 ASN g 64 GLN g 106 ASN h 18 ASN h 57 GLN ** i 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 78 ASN k 101 GLN ** k 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 HIS l 125 GLN n 38 HIS n 52 GLN ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 62 HIS p 83 HIS p 88 ASN q 6 ASN r 56 GLN s 22 GLN s 57 HIS ** t 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 GLN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 ASN E 29 ASN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 145 ASN E 169 ASN F 172 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN K 113 ASN L 3 GLN M 4 HIS M 38 GLN O 87 GLN P 101 HIS P 114 ASN Q 104 HIS R 52 GLN ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 81 HIS S 81 HIS S 88 HIS ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 58 ASN W 78 GLN X 87 GLN Y 17 ASN Y 23 ASN Y 32 ASN 0 40 ASN 2 40 HIS 3 26 ASN 3 33 GLN 4 6 GLN 5 4 GLN 5 31 HIS 5 60 GLN Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.968 152361 Z= 0.322 Angle : 0.657 18.148 228576 Z= 0.336 Chirality : 0.037 0.745 29337 Planarity : 0.005 0.105 11761 Dihedral : 23.824 179.883 77552 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.83 % Favored : 89.04 % Rotamer: Outliers : 4.52 % Allowed : 12.87 % Favored : 82.61 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.26 % Twisted Proline : 1.04 % 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: -3.56 (0.10), residues: 5089 helix: -1.62 (0.12), residues: 1397 sheet: -1.82 (0.17), residues: 889 loop : -3.04 (0.10), residues: 2803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 61 HIS 0.010 0.001 HIS 0 52 PHE 0.020 0.002 PHE N 69 TYR 0.029 0.002 TYR C 62 ARG 0.008 0.001 ARG q 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1240 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 1043 time to evaluate : 5.844 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 TARDY: cannot create tardy model for: "ARG F 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARG G 69 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP K 61 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN M 133 " (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: "ARG X 50 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE 0 6 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU 5 62 " (corrupted residue). Skipping it. REVERT: c 175 HIS cc_start: 0.7368 (OUTLIER) cc_final: 0.6379 (t-170) REVERT: j 32 THR cc_start: 0.6943 (p) cc_final: 0.6522 (p) REVERT: j 67 MET cc_start: 0.6119 (mmm) cc_final: 0.5890 (ttt) REVERT: l 32 LYS cc_start: 0.6697 (pmmt) cc_final: 0.6130 (pttt) REVERT: l 80 ILE cc_start: 0.6542 (OUTLIER) cc_final: 0.5915 (tp) REVERT: o 12 ILE cc_start: 0.8762 (pt) cc_final: 0.8489 (pt) REVERT: o 59 LYS cc_start: 0.7529 (mttt) cc_final: 0.6940 (mmmm) REVERT: r 49 THR cc_start: 0.8372 (p) cc_final: 0.8086 (m) REVERT: s 6 LYS cc_start: 0.6164 (pmtt) cc_final: 0.5688 (tppt) REVERT: C 171 TYR cc_start: 0.5700 (m-10) cc_final: 0.5489 (m-10) REVERT: C 274 ARG cc_start: 0.7015 (tpt90) cc_final: 0.6698 (tpt90) REVERT: D 46 TYR cc_start: 0.5505 (m-10) cc_final: 0.5289 (m-10) REVERT: E 34 TYR cc_start: 0.7811 (t80) cc_final: 0.7370 (t80) REVERT: E 74 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7104 (ptt90) REVERT: E 197 THR cc_start: 0.4538 (OUTLIER) cc_final: 0.4109 (p) REVERT: N 1 MET cc_start: 0.4115 (mmm) cc_final: 0.2993 (mmm) REVERT: N 94 VAL cc_start: 0.7990 (OUTLIER) cc_final: 0.5932 (m) REVERT: N 98 LYS cc_start: 0.4919 (tptt) cc_final: 0.4712 (tptt) REVERT: R 36 LYS cc_start: 0.6156 (mttp) cc_final: 0.5880 (mttt) REVERT: R 52 GLN cc_start: 0.4980 (mt0) cc_final: 0.4143 (mt0) REVERT: T 51 ILE cc_start: 0.7620 (mt) cc_final: 0.7419 (mm) REVERT: U 81 THR cc_start: 0.7508 (m) cc_final: 0.7243 (p) REVERT: 3 24 ARG cc_start: 0.8393 (mmm160) cc_final: 0.8143 (mmm160) REVERT: 6 10 MET cc_start: 0.3457 (mmt) cc_final: 0.3054 (mmt) outliers start: 197 outliers final: 107 residues processed: 1153 average time/residue: 1.1981 time to fit residues: 2409.5733 Evaluate side-chains 951 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 839 time to evaluate : 5.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 175 HIS Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain d residue 2 SER Chi-restraints excluded: chain d residue 127 VAL Chi-restraints excluded: chain d residue 152 ILE Chi-restraints excluded: chain d residue 190 ILE Chi-restraints excluded: chain e residue 122 ASP Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain h residue 105 ILE Chi-restraints excluded: chain h residue 115 ASP Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 30 VAL Chi-restraints excluded: chain i residue 83 ILE Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 61 SER Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 94 SER Chi-restraints excluded: chain k residue 17 GLU Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 75 MET Chi-restraints excluded: chain k residue 112 ASP Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain k residue 121 CYS Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 43 VAL Chi-restraints excluded: chain m residue 101 ASN Chi-restraints excluded: chain n residue 52 GLN Chi-restraints excluded: chain p residue 50 VAL Chi-restraints excluded: chain p residue 58 ASP Chi-restraints excluded: chain p residue 85 GLU Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain s residue 41 PHE Chi-restraints excluded: chain s residue 69 HIS Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 62 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain D residue 119 PHE Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 77 ARG Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain N residue 9 HIS Chi-restraints excluded: chain N residue 48 GLU Chi-restraints excluded: chain N residue 94 VAL Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain P residue 81 GLU Chi-restraints excluded: chain P residue 101 HIS Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain U residue 89 ILE Chi-restraints excluded: chain V residue 31 ASP Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain X residue 19 THR Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 41 ASP Chi-restraints excluded: chain Z residue 53 ILE Chi-restraints excluded: chain 0 residue 49 THR Chi-restraints excluded: chain 0 residue 56 VAL Chi-restraints excluded: chain 1 residue 48 VAL Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 41 VAL Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 31 HIS Chi-restraints excluded: chain 6 residue 3 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 958 random chunks: chunk 483 optimal weight: 10.0000 chunk 270 optimal weight: 0.0270 chunk 724 optimal weight: 7.9990 chunk 592 optimal weight: 10.0000 chunk 239 optimal weight: 7.9990 chunk 871 optimal weight: 0.9990 chunk 941 optimal weight: 4.9990 chunk 776 optimal weight: 2.9990 chunk 864 optimal weight: 6.9990 chunk 297 optimal weight: 10.0000 chunk 699 optimal weight: 0.0000 overall best weight: 1.8048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 153 HIS i 75 GLN i 126 GLN ** j 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 52 GLN o 83 GLN t 18 ASN ** t 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 HIS ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 GLN D 14 GLN ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 HIS F 2 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 124 ASN K 131 HIS K 136 GLN L 4 GLN P 101 HIS Q 104 HIS R 52 GLN ** R 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 18 GLN S 75 GLN S 86 GLN ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 38 GLN 2 48 HIS ** 3 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 4 GLN ** 5 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 60 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.972 152361 Z= 0.294 Angle : 0.580 18.692 228576 Z= 0.296 Chirality : 0.033 0.758 29337 Planarity : 0.005 0.097 11761 Dihedral : 23.635 179.643 77549 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.41 % Favored : 89.49 % Rotamer: Outliers : 4.11 % Allowed : 15.88 % Favored : 80.01 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.26 % Twisted Proline : 0.52 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.11), residues: 5089 helix: -0.79 (0.13), residues: 1413 sheet: -1.42 (0.17), residues: 863 loop : -2.82 (0.11), residues: 2813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 213 HIS 0.035 0.002 HIS c 175 PHE 0.027 0.002 PHE N 69 TYR 0.025 0.002 TYR N 74 ARG 0.008 0.001 ARG j 31 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1150 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 971 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 