Starting phenix.real_space_refine on Sun Sep 29 21:20:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yhd_39287/09_2024/8yhd_39287_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yhd_39287/09_2024/8yhd_39287.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yhd_39287/09_2024/8yhd_39287.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yhd_39287/09_2024/8yhd_39287.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yhd_39287/09_2024/8yhd_39287_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yhd_39287/09_2024/8yhd_39287_neut.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.048 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 11 6.06 5 P 88 5.49 5 S 97 5.16 5 C 14731 2.51 5 N 4109 2.21 5 O 4823 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 23859 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1157 Classifications: {'peptide': 163} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 158} Chain breaks: 2 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1531 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1547 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain: "D" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1537 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1541 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1523 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1703 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 7, 'TRANS': 226} Chain breaks: 2 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "H" Number of atoms: 4083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4083 Classifications: {'peptide': 518} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 17, 'TRANS': 500} Chain breaks: 11 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 6, 'ASP:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 99 Chain: "I" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1318 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 153} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1543 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1781 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 9, 'TRANS': 209} Chain breaks: 5 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "L" Number of atoms: 1301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1301 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 6, 'TRANS': 153} Chain breaks: 2 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "M" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1110 Classifications: {'RNA': 53} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 17, 'rna3p_pur': 14, 'rna3p_pyr': 12} Link IDs: {'rna2p': 26, 'rna3p': 26} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {' G%rna2p_pur:plan': 1, ' G%rna2p_pur:plan2': 1} Unresolved non-hydrogen planarities: 12 Chain: "N" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 748 Classifications: {'RNA': 35} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 19, 'rna3p_pyr': 15} Link IDs: {'rna2p': 1, 'rna3p': 33} Chain: "O" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1425 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" 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 387 SG CYS A 71 66.221 74.478 34.287 1.00 97.08 S ATOM 455 SG CYS A 81 64.250 76.911 36.324 1.00 98.11 S ATOM 476 SG CYS A 84 63.634 76.844 32.921 1.00 97.15 S ATOM 496 SG CYS A 87 62.301 73.826 34.638 1.00102.07 S ATOM 1697 SG CYS B 71 38.908 68.915 54.630 1.00 80.40 S ATOM 1771 SG CYS B 81 36.316 68.610 56.875 1.00 86.09 S ATOM 1792 SG CYS B 84 35.678 66.756 53.691 1.00 63.94 S ATOM 1812 SG CYS B 87 38.323 65.326 55.660 1.00 80.96 S ATOM 3240 SG CYS C 71 28.301 45.411 77.362 1.00 75.46 S ATOM 3314 SG CYS C 81 25.640 43.578 79.513 1.00 66.21 S ATOM 3335 SG CYS C 84 27.331 41.670 76.805 1.00 66.73 S ATOM 3355 SG CYS C 87 29.319 42.600 79.701 1.00 64.66 S ATOM 4781 SG CYS D 71 62.024 23.528 127.678 1.00 73.62 S ATOM 4855 SG CYS D 81 64.142 21.872 130.529 1.00 65.29 S ATOM 4876 SG CYS D 84 65.586 22.260 127.677 1.00 80.91 S ATOM 4896 SG CYS D 87 64.503 25.681 129.518 1.00 62.57 S ATOM 6318 SG CYS E 71 76.247 43.511 151.534 1.00 52.48 S ATOM 6392 SG CYS E 81 79.026 44.327 154.171 1.00 61.95 S ATOM 6413 SG CYS E 84 78.444 46.636 151.294 1.00 63.38 S ATOM 6433 SG CYS E 87 75.797 46.474 153.723 1.00 61.92 S ATOM 7851 SG CYS F 71 68.778 67.596 173.556 1.00 69.83 S ATOM 7925 SG CYS F 81 69.755 70.001 176.411 1.00 69.81 S ATOM 7946 SG CYS F 84 68.654 71.564 173.633 1.00 70.95 S ATOM 7966 SG CYS F 87 65.958 69.125 174.870 1.00 63.57 S ATOM 9347 SG CYS G 70 33.221 30.792 203.938 1.00 30.00 S ATOM 9459 SG CYS G 85 34.444 29.963 206.252 1.00 30.00 S ATOM 9478 SG CYS G 88 35.851 28.506 203.826 1.00 30.00 S ATOM 16488 SG CYS J 71 39.862 25.256 102.126 1.00 67.54 S ATOM 16562 SG CYS J 81 39.210 