TARDY: cannot create tardy model for: "ARG F 80 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG G 69 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP K 61 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN M 133 " (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: "ARG X 50 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE 0 6 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYS 2 57 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU 5 62 " (corrupted residue). Skipping it. REVERT: c 175 HIS cc_start: 0.7330 (OUTLIER) cc_final: 0.7126 (t70) REVERT: e 76 MET cc_start: 0.5820 (ttm) cc_final: 0.5570 (mtt) REVERT: h 61 ARG cc_start: 0.6959 (ttp80) cc_final: 0.6401 (ttp80) REVERT: k 33 MET cc_start: 0.5634 (OUTLIER) cc_final: 0.5324 (ttp) REVERT: l 32 LYS cc_start: 0.6771 (OUTLIER) cc_final: 0.6297 (pttt) REVERT: l 80 ILE cc_start: 0.6100 (pp) cc_final: 0.5768 (mt) REVERT: m 13 LYS cc_start: 0.3155 (mmtt) cc_final: 0.2602 (mmtt) REVERT: q 7 GLN cc_start: 0.6465 (tm-30) cc_final: 0.6126 (tm-30) REVERT: r 47 ARG cc_start: 0.8389 (mtm110) cc_final: 0.8155 (ptp-110) REVERT: s 6 LYS cc_start: 0.6128 (pmtt) cc_final: 0.5637 (tppt) REVERT: E 34 TYR cc_start: 0.7725 (t80) cc_final: 0.7366 (t80) REVERT: K 81 TYR cc_start: 0.8044 (m-80) cc_final: 0.7796 (m-80) REVERT: N 1 MET cc_start: 0.4056 (mmm) cc_final: 0.2705 (mmm) REVERT: N 83 MET cc_start: 0.6590 (mmt) cc_final: 0.6374 (mmp) REVERT: N 113 VAL cc_start: 0.7408 (t) cc_final: 0.7187 (t) REVERT: T 83 GLU cc_start: 0.5086 (tt0) cc_final: 0.4877 (tt0) REVERT: U 81 THR cc_start: 0.7520 (m) cc_final: 0.7296 (p) REVERT: W 96 MET cc_start: 0.6215 (ptt) cc_final: 0.5468 (ptp) REVERT: 0 17 GLN cc_start: 0.6054 (OUTLIER) cc_final: 0.5734 (mp10) REVERT: 0 50 ILE cc_start: 0.7334 (mm) cc_final: 0.7122 (mm) REVERT: 3 23 LYS cc_start: 0.8969 (pttt) cc_final: 0.8609 (pttm) outliers start: 179 outliers final: 97 residues processed: 1070 average time/residue: 1.2646 time to fit residues: 2373.8805 Evaluate side-chains 913 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 812 time to evaluate : 5.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 175 HIS Chi-restraints excluded: chain d residue 2 SER Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain h residue 105 ILE Chi-restraints excluded: chain h residue 110 GLU Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 30 VAL Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 94 SER Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 33 MET Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain l residue 14 SER Chi-restraints excluded: chain l residue 32 LYS Chi-restraints excluded: chain l residue 70 LEU Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 43 VAL Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 52 GLN Chi-restraints excluded: chain p residue 50 VAL Chi-restraints excluded: chain p residue 58 ASP Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 85 GLU Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 80 GLU Chi-restraints excluded: chain r residue 25 ILE Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain s residue 41 PHE Chi-restraints excluded: chain s residue 69 HIS Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain D residue 119 PHE Chi-restraints excluded: chain D residue 139 TYR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 161 ASN Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 120 LYS Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain N residue 9 HIS Chi-restraints excluded: chain N residue 17 MET Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 94 VAL Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain S residue 18 GLN Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain U residue 89 ILE Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain W residue 83 THR Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 41 ASP Chi-restraints excluded: chain Z residue 53 ILE Chi-restraints excluded: chain 0 residue 17 GLN Chi-restraints excluded: chain 0 residue 31 VAL Chi-restraints excluded: chain 0 residue 49 THR Chi-restraints excluded: chain 0 residue 56 VAL Chi-restraints excluded: chain 0 residue 59 VAL Chi-restraints excluded: chain 2 residue 32 ASN Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 5 residue 31 HIS Chi-restraints excluded: chain 6 residue 3 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 958 random chunks: chunk 861 optimal weight: 0.3980 chunk 655 optimal weight: 20.0000 chunk 452 optimal weight: 30.0000 chunk 96 optimal weight: 20.0000 chunk 415 optimal weight: 10.0000 chunk 585 optimal weight: 10.0000 chunk 874 optimal weight: 9.9990 chunk 926 optimal weight: 9.9990 chunk 456 optimal weight: 10.0000 chunk 828 optimal weight: 9.9990 chunk 249 optimal weight: 0.4980 overall best weight: 6.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 175 HIS e 43 ASN f 67 ASN ** j 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 101 GLN l 25 ASN l 88 GLN o 83 GLN s 22 GLN ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 GLN ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 GLN D 37 GLN D 135 HIS E 40 GLN ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 131 HIS K 136 GLN M 83 ASN Q 10 GLN Q 41 GLN R 72 ASN ** S 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 75 GLN ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 102 ASN V 53 GLN W 55 HIS Z 60 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.968 152361 Z= 0.393 Angle : 0.700 18.259 228576 Z= 0.354 Chirality : 0.039 0.751 29337 Planarity : 0.005 0.095 11761 Dihedral : 23.702 179.810 77544 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.67 % Favored : 87.19 % Rotamer: Outliers : 5.28 % Allowed : 17.55 % Favored : 77.17 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.26 % Twisted Proline : 0.52 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.11), residues: 5089 helix: -0.48 (0.13), residues: 1388 sheet: -1.52 (0.17), residues: 890 loop : -2.76 (0.11), residues: 2811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP p 59 HIS 0.010 0.002 HIS h 22 PHE 0.032 0.002 PHE h 63 TYR 0.030 0.002 TYR r 27 ARG 0.018 0.001 ARG h 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1073 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 843 time to evaluate : 5.981 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 TARDY: cannot create tardy model for: "ARG F 80 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ARG G 69 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP K 61 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN M 133 " (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: "ARG X 50 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS 2 57 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU 5 62 " (corrupted residue). Skipping it. REVERT: c 175 HIS cc_start: 0.7305 (OUTLIER) cc_final: 0.6255 (t-170) REVERT: k 33 MET cc_start: 0.5740 (OUTLIER) cc_final: 0.5468 (ttp) REVERT: l 32 LYS cc_start: 0.6874 (OUTLIER) cc_final: 0.6379 (pttt) REVERT: q 7 GLN cc_start: 0.6738 (tm-30) cc_final: 0.6517 (tm-30) REVERT: q 20 MET cc_start: 0.4797 (mtp) cc_final: 0.4552 (mtm) REVERT: q 40 ARG cc_start: 0.7156 (tpt170) cc_final: 0.6671 (ttt180) REVERT: C 274 ARG cc_start: 0.7295 (tpt90) cc_final: 0.7091 (tpt90) REVERT: D 46 TYR cc_start: 0.5573 (m-10) cc_final: 0.5233 (m-80) REVERT: D 168 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.6646 (ptt180) REVERT: E 34 TYR cc_start: 0.7924 (t80) cc_final: 0.7606 (t80) REVERT: G 134 LYS cc_start: 0.4675 (OUTLIER) cc_final: 0.4100 (mtmm) REVERT: N 1 MET cc_start: 0.4076 (mmm) cc_final: 0.2673 (mmm) REVERT: R 79 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8216 (tp) REVERT: W 96 MET cc_start: 0.6201 (ptt) cc_final: 0.5574 (ptp) REVERT: 0 17 GLN cc_start: 0.6269 (OUTLIER) cc_final: 0.5921 (mp10) REVERT: 3 23 LYS cc_start: 0.8812 (pttt) cc_final: 0.8435 (pttm) REVERT: 4 1 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.7339 (mmt) REVERT: 4 28 ARG cc_start: 0.7765 (mmt90) cc_final: 0.7455 (mpt-90) outliers start: 230 outliers final: 157 residues processed: 995 average time/residue: 1.2357 time to fit residues: 2174.1493 Evaluate side-chains 935 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 770 time to evaluate : 5.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 175 HIS Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain d residue 2 SER Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain d residue 127 VAL Chi-restraints excluded: chain e residue 122 ASP Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 105 ILE Chi-restraints excluded: chain h residue 110 GLU Chi-restraints excluded: chain h residue 115 ASP Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 30 VAL Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 94 SER Chi-restraints excluded: chain k residue 16 ILE Chi-restraints excluded: chain k residue 28 ASN Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 33 MET Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 112 ASP Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 14 SER Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 32 LYS Chi-restraints excluded: chain l residue 70 LEU Chi-restraints excluded: chain l residue 86 ASN Chi-restraints excluded: chain l residue 88 GLN Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 101 ASN Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 81 LEU Chi-restraints excluded: chain p residue 50 VAL Chi-restraints excluded: chain p residue 58 ASP Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 85 GLU Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain r residue 25 ILE Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain s residue 20 GLU Chi-restraints excluded: chain s residue 41 PHE Chi-restraints excluded: chain s residue 57 HIS Chi-restraints excluded: chain s residue 69 HIS Chi-restraints excluded: chain t residue 25 THR Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 62 THR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 119 PHE Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 161 ASN Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain K residue 77 ARG Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 83 ASN Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 120 LYS Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain N residue 9 HIS Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 137 MET Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 23 ASP Chi-restraints excluded: chain O residue 57 HIS Chi-restraints excluded: chain O residue 61 GLN Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain S residue 18 GLN Chi-restraints excluded: chain T residue 36 ASP Chi-restraints excluded: chain T residue 40 ILE Chi-restraints excluded: chain T residue 67 PHE Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain U residue 62 PHE Chi-restraints excluded: chain U residue 89 ILE Chi-restraints excluded: chain V residue 31 ASP Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain W residue 83 THR Chi-restraints excluded: chain X residue 19 THR Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 41 ASP Chi-restraints excluded: chain Z residue 45 GLU Chi-restraints excluded: chain Z residue 53 ILE Chi-restraints excluded: chain 0 residue 17 GLN Chi-restraints excluded: chain 0 residue 49 THR Chi-restraints excluded: chain 0 residue 56 VAL Chi-restraints excluded: chain 1 residue 48 VAL Chi-restraints excluded: chain 2 residue 32 ASN Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 3 residue 28 ASP Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 6 residue 3 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 958 random chunks: chunk 771 optimal weight: 2.9990 chunk 525 optimal weight: 10.0000 chunk 13 optimal weight: 30.0000 chunk 689 optimal weight: 1.9990 chunk 382 optimal weight: 10.0000 chunk 790 optimal weight: 8.9990 chunk 640 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 472 optimal weight: 50.0000 chunk 831 optimal weight: 10.0000 chunk 233 optimal weight: 10.0000 overall best weight: 6.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 61 ASN c 175 HIS d 64 ASN d 67 GLN g 106 ASN i 14 ASN ** j 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 101 GLN ** l 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 83 GLN ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 GLN D 68 HIS ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 131 HIS M 83 ASN ** P 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 20 ASN S 18 GLN ** S 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 86 GLN ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.969 152361 Z= 0.405 Angle : 0.716 18.187 228576 Z= 0.361 Chirality : 0.040 0.732 29337 Planarity : 0.005 0.098 11761 Dihedral : 23.728 179.959 77543 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.99 % Favored : 86.89 % Rotamer: Outliers : 5.71 % Allowed : 18.45 % Favored : 75.84 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.26 % Twisted Proline : 0.52 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.11), residues: 5089 helix: -0.47 (0.13), residues: 1409 sheet: -1.57 (0.17), residues: 928 loop : -2.78 (0.11), residues: 2752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP p 59 HIS 0.031 0.002 HIS c 175 PHE 0.036 0.002 PHE h 63 TYR 0.023 0.002 TYR d 61 ARG 0.013 0.001 ARG 4 36 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1065 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 816 time to evaluate : 5.218 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 TARDY: cannot create tardy model for: "ARG F 80 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ARG G 69 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP K 61 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN M 133 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG X 50 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYS 2 57 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU 5 62 " (corrupted residue). Skipping it. REVERT: c 175 HIS cc_start: 0.7300 (OUTLIER) cc_final: 0.6646 (t-170) REVERT: h 69 ASN cc_start: 0.8328 (p0) cc_final: 0.7788 (p0) REVERT: k 33 MET cc_start: 0.5790 (OUTLIER) cc_final: 0.5491 (ttp) REVERT: l 32 LYS cc_start: 0.6906 (OUTLIER) cc_final: 0.6381 (pttt) REVERT: l 54 THR cc_start: 0.7213 (t) cc_final: 0.6913 (p) REVERT: q 40 ARG cc_start: 0.7160 (tpt170) cc_final: 0.6740 (ttt180) REVERT: D 168 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.6683 (ptt180) REVERT: E 34 TYR cc_start: 0.8089 (t80) cc_final: 0.7691 (t80) REVERT: G 95 ARG cc_start: 0.4585 (mtm-85) cc_final: 0.4293 (mtm-85) REVERT: G 134 LYS cc_start: 0.4646 (OUTLIER) cc_final: 0.3871 (mtmm) REVERT: N 1 MET cc_start: 0.3928 (mmm) cc_final: 0.2469 (mmm) REVERT: N 11 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.5398 (mtp85) REVERT: W 96 MET cc_start: 0.6056 (ptt) cc_final: 0.5495 (ptp) REVERT: 6 10 MET cc_start: 0.4472 (mmt) cc_final: 0.4169 (mmt) outliers start: 249 outliers final: 184 residues processed: 972 average time/residue: 1.2156 time to fit residues: 2094.3609 Evaluate side-chains 951 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 761 time to evaluate : 5.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 17 ASP Chi-restraints excluded: chain c residue 34 GLU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 61 ASN Chi-restraints excluded: chain c residue 175 HIS Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain d residue 2 SER Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain d residue 127 VAL Chi-restraints excluded: chain d residue 129 ILE Chi-restraints excluded: chain e residue 72 VAL Chi-restraints excluded: chain e residue 122 ASP Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain g residue 59 LEU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain h residue 92 ASP Chi-restraints excluded: chain h residue 105 ILE Chi-restraints excluded: chain h residue 110 GLU Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 115 ASP Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 30 VAL Chi-restraints excluded: chain i residue 98 LEU Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 94 SER Chi-restraints excluded: chain k residue 17 GLU Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 33 MET Chi-restraints excluded: chain k residue 42 LEU Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 112 ASP Chi-restraints excluded: chain l residue 14 SER Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 32 LYS Chi-restraints excluded: chain l residue 86 ASN Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 101 ASN Chi-restraints excluded: chain n residue 23 ARG Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain p residue 34 ILE Chi-restraints excluded: chain p residue 50 VAL Chi-restraints excluded: chain p residue 58 ASP Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 85 GLU Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 80 GLU Chi-restraints excluded: chain r residue 25 ILE Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain s residue 20 GLU Chi-restraints excluded: chain s residue 41 PHE Chi-restraints excluded: chain s residue 57 HIS Chi-restraints excluded: chain s residue 69 HIS Chi-restraints excluded: chain t residue 24 GLN Chi-restraints excluded: chain t residue 25 THR Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 62 THR Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 