22.216 104.275 1.00 67.10 S ATOM 16583 SG CYS J 84 42.228 22.246 101.745 1.00 72.20 S ATOM 16603 SG CYS J 87 42.258 24.389 104.756 1.00 63.34 S ATOM 22957 SG CYS O 71 43.748 76.906 194.626 1.00 92.25 S ATOM 22990 SG CYS O 81 41.968 79.432 197.278 1.00 97.53 S ATOM 23005 SG CYS O 84 40.385 77.615 194.321 1.00 95.27 S ATOM 23025 SG CYS O 87 41.384 75.618 197.330 1.00 91.14 S Time building chain proxies: 13.98, per 1000 atoms: 0.59 Number of scatterers: 23859 At special positions: 0 Unit cell: (94.05, 120.65, 241.3, 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 11 29.99 S 97 16.00 P 88 15.00 O 4823 8.00 N 4109 7.00 C 14731 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 - 3.00 Amino acid : True - 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: 6.28 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 84 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 71 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 81 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 87 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 84 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 87 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 71 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 81 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 84 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 87 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 81 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 71 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 84 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 81 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 71 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 87 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 87 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 84 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 71 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 81 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 71 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 84 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 87 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 81 " pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 88 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 85 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 70 " pdb=" ZN H 701 " pdb="ZN ZN H 701 " - pdb=" ND1 HIS H 64 " pdb="ZN ZN H 701 " - pdb=" NE2 HIS H 62 " pdb="ZN ZN H 701 " - pdb=" ND1 HIS H 148 " pdb=" ZN H 702 " pdb="ZN ZN H 702 " - pdb=" NE2 HIS H 67 " pdb=" ZN J 301 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 87 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 71 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 81 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 84 " pdb=" ZN O 301 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 84 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 87 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 81 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 71 " Number of angles added : 48 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5330 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 39 sheets defined 35.4% alpha, 22.2% beta 23 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 8.51 Creating SS restraints... Processing helix chain 'A' and resid 51 through 66 Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 109 through 114 removed outlier: 3.548A pdb=" N ILE A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 172 removed outlier: 3.586A pdb=" N LYS A 166 " --> pdb=" O GLN A 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 32 Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'B' and resid 156 through 172 Processing helix chain 'B' and resid 176 through 180 removed outlier: 3.859A pdb=" N GLY B 180 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 32 Processing helix chain 'C' and resid 54 through 67 Processing helix chain 'C' and resid 84 through 91 Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 157 through 172 Processing helix chain 'D' and resid 24 through 32 Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 85 through 91 Processing helix chain 'D' and resid 155 through 172 removed outlier: 4.545A pdb=" N SER D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 198 No H-bonds generated for 'chain 'D' and resid 196 through 198' Processing helix chain 'E' and resid 24 through 32 Processing helix chain 'E' and resid 51 through 67 Processing helix chain 'E' and resid 84 through 90 Processing helix chain 'E' and resid 109 through 113 Processing helix chain 'E' and resid 156 through 172 Processing helix chain 'F' and resid 24 through 32 Processing helix chain 'F' and resid 51 through 67 Processing helix chain 'F' and resid 85 through 90 Processing