119 PHE Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 172 GLN Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 161 ASN Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain K residue 48 HIS Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 83 ASN Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 120 LYS Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain N residue 9 HIS Chi-restraints excluded: chain N residue 11 ARG Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 48 GLU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 23 ASP Chi-restraints excluded: chain O residue 57 HIS Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 18 GLN Chi-restraints excluded: chain T residue 36 ASP Chi-restraints excluded: chain T residue 40 ILE Chi-restraints excluded: chain T residue 67 PHE Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 102 ASN Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain U residue 89 ILE Chi-restraints excluded: chain V residue 31 ASP Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain W residue 83 THR Chi-restraints excluded: chain X residue 19 THR Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 69 PHE Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 41 ASP Chi-restraints excluded: chain Z residue 53 ILE Chi-restraints excluded: chain 0 residue 49 THR Chi-restraints excluded: chain 0 residue 56 VAL Chi-restraints excluded: chain 1 residue 48 VAL Chi-restraints excluded: chain 2 residue 32 ASN Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 28 ASP Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 6 residue 3 VAL Chi-restraints excluded: chain 6 residue 12 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 958 random chunks: chunk 311 optimal weight: 3.9990 chunk 833 optimal weight: 0.2980 chunk 183 optimal weight: 20.0000 chunk 543 optimal weight: 10.0000 chunk 228 optimal weight: 6.9990 chunk 926 optimal weight: 9.9990 chunk 769 optimal weight: 0.0770 chunk 429 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 306 optimal weight: 30.0000 chunk 486 optimal weight: 10.0000 overall best weight: 4.2744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 175 HIS ** j 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 101 GLN ** n 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 83 GLN ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 72 ASN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN D 85 ASN ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 ASN N 35 GLN Q 10 GLN ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 75 GLN ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.969 152361 Z= 0.336 Angle : 0.641 18.148 228576 Z= 0.325 Chirality : 0.036 0.747 29337 Planarity : 0.005 0.096 11761 Dihedral : 23.653 179.891 77543 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.12 % Favored : 87.76 % Rotamer: Outliers : 5.69 % Allowed : 19.60 % Favored : 74.71 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.26 % Twisted Proline : 0.52 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.11), residues: 5089 helix: -0.25 (0.14), residues: 1417 sheet: -1.42 (0.17), residues: 915 loop : -2.66 (0.11), residues: 2757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP p 59 HIS 0.013 0.001 HIS c 175 PHE 0.020 0.002 PHE P 34 TYR 0.020 0.002 TYR U 68 ARG 0.010 0.001 ARG c 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1052 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 804 time to evaluate : 5.831 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 TARDY: cannot create tardy model for: "ARG F 80 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ARG G 69 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP K 61 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN M 133 " (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: "ARG X 50 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS 2 57 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU 5 62 " (corrupted residue). Skipping it. REVERT: k 33 MET cc_start: 0.5710 (OUTLIER) cc_final: 0.5413 (ttp) REVERT: l 32 LYS cc_start: 0.6787 (OUTLIER) cc_final: 0.6262 (pttt) REVERT: l 54 THR cc_start: 0.7298 (t) cc_final: 0.6980 (p) REVERT: m 13 LYS cc_start: 0.3347 (mmtp) cc_final: 0.2641 (mmtt) REVERT: q 40 ARG cc_start: 0.7226 (tpt170) cc_final: 0.6813 (ttt180) REVERT: s 66 MET cc_start: 0.5126 (OUTLIER) cc_final: 0.4411 (ppp) REVERT: C 180 GLU cc_start: 0.5370 (mp0) cc_final: 0.5058 (mp0) REVERT: D 46 TYR cc_start: 0.5457 (m-10) cc_final: 0.5098 (m-80) REVERT: D 120 GLN cc_start: 0.7385 (mm-40) cc_final: 0.7057 (mm-40) REVERT: D 168 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6734 (ptt180) REVERT: E 34 TYR cc_start: 0.8019 (t80) cc_final: 0.7621 (t80) REVERT: G 134 LYS cc_start: 0.4732 (OUTLIER) cc_final: 0.3913 (mtmm) REVERT: N 1 MET cc_start: 0.3868 (mmm) cc_final: 0.2391 (mmm) REVERT: N 11 ARG cc_start: 0.6966 (OUTLIER) cc_final: 0.5558 (mtp85) REVERT: R 19 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.7175 (ttmm) REVERT: W 96 MET cc_start: 0.5970 (ptt) cc_final: 0.5436 (ptp) REVERT: Z 18 GLU cc_start: 0.2849 (pp20) cc_final: 0.2049 (pp20) REVERT: 3 23 LYS cc_start: 0.8676 (pttt) cc_final: 0.8351 (pttm) outliers start: 248 outliers final: 186 residues processed: 960 average time/residue: 1.1653 time to fit residues: 1969.5496 Evaluate side-chains 958 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 765 time to evaluate : 5.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 17 ASP Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 175 HIS Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain d residue 2 SER Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 97 ASN Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain d residue 127 VAL Chi-restraints excluded: chain d residue 166 VAL Chi-restraints excluded: chain d residue 191 ASP Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 122 ASP Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 59 LEU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain h residue 92 ASP Chi-restraints excluded: chain h residue 105 ILE Chi-restraints excluded: chain h residue 110 GLU Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 115 ASP Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 30 VAL Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 63 GLU Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 94 SER Chi-restraints excluded: chain k residue 28 ASN Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 33 MET Chi-restraints excluded: chain k residue 42 LEU Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 107 VAL Chi-restraints excluded: chain k residue 112 ASP Chi-restraints excluded: chain l residue 14 SER Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 32 LYS Chi-restraints excluded: chain l residue 70 LEU Chi-restraints excluded: chain l residue 86 ASN Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 101 ASN Chi-restraints excluded: chain n residue 23 ARG Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 81 LEU Chi-restraints excluded: chain p residue 26 ARG Chi-restraints excluded: chain p residue 41 ASN Chi-restraints excluded: chain p residue 50 VAL Chi-restraints excluded: chain p residue 58 ASP Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 85 GLU Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 80 GLU Chi-restraints excluded: chain r residue 25 ILE Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain s residue 41 PHE Chi-restraints excluded: chain s residue 57 HIS Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain s residue 69 HIS Chi-restraints excluded: chain t residue 24 GLN Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 62 THR Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 119 PHE Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 172 GLN Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 161 ASN Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain K residue 95 ASP Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 58 PHE Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 83 ASN Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 120 LYS Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain N residue 9 HIS Chi-restraints excluded: chain N residue 11 ARG Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 48 GLU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 23 ASP Chi-restraints excluded: chain O residue 57 HIS Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 63 LYS Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain R residue 19 LYS Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain S residue 18 GLN Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 36 ASP Chi-restraints excluded: chain T residue 67 PHE Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain U residue 89 ILE Chi-restraints excluded: chain V residue 31 ASP Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain W residue 83 THR Chi-restraints excluded: chain X residue 19 THR Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 69 PHE Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 41 ASP Chi-restraints excluded: chain Z residue 9 LEU Chi-restraints excluded: chain Z residue 45 GLU Chi-restraints excluded: chain Z residue 53 ILE Chi-restraints excluded: chain 0 residue 18 ASN Chi-restraints excluded: chain 0 residue 49 THR Chi-restraints excluded: chain 0 residue 56 VAL Chi-restraints excluded: chain 1 residue 48 VAL Chi-restraints excluded: chain 2 residue 32 ASN Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 28 ASP Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 65 MET Chi-restraints excluded: chain 6 residue 3 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 958 random chunks: chunk 893 optimal weight: 50.0000 chunk 104 optimal weight: 20.0000 chunk 528 optimal weight: 10.0000 chunk 676 optimal weight: 3.9990 chunk 524 optimal weight: 10.0000 chunk 780 optimal weight: 5.9990 chunk 517 optimal weight: 20.0000 chunk 923 optimal weight: 8.9990 chunk 577 optimal weight: 30.0000 chunk 562 optimal weight: 10.0000 chunk 426 optimal weight: 10.0000 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 61 ASN c 175 HIS d 133 HIS ** j 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 101 GLN ** n 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 83 GLN ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 GLN D 37 GLN D 68 HIS E 82 GLN ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 ASN N 35 GLN Q 10 GLN ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 75 GLN ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.968 152361 Z= 0.437 Angle : 0.750 18.150 228576 Z= 0.377 Chirality : 0.041 0.733 29337 Planarity : 0.005 0.099 11761 Dihedral : 23.759 179.844 77543 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 14.13 % Favored : 85.73 % Rotamer: Outliers : 6.20 % Allowed : 20.08 % Favored : 73.73 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.26 % Twisted Proline : 0.52 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.11), residues: 5089 helix: -0.45 (0.13), residues: 1417 sheet: -1.46 (0.17), residues: 917 loop : -2.77 (0.11), residues: 2755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP p 59 HIS 0.013 0.002 HIS c 175 PHE 0.022 0.002 PHE 1 23 TYR 0.022 0.002 TYR d 61 ARG 0.008 0.001 ARG m 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1049 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 779 time to evaluate : 5.958 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 TARDY: cannot create tardy model for: "ARG F 80 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ARG G 69 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN M 133 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG X 50 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYS 2 57 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU 5 62 " (corrupted residue). Skipping it. REVERT: k 33 MET cc_start: 0.5756 (OUTLIER) cc_final: 0.5484 (ttp) REVERT: k 75 MET cc_start: 0.8033 (mmm) cc_final: 0.7790 (mmm) REVERT: k 127 ARG cc_start: 0.7781 (mtp-110) cc_final: 0.7505 (mtp-110) REVERT: l 32 LYS cc_start: 0.6991 (OUTLIER) cc_final: 0.6418 (pttt) REVERT: q 40 ARG cc_start: 0.7227 (tpt170) cc_final: 0.6775 (tpt170) REVERT: s 66 MET cc_start: 0.5121 (OUTLIER) cc_final: 0.4444 (ppp) REVERT: D 168 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.6687 (ptt180) REVERT: G 134 LYS cc_start: 0.4895 (OUTLIER) cc_final: 0.4147 (mtmm) REVERT: N 1 MET cc_start: 0.3961 (mmm) cc_final: 0.2368 (mmm) REVERT: N 11 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.5854 (mtp85) REVERT: O 16 MET cc_start: 0.6891 (mtp) cc_final: 0.6466 (ttm) REVERT: O 57 HIS cc_start: 0.7783 (OUTLIER) cc_final: 0.6702 (t-90) REVERT: W 96 MET cc_start: 0.6022 (ptt) cc_final: 0.5480 (ptp) REVERT: 3 23 LYS cc_start: 0.8685 (pttt) cc_final: 0.8405 (pttm) REVERT: 6 10 MET cc_start: 0.4551 (mmt) cc_final: 0.4304 (mmt) outliers start: 270 outliers final: 207 residues processed: 957 average time/residue: 1.2669 time to fit residues: 2154.4189 Evaluate side-chains 957 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 743 time to evaluate : 5.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 17 ASP Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 61 ASN Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 122 GLN Chi-restraints excluded: chain c residue 175 HIS Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain d residue 2 SER Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 97 ASN Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain d residue 127 VAL Chi-restraints excluded: chain d residue 129 ILE Chi-restraints excluded: chain d residue 166 VAL Chi-restraints excluded: chain e residue 43 ASN Chi-restraints excluded: chain e residue 72 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 122 ASP Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain f residue 23 THR Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain g residue 59 LEU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain h residue 92 ASP Chi-restraints excluded: chain h residue 105 ILE Chi-restraints excluded: chain h residue 110 GLU Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 115 ASP Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 30 VAL Chi-restraints excluded: chain i residue 98 LEU Chi-restraints excluded: chain i residue 103 LEU Chi-restraints excluded: chain i residue 127 PHE Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 94 SER Chi-restraints excluded: chain k residue 17 GLU Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 33 MET Chi-restraints excluded: chain k residue 42 LEU Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 107 VAL Chi-restraints excluded: chain k residue 112 ASP Chi-restraints excluded: chain k residue 121 CYS Chi-restraints excluded: chain l residue 14 SER Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 32 LYS Chi-restraints excluded: chain l residue 70 LEU Chi-restraints excluded: chain l residue 86 ASN Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain m residue 89 ILE Chi-restraints excluded: chain m residue 101 ASN Chi-restraints excluded: chain n residue 23 ARG Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 81 LEU Chi-restraints excluded: chain p residue 34 ILE Chi-restraints excluded: chain p residue 41 ASN Chi-restraints excluded: chain p residue 50 VAL Chi-restraints excluded: chain p residue 58 ASP Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 85 GLU Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 80 GLU Chi-restraints excluded: chain r residue 25 ILE Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain s residue 41 PHE Chi-restraints excluded: chain s residue 57 HIS Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain s residue 69 HIS Chi-restraints excluded: chain t residue 24 GLN Chi-restraints excluded: chain t residue 25 THR Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 62 THR Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 119 PHE Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 172 GLN Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 161 ASN Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain K residue 95 ASP Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 58 PHE Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 83 ASN Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 120 LYS Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain N residue 9 HIS Chi-restraints excluded: chain N residue 11 ARG Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 48 GLU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 23 ASP Chi-restraints excluded: chain O residue 57 HIS Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 63 LYS Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 36 ASP Chi-restraints excluded: chain T residue 40 ILE Chi-restraints excluded: chain T residue 67 PHE Chi-restraints excluded: chain T residue 68 ASP Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 102 ASN Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 89 ILE Chi-restraints excluded: chain V residue 31 ASP Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain W residue 83 THR Chi-restraints excluded: chain X residue 19 THR Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 69 PHE Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 41 ASP Chi-restraints excluded: chain Z residue 9 LEU Chi-restraints excluded: chain Z residue 53 ILE Chi-restraints excluded: chain 0 residue 18 ASN Chi-restraints excluded: chain 0 residue 49 THR Chi-restraints excluded: chain 0 residue 56 VAL Chi-restraints excluded: chain 2 residue 32 ASN Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 28 ASP Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 41 VAL Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 65 MET Chi-restraints excluded: chain 6 residue 3 VAL Chi-restraints excluded: chain 6 residue 12 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 958 random chunks: chunk 571 optimal weight: 40.0000 chunk 368 optimal weight: 10.0000 chunk 551 optimal weight: 30.0000 chunk 278 optimal weight: 8.9990 chunk 181 optimal weight: 8.9990 chunk 178 optimal weight: 4.9990 chunk 587 optimal weight: 10.0000 chunk 629 optimal weight: 10.0000 chunk 456 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 725 optimal weight: 2.