helix chain 'F' and resid 109 through 113 Processing helix chain 'F' and resid 156 through 172 Processing helix chain 'F' and resid 196 through 198 No H-bonds generated for 'chain 'F' and resid 196 through 198' Processing helix chain 'G' and resid 28 through 43 Processing helix chain 'G' and resid 47 through 53 Processing helix chain 'G' and resid 127 through 142 Processing helix chain 'G' and resid 148 through 152 Processing helix chain 'H' and resid 42 through 53 removed outlier: 3.752A pdb=" N GLY H 53 " --> pdb=" O ILE H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 77 removed outlier: 3.840A pdb=" N LEU H 74 " --> pdb=" O LEU H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 107 Processing helix chain 'H' and resid 114 through 122 removed outlier: 3.515A pdb=" N PHE H 122 " --> pdb=" O ILE H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 219 removed outlier: 3.773A pdb=" N LEU H 211 " --> pdb=" O ASP H 207 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS H 216 " --> pdb=" O LEU H 212 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS H 219 " --> pdb=" O ALA H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 234 through 245 Processing helix chain 'H' and resid 255 through 268 removed outlier: 4.316A pdb=" N LYS H 260 " --> pdb=" O PRO H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 272 Processing helix chain 'H' and resid 273 through 277 Processing helix chain 'H' and resid 295 through 304 Processing helix chain 'H' and resid 323 through 332 Processing helix chain 'H' and resid 375 through 384 Processing helix chain 'H' and resid 400 through 413 Processing helix chain 'H' and resid 470 through 479 removed outlier: 3.709A pdb=" N PHE H 474 " --> pdb=" O ASP H 470 " (cutoff:3.500A) Processing helix chain 'H' and resid 509 through 523 Processing helix chain 'H' and resid 527 through 541 Processing helix chain 'H' and resid 541 through 554 Processing helix chain 'H' and resid 572 through 592 removed outlier: 3.774A pdb=" N LYS H 592 " --> pdb=" O LEU H 588 " (cutoff:3.500A) Processing helix chain 'H' and resid 594 through 603 Processing helix chain 'I' and resid 470 through 490 Processing helix chain 'I' and resid 509 through 523 Processing helix chain 'I' and resid 527 through 540 Processing helix chain 'I' and resid 541 through 554 Processing helix chain 'I' and resid 572 through 592 removed outlier: 4.034A pdb=" N LYS I 592 " --> pdb=" O LEU I 588 " (cutoff:3.500A) Processing helix chain 'I' and resid 594 through 604 removed outlier: 4.006A pdb=" N ASN I 604 " --> pdb=" O ASN I 600 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 32 Processing helix chain 'J' and resid 51 through 67 Processing helix chain 'J' and resid 84 through 91 Processing helix chain 'J' and resid 109 through 113 Processing helix chain 'J' and resid 156 through 172 Processing helix chain 'J' and resid 176 through 180 removed outlier: 3.570A pdb=" N GLY J 180 " --> pdb=" O LEU J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 378 through 386 Processing helix chain 'K' and resid 405 through 413 Processing helix chain 'K' and resid 470 through 488 removed outlier: 3.792A pdb=" N PHE K 474 " --> pdb=" O ASP K 470 " (cutoff:3.500A) Processing helix chain 'K' and resid 509 through 523 removed outlier: 3.785A pdb=" N ASN K 522 " --> pdb=" O GLU K 518 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE K 523 " --> pdb=" O TYR K 519 " (cutoff:3.500A) Processing helix chain 'K' and resid 527 through 540 removed outlier: 3.657A pdb=" N LYS K 540 " --> pdb=" O GLU K 536 " (cutoff:3.500A) Processing helix chain 'K' and resid 541 through 553 removed outlier: 3.523A pdb=" N ALA K 545 " --> pdb=" O GLY K 541 " (cutoff:3.500A) Processing helix chain 'K' and resid 572 through 592 removed outlier: 3.955A pdb=" N LYS K 592 " --> pdb=" O LEU K 588 " (cutoff:3.500A) Processing helix chain 'K' and resid 594 through 603 removed outlier: 3.923A pdb=" N ILE K 601 " --> pdb=" O LYS K 597 " (cutoff:3.500A) Processing helix chain 'L' and resid 470 through 486 Processing helix chain 'L' and resid 509 through 523 Processing helix chain 'L' and resid 527 through 539 Processing helix chain 'L' and resid 542 through 553 Processing helix chain 'L' and resid 572 through 592 removed outlier: 3.746A pdb=" N LYS L 592 " --> pdb=" O LEU L 588 " (cutoff:3.500A) Processing helix chain 'L' and resid 594 through 603 Processing helix chain 'O' and resid 24 through 32 Processing helix chain 'O' and resid 51 through 67 Processing helix chain 'O' and resid 84 through 91 Processing helix chain 'O' and resid 109 through 113 Processing helix chain 'O' and resid 157 through 172 Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 101 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.572A pdb=" N ILE A 49 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 104 " --> pdb=" O ILE A 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 99 through 100 Processing sheet with id=AA4, first strand: chain 'B' and resid 99 through 100 Processing sheet with id=AA5, first strand: chain 'B' and resid 114 through 122 Processing sheet with id=AA6, first strand: chain 'C' and resid 41 through 42 removed outlier: 5.544A pdb=" N VAL C 47 " --> pdb=" O SER C 106 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE C 49 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 41 through 42 removed outlier: 5.544A pdb=" N VAL C 47 " --> pdb=" O SER C 106 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE C 49 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 114 through 122 Processing sheet with id=AA9, first strand: chain 'D' and resid 48 through 49 Processing sheet with id=AB1, first strand: chain 'D' and resid 48 through 49 Processing sheet with id=AB2, first strand: chain 'D' and resid 114 through 122 Processing sheet with id=AB3, first strand: chain 'E' and resid 99 through 101 Processing sheet with id=AB4, first strand: chain 'E' and resid 99 through 101 Processing sheet with id=AB5, first strand: chain 'E' and resid 114 through 122 Processing sheet with id=AB6, first strand: chain 'F' and resid 99 through 101 Processing sheet with id=AB7, first strand: chain 'F' and resid 99 through 101 Processing sheet with id=AB8, first strand: chain 'F' and resid 114 through 122 Processing sheet with id=AB9, first strand: chain 'G' and resid 115 through 117 removed outlier: 7.032A pdb=" N LYS G 5 " --> pdb=" O TYR G 161 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR G 161 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ILE G 7 " --> pdb=" O LYS G 159 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 59 through 61 Processing sheet with id=AC2, first strand: chain 'G' and resid 75 through 76 removed outlier: 3.794A pdb=" N TYR G 75 " --> pdb=" O LYS G 84 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 97 through 102 Processing sheet with id=AC4, first strand: chain 'G' and resid 214 through 216 Processing sheet with id=AC5, first strand: chain 'G' and resid 187 through 192 Processing sheet with id=AC6, first strand: chain 'H' and resid 2 through 4 removed outlier: 6.671A pdb=" N LYS H 24 " --> pdb=" O ALA H 55 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASP H 56 " --> pdb=" O LYS H 82 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE H 84 " --> pdb=" O ASP H 56 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N CYS H 58 " --> pdb=" O ILE H 84 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ASP H 126 " --> pdb=" O ASN H 81 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ILE H 83 " --> pdb=" O ASP H 126 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 134 through 136 removed outlier: 6.344A pdb=" N ASN H 163 " --> pdb=" O TYR H 191 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU H 192 " --> pdb=" O PHE H 394 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU H 418 " --> pdb=" O VAL H 393 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 226 through 228 removed outlier: 3.969A pdb=" N SER H 313 " --> pdb=" O ILE H 227 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N TYR H 252 " --> pdb=" O ILE H 312 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 339 through 340 Processing sheet with id=AD1, first strand: chain 'H' and resid 435 through 436 Processing sheet with id=AD2, first strand: chain 'H' and resid 435 through 436 removed outlier: 4.024A pdb=" N ARG H 451 " --> pdb=" O GLU K 461 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL K 435 " --> pdb=" O ILE K 466 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE K 468 " --> pdb=" O VAL K 435 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU K 437 " --> pdb=" O ILE K 468 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 445 through 447 Processing sheet with id=AD4, first strand: chain 'I' and resid 445 through 447 removed outlier: 4.126A pdb=" N ARG I 451 " --> pdb=" O GLU L 461 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 48 through 49 Processing sheet with id=AD6, first strand: chain 'J' and resid 48 through 49 Processing sheet with id=AD7, first strand: chain 'J' and resid 114 through 122 Processing sheet with id=AD8, first strand: chain 'K' and resid 164 through 165 removed outlier: 6.777A pdb=" N LEU K 192 " --> pdb=" O PHE K 394 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 445 through 447 Processing sheet with id=AE1, first strand: chain 'O' and resid 99 through 100 Processing sheet with id=AE2, first strand: chain 'O' and resid 105 through 106 removed outlier: 3.554A pdb=" N MET O 5 " --> pdb=" O VAL O 193 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 114 through 122 1018 hydrogen bonds defined for protein. 