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 175 HIS ** j 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 101 GLN ** n 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN D 68 HIS D 85 ASN ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 GLN S 75 GLN S 86 GLN ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.968 152361 Z= 0.419 Angle : 0.739 18.079 228576 Z= 0.372 Chirality : 0.041 0.736 29337 Planarity : 0.005 0.099 11761 Dihedral : 23.766 179.732 77543 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.64 % Favored : 86.23 % Rotamer: Outliers : 5.78 % Allowed : 20.58 % Favored : 73.63 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.26 % Twisted Proline : 0.52 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.11), residues: 5089 helix: -0.44 (0.13), residues: 1417 sheet: -1.50 (0.17), residues: 904 loop : -2.77 (0.11), residues: 2768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP p 59 HIS 0.021 0.002 HIS c 175 PHE 0.022 0.002 PHE P 34 TYR 0.020 0.002 TYR d 61 ARG 0.007 0.001 ARG r 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 756 time to evaluate : 5.761 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 TARDY: cannot create tardy model for: "ARG F 80 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ARG G 69 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN M 133 " (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: "ARG X 50 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS 2 57 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU 5 62 " (corrupted residue). Skipping it. REVERT: c 175 HIS cc_start: 0.7337 (OUTLIER) cc_final: 0.6333 (t-170) REVERT: d 88 MET cc_start: 0.8161 (mmm) cc_final: 0.7594 (mmm) REVERT: d 165 PHE cc_start: 0.4265 (p90) cc_final: 0.3613 (p90) REVERT: k 33 MET cc_start: 0.5693 (OUTLIER) cc_final: 0.5413 (ttp) REVERT: k 127 ARG cc_start: 0.7799 (mtp180) cc_final: 0.7562 (mtp-110) REVERT: l 32 LYS cc_start: 0.7013 (OUTLIER) cc_final: 0.6427 (pttt) REVERT: l 54 THR cc_start: 0.7303 (t) cc_final: 0.6701 (m) REVERT: q 40 ARG cc_start: 0.7262 (tpt170) cc_final: 0.6807 (tpt170) REVERT: s 66 MET cc_start: 0.5243 (OUTLIER) cc_final: 0.4499 (ppp) REVERT: C 225 MET cc_start: 0.8243 (mmt) cc_final: 0.8000 (mmt) REVERT: D 107 VAL cc_start: 0.7876 (OUTLIER) cc_final: 0.7665 (m) REVERT: D 168 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6672 (ptt180) REVERT: G 134 LYS cc_start: 0.5013 (OUTLIER) cc_final: 0.4241 (mtmm) REVERT: N 1 MET cc_start: 0.3933 (mmm) cc_final: 0.2332 (mmm) REVERT: N 4 PRO cc_start: 0.6815 (Cg_endo) cc_final: 0.6469 (Cg_exo) REVERT: N 11 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.5828 (mtp85) REVERT: O 16 MET cc_start: 0.6976 (mtp) cc_final: 0.6547 (ttm) REVERT: O 57 HIS cc_start: 0.7843 (OUTLIER) cc_final: 0.6664 (t-90) REVERT: W 96 MET cc_start: 0.6276 (ptt) cc_final: 0.5741 (ptp) REVERT: 3 23 LYS cc_start: 0.8735 (pttt) cc_final: 0.8434 (pttm) REVERT: 6 10 MET cc_start: 0.4509 (mmt) cc_final: 0.4277 (mmt) outliers start: 252 outliers final: 213 residues processed: 918 average time/residue: 1.1556 time to fit residues: 1879.4710 Evaluate side-chains 956 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 734 time to evaluate : 9.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 17 ASP Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 122 GLN Chi-restraints excluded: chain c residue 175 HIS Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain d residue 2 SER Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 97 ASN Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain d residue 127 VAL Chi-restraints excluded: chain d residue 129 ILE Chi-restraints excluded: chain d residue 166 VAL Chi-restraints excluded: chain e residue 43 ASN Chi-restraints excluded: chain e residue 72 VAL Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 122 ASP Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain f residue 23 THR Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain g residue 21 LYS Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain g residue 59 LEU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain h residue 92 ASP Chi-restraints excluded: chain h residue 93 GLU Chi-restraints excluded: chain h residue 105 ILE Chi-restraints excluded: chain h residue 110 GLU Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 115 ASP Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 98 LEU Chi-restraints excluded: chain i residue 103 LEU Chi-restraints excluded: chain i residue 127 PHE Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 94 SER Chi-restraints excluded: chain k residue 17 GLU Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 33 MET Chi-restraints excluded: chain k residue 42 LEU Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 107 VAL Chi-restraints excluded: chain k residue 112 ASP Chi-restraints excluded: chain k residue 121 CYS Chi-restraints excluded: chain l residue 14 SER Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 32 LYS Chi-restraints excluded: chain l residue 86 ASN Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 89 ILE Chi-restraints excluded: chain m residue 101 ASN Chi-restraints excluded: chain n residue 23 ARG Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 81 LEU Chi-restraints excluded: chain p residue 34 ILE Chi-restraints excluded: chain p residue 41 ASN Chi-restraints excluded: chain p residue 50 VAL Chi-restraints excluded: chain p residue 58 ASP Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 85 GLU Chi-restraints excluded: chain q residue 7 GLN Chi-restraints excluded: chain q residue 43 TYR Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 80 GLU Chi-restraints excluded: chain r residue 25 ILE Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain s residue 41 PHE Chi-restraints excluded: chain s residue 57 HIS Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain s residue 69 HIS Chi-restraints excluded: chain t residue 24 GLN Chi-restraints excluded: chain t residue 25 THR Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 62 THR Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 119 PHE Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 172 GLN Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 161 ASN Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain K residue 95 ASP Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 58 PHE Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 120 LYS Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain N residue 9 HIS Chi-restraints excluded: chain N residue 11 ARG Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 48 GLU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 23 ASP Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 57 HIS Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain O residue 109 LYS Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 63 LYS Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 29 HIS Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 36 ASP Chi-restraints excluded: chain T residue 67 PHE Chi-restraints excluded: chain T residue 80 PHE Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 102 ASN Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain U residue 89 ILE Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 31 ASP Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain W residue 83 THR Chi-restraints excluded: chain X residue 19 THR Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 69 PHE Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 41 ASP Chi-restraints excluded: chain Z residue 9 LEU Chi-restraints excluded: chain Z residue 53 ILE Chi-restraints excluded: chain 0 residue 18 ASN Chi-restraints excluded: chain 0 residue 49 THR Chi-restraints excluded: chain 0 residue 56 VAL Chi-restraints excluded: chain 2 residue 32 ASN Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 28 ASP Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 41 VAL Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 65 MET Chi-restraints excluded: chain 6 residue 3 VAL Chi-restraints excluded: chain 6 residue 12 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 958 random chunks: chunk 839 optimal weight: 0.8980 chunk 884 optimal weight: 5.9990 chunk 807 optimal weight: 0.1980 chunk 860 optimal weight: 3.9990 chunk 517 optimal weight: 10.0000 chunk 374 optimal weight: 10.0000 chunk 675 optimal weight: 1.9990 chunk 264 optimal weight: 2.9990 chunk 777 optimal weight: 9.9990 chunk 813 optimal weight: 4.9990 chunk 857 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 175 HIS ** j 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 101 GLN ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 46 HIS ** o 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 ASN ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 48 HIS ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 GLN ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 75 GLN ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.970 152361 Z= 0.296 Angle : 0.597 18.074 228576 Z= 0.302 Chirality : 0.034 0.760 29337 Planarity : 0.004 0.095 11761 Dihedral : 23.584 178.920 77543 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.26 % Favored : 89.64 % Rotamer: Outliers : 4.45 % Allowed : 21.89 % Favored : 73.66 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.26 % Twisted Proline : 0.52 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.11), residues: 5089 helix: 0.05 (0.14), residues: 1408 sheet: -1.23 (0.17), residues: 909 loop : -2.58 (0.11), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP p 59 HIS 0.022 0.001 HIS c 175 PHE 0.021 0.002 PHE P 34 TYR 0.022 0.001 TYR F 128 ARG 0.012 0.000 ARG h 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1027 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 833 time to evaluate : 5.843 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 TARDY: cannot create tardy model for: "ARG F 80 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG G 69 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN M 133 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG X 50 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYS 2 57 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU 5 62 " (corrupted residue). Skipping it. REVERT: h 61 ARG cc_start: 0.6494 (ttp80) cc_final: 0.5777 (ttp80) REVERT: k 33 MET cc_start: 0.5601 (OUTLIER) cc_final: 0.5323 (ttp) REVERT: l 32 LYS cc_start: 0.6733 (OUTLIER) cc_final: 0.6149 (pttt) REVERT: l 54 THR cc_start: 0.7185 (t) cc_final: 0.6559 (m) REVERT: q 40 ARG cc_start: 0.7291 (tpt170) cc_final: 0.6672 (tpt170) REVERT: r 47 ARG cc_start: 0.8450 (mtm110) cc_final: 0.8151 (ptp-110) REVERT: s 66 MET cc_start: 0.5099 (OUTLIER) cc_final: 0.4418 (ppp) REVERT: C 225 MET cc_start: 0.8124 (mmt) cc_final: 0.7814 (mmt) REVERT: D 46 TYR cc_start: 0.5249 (m-10) cc_final: 0.4946 (m-80) REVERT: D 120 GLN cc_start: 0.7452 (mm-40) cc_final: 0.7169 (mm-40) REVERT: D 168 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6710 (ptt180) REVERT: E 34 TYR cc_start: 0.7860 (t80) cc_final: 0.7512 (t80) REVERT: L 2 ILE cc_start: 0.8223 (mm) cc_final: 0.8020 (mm) REVERT: N 1 MET cc_start: 0.3808 (mmm) cc_final: 0.2225 (mmm) REVERT: N 11 ARG cc_start: 0.6660 (OUTLIER) cc_final: 0.4864 (mtp85) REVERT: O 16 MET cc_start: 0.6592 (mtp) cc_final: 0.5985 (ttm) REVERT: O 21 THR cc_start: 0.8052 (p) cc_final: 0.7844 (t) REVERT: O 57 HIS cc_start: 0.7785 (OUTLIER) cc_final: 0.6744 (t-90) REVERT: O 120 MET cc_start: 0.6404 (mmm) cc_final: 0.6141 (mmm) REVERT: U 68 TYR cc_start: 0.6602 (m-80) cc_final: 0.6343 (m-80) REVERT: V 99 GLU cc_start: -0.0219 (mp0) cc_final: -0.0467 (mp0) REVERT: W 74 MET cc_start: 0.6358 (tmm) cc_final: 0.5956 (tmm) outliers start: 194 outliers final: 144 residues processed: 954 average time/residue: 1.1411 time to fit residues: 1916.4796 Evaluate side-chains 924 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 774 time to evaluate : 5.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 17 ASP Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 175 HIS Chi-restraints excluded: chain d residue 2 SER Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain d residue 127 VAL Chi-restraints excluded: chain d residue 166 VAL Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 122 ASP Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain g residue 21 LYS Chi-restraints excluded: chain g residue 59 LEU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain h residue 110 GLU Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 115 ASP Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 103 LEU Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 94 SER Chi-restraints excluded: chain k residue 33 MET Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 112 ASP Chi-restraints excluded: chain l residue 14 SER Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 32 LYS Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 101 ASN Chi-restraints excluded: chain n residue 23 ARG Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain p residue 34 ILE Chi-restraints excluded: chain p residue 41 ASN Chi-restraints excluded: chain p residue 50 VAL Chi-restraints excluded: chain p residue 58 ASP Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 85 GLU Chi-restraints excluded: chain q residue 43 TYR Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 80 GLU Chi-restraints excluded: chain r residue 25 ILE Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain s residue 41 PHE Chi-restraints excluded: chain s residue 57 HIS Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain s residue 69 HIS Chi-restraints excluded: chain t residue 20 LYS Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 119 PHE Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 161 ASN Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 58 PHE Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 120 LYS Chi-restraints excluded: chain N residue 9 HIS Chi-restraints excluded: chain N residue 11 ARG Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 48 GLU Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 23 ASP Chi-restraints excluded: chain O residue 57 HIS Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 63 LYS Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain T residue 36 ASP Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain U residue 89 ILE Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain X residue 19 THR Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 69 PHE Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 41 ASP Chi-restraints excluded: chain Z residue 9 LEU Chi-restraints excluded: chain 0 residue 18 ASN Chi-restraints excluded: chain 0 residue 56 VAL Chi-restraints excluded: chain 2 residue 32 ASN Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 28 ASP Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 5 residue 65 MET Chi-restraints excluded: chain 6 residue 3 VAL Chi-restraints excluded: chain 6 residue 27 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 958 random chunks: chunk 565 optimal weight: 10.0000 chunk 909 optimal weight: 9.9990 chunk 555 optimal weight: 10.0000 chunk 431 optimal weight: 10.0000 chunk 632 optimal weight: 10.0000 chunk 954 optimal weight: 8.9990 chunk 878 optimal weight: 2.9990 chunk 760 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 587 optimal weight: 10.0000 chunk 466 optimal weight: 20.0000 overall best weight: 8.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 61 ASN ** c 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 175 HIS d 147 GLN ** j 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 76 ASN ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 62 HIS ** o 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 55 ASN ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 GLN D 37 GLN D 68 HIS E 29 ASN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 131 HIS N 35 GLN ** Q 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 44 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.967 152361 Z= 0.459 Angle : 0.787 18.107 228576 Z= 0.394 Chirality : 0.042 0.739 29337 Planarity : 0.006 0.099 11761 Dihedral : 23.773 179.876 77543 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 14.48 % Favored : 85.38 % Rotamer: Outliers : 4.18 % Allowed : 22.74 % Favored : 73.08 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.26 % Twisted Proline : 0.52 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.11), residues: 5089 helix: -0.32 (0.14), residues: 1394 sheet: -1.50 (0.17), residues: 940 loop : -2.74 (0.11), residues: 2755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.004 TRP C 213 HIS 0.015 0.002 HIS c 175 PHE 0.022 0.003 PHE R 106 TYR 0.022 0.002 TYR d 61 ARG 0.018 0.001 ARG C 274 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 923 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 741 time to evaluate : 5.770 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 TARDY: cannot create tardy model for: "ARG F 80 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ARG G 69 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP K 61 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN M 133 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG X 50 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYS 2 57 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU 5 62 " (corrupted residue). Skipping it. REVERT: d 88 MET cc_start: 0.8012 (mmm) cc_final: 0.7597 (mmm) REVERT: d 165 PHE cc_start: 0.4139 (p90) cc_final: 0.3807 (p90) REVERT: e 54 GLN cc_start: 0.8460 (tp40) cc_final: 0.8201 (tp-100) REVERT: k 33 MET cc_start: 0.5726 (OUTLIER) cc_final: 0.5447 (ttp) REVERT: l 32 LYS cc_start: 0.6996 (OUTLIER) cc_final: 0.6425 (pttt) REVERT: l 54 THR cc_start: 0.7304 (t) cc_final: 0.6699 (m) REVERT: o 58 LYS cc_start: 0.8454 (mptt) cc_final: 0.8154 (mptt) REVERT: q 40 ARG cc_start: 0.7261 (tpt170) cc_final: 0.6707 (ttt180) REVERT: q 46 LYS cc_start: 0.8040 (mmmt) cc_final: 0.7636 (mmmt) REVERT: r 47 ARG cc_start: 0.8499 (mtm110) cc_final: 0.8246 (ptp-110) REVERT: s 66 MET cc_start: 0.5277 (OUTLIER) cc_final: 0.4778 (ppp) REVERT: C 225 MET cc_start: 0.8315 (mmt) cc_final: 0.8019 (mmt) REVERT: D 85 ASN cc_start: 0.8122 (OUTLIER) cc_final: 0.7846 (p0) REVERT: D 168 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6745 (ptt180) REVERT: N 1 MET cc_start: 0.3775 (mmm) cc_final: 0.2122 (mmm) REVERT: N 4 PRO cc_start: 0.6696 (Cg_endo) cc_final: 0.6347 (Cg_exo) REVERT: N 11 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.4997 (mtp85) REVERT: O 16 MET cc_start: 0.6819 (mtp) cc_final: 0.6442 (ttm) REVERT: O 57 HIS cc_start: 0.7922 (OUTLIER) cc_final: 0.6835 (t-90) REVERT: R 36 LYS cc_start: 0.6224 (mttt) cc_final: 0.5577 (mttp) REVERT: U 68 TYR cc_start: 0.6613 (m-80) cc_final: 0.6412 (m-80) REVERT: V 99 GLU cc_start: 0.0153 (mp0) cc_final: -0.0117 (mp0) REVERT: W 65 VAL cc_start: 0.1853 (OUTLIER) cc_final: 0.1611 (m) REVERT: 6 10 MET cc_start: 0.3929 (mmt) cc_final: 0.3562 (mmt) outliers start: 182 outliers final: 159 residues processed: 861 average time/residue: 1.1713 time to fit residues: 1785.3928 Evaluate side-chains 888 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 721 time to evaluate : 5.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 17 ASP Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 61 ASN Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 175 HIS Chi-restraints excluded: chain d residue 2 SER Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain d residue 127 VAL Chi-restraints excluded: chain d residue 166 VAL Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 122 ASP Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain g residue 21 LYS Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 59 LEU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain h residue 92 ASP Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 115 ASP Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 94 PHE Chi-restraints excluded: chain i residue 103 LEU Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 94 SER Chi-restraints excluded: chain k residue 17 GLU Chi-restraints excluded: chain k residue 33 MET Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain k residue 112 ASP Chi-restraints excluded: chain l residue 14 SER Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 32 LYS Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain m residue 101 ASN Chi-restraints excluded: chain n residue 23 ARG Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 62 HIS Chi-restraints excluded: chain p residue 34 ILE Chi-restraints excluded: chain p residue 40 TYR Chi-restraints excluded: chain p residue 41 ASN Chi-restraints excluded: chain p residue 50 VAL Chi-restraints excluded: chain p residue 58 ASP Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 85 GLU Chi-restraints excluded: chain q residue 43 TYR Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 80 GLU Chi-restraints excluded: chain r residue 25 ILE Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain s residue 41 PHE Chi-restraints excluded: chain s residue 57 HIS Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain s residue 69 HIS Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 62 THR Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 119 PHE Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 161 ASN Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain K residue 95 ASP Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 58 PHE Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 120 LYS Chi-restraints excluded: chain N residue 9 HIS Chi-restraints excluded: chain N residue 11 ARG Chi-restraints excluded: chain N residue 17 MET Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 48 GLU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 23 ASP Chi-restraints excluded: chain O residue 57 HIS Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 63 LYS Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain T residue 36 ASP Chi-restraints excluded: chain T residue 67 PHE Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 89 ILE Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 31 ASP Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain X residue 19 THR Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 69 PHE Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 41 ASP Chi-restraints excluded: chain Z residue 9 LEU Chi-restraints excluded: chain Z residue 38 GLU Chi-restraints excluded: chain Z residue 53 ILE Chi-restraints excluded: chain 0 residue 13 ILE Chi-restraints excluded: chain 0 residue 18 ASN Chi-restraints excluded: chain 0 residue 56 VAL Chi-restraints excluded: chain 2 residue 32 ASN Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 3 residue 28 ASP Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 41 VAL Chi-restraints excluded: chain 5 residue 65 MET Chi-restraints excluded: chain 6 residue 3 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 958 random chunks: chunk 603 optimal weight: 10.0000 chunk 809 optimal weight: 5.9990 chunk 232 optimal weight: 2.9990 chunk 700 optimal weight: 5.9990 chunk 112 optimal weight: 30.0000 chunk 211 optimal weight: 0.2980 chunk 761 optimal weight: 9.9990 chunk 318 optimal weight: 8.9990 chunk 781 optimal weight: 2.9990 chunk 96 optimal weight: 20.0000 chunk 140 optimal weight: 10.0000 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 175 HIS ** j 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 125 GLN ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 62 HIS ** o 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN D 68 HIS ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 ASN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 48 HIS K 124 ASN ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 60 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.070404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.053800 restraints weight = 663352.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 76)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.055273 restraints weight = 212643.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.056158 restraints weight = 110040.375| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.969 152361 Z= 0.325 Angle : 0.640 18.016 228576 Z= 0.324 Chirality : 0.036 0.758 29337 Planarity : 0.005 0.097 11761 Dihedral : 23.610 179.979 77543 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.83 % Favored : 89.07 % Rotamer: Outliers : 3.97 % Allowed : 23.34 % Favored : 72.69 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.26 % Twisted Proline : 0.52 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.11), residues: 5089 helix: -0.07 (0.14), residues: 1403 sheet: -1.34 (0.17), residues: 916 loop : -2.62 (0.11), residues: 2770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP C 213 HIS 0.033 0.002 HIS o 62 PHE 0.039 0.002 PHE S 74 TYR 0.025 0.002 TYR U 68 ARG 0.011 0.001 ARG C 274 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32449.60 seconds wall clock time: 569 minutes 40.68 seconds (34180.68 seconds total)