2949 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 57 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 8.20 Time building geometry restraints manager: 7.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5806 1.33 - 1.45: 5451 1.45 - 1.58: 12818 1.58 - 1.70: 177 1.70 - 1.82: 148 Bond restraints: 24400 Sorted by residual: bond pdb=" C ARG C 40 " pdb=" N LYS C 41 " ideal model delta sigma weight residual 1.331 1.222 0.110 1.38e-02 5.25e+03 6.30e+01 bond pdb=" C ALA G 40 " pdb=" N PHE G 41 " ideal model delta sigma weight residual 1.334 1.435 -0.100 1.33e-02 5.65e+03 5.68e+01 bond pdb=" C ALA H 407 " pdb=" N LYS H 408 " ideal model delta sigma weight residual 1.334 1.238 0.096 1.33e-02 5.65e+03 5.21e+01 bond pdb=" C SER C 117 " pdb=" N THR C 118 " ideal model delta sigma weight residual 1.331 1.426 -0.095 1.33e-02 5.65e+03 5.08e+01 bond pdb=" C ARG B 40 " pdb=" N LYS B 41 " ideal model delta sigma weight residual 1.330 1.230 0.100 1.45e-02 4.76e+03 4.80e+01 ... (remaining 24395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 31561 2.61 - 5.22: 1468 5.22 - 7.83: 227 7.83 - 10.43: 60 10.43 - 13.04: 4 Bond angle restraints: 33320 Sorted by residual: angle pdb=" N HIS H 67 " pdb=" CA HIS H 67 " pdb=" C HIS H 67 " ideal model delta sigma weight residual 114.12 103.74 10.38 1.39e+00 5.18e-01 5.58e+01 angle pdb=" N ALA C 54 " pdb=" CA ALA C 54 " pdb=" C ALA C 54 " ideal model delta sigma weight residual 113.50 104.97 8.53 1.23e+00 6.61e-01 4.81e+01 angle pdb=" N GLY C 53 " pdb=" CA GLY C 53 " pdb=" C GLY C 53 " ideal model delta sigma weight residual 113.58 106.39 7.19 1.07e+00 8.73e-01 4.51e+01 angle pdb=" N PRO G 86 " pdb=" CA PRO G 86 " pdb=" C PRO G 86 " ideal model delta sigma weight residual 113.81 104.40 9.41 1.45e+00 4.76e-01 4.22e+01 angle pdb=" N LYS E 33 " pdb=" CA LYS E 33 " pdb=" C LYS E 33 " ideal model delta sigma weight residual 112.90 104.51 8.39 1.31e+00 5.83e-01 4.10e+01 ... (remaining 33315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 14291 35.97 - 71.95: 595 71.95 - 107.92: 41 107.92 - 143.89: 0 143.89 - 179.86: 4 Dihedral angle restraints: 14931 sinusoidal: 6717 harmonic: 8214 Sorted by residual: dihedral pdb=" O4' U M 5 " pdb=" C1' U M 5 " pdb=" N1 U M 5 " pdb=" C2 U M 5 " ideal model delta sinusoidal sigma weight residual -128.00 51.86 -179.86 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U M 11 " pdb=" C1' U M 11 " pdb=" N1 U M 11 " pdb=" C2 U M 11 " ideal model delta sinusoidal sigma weight residual -128.00 50.86 -178.86 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U M 23 " pdb=" C1' U M 23 " pdb=" N1 U M 23 " pdb=" C2 U M 23 " ideal model delta sinusoidal sigma weight residual -128.00 41.61 -169.61 1 1.70e+01 3.46e-03 6.59e+01 ... (remaining 14928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3295 0.098 - 0.196: 512 0.196 - 0.293: 40 0.293 - 0.391: 10 0.391 - 0.489: 13 Chirality restraints: 3870 Sorted by residual: chirality pdb=" CB VAL O 23 " pdb=" CA VAL O 23 " pdb=" CG1 VAL O 23 " pdb=" CG2 VAL O 23 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 5.97e+00 chirality pdb=" P U M 23 " pdb=" OP1 U M 23 " pdb=" OP2 U M 23 " pdb=" O5' U M 23 " both_signs ideal model delta sigma weight residual True 2.41 -2.90 -0.49 2.00e-01 2.50e+01 5.95e+00 chirality pdb=" CB ILE H 57 " pdb=" CA ILE H 57 " pdb=" CG1 ILE H 57 " pdb=" CG2 ILE H 57 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.71e+00 ... (remaining 3867 not shown) Planarity restraints: 3956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 78 " -0.520 9.50e-02 1.11e+02 2.33e-01 3.32e+01 pdb=" NE ARG H 78 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG H 78 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG H 78 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG H 78 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR H 133 " -0.023 2.00e-02 2.50e+03 4.72e-02 2.23e+01 pdb=" C THR H 133 " 0.082 2.00e-02 2.50e+03 pdb=" O THR H 133 " -0.032 2.00e-02 2.50e+03 pdb=" N ILE H 134 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 554 " -0.420 9.50e-02 1.11e+02 1.88e-01 2.18e+01 pdb=" NE ARG L 554 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG L 554 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG L 554 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG L 554 " -0.014 2.00e-02 2.50e+03 ... (remaining 3953 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5009 2.78 - 3.31: 21634 3.31 - 3.84: 42262 3.84 - 4.37: 50810 4.37 - 4.90: 83635 Nonbonded interactions: 203350 Sorted by model distance: nonbonded pdb=" OG SER D 117 " pdb=" OE2 GLU D 137 " model vdw 2.251 3.040 nonbonded pdb=" OE1 GLU C 123 " pdb=" OG SER C 128 " model vdw 2.273 3.040 nonbonded pdb=" OG SER K 527 " pdb=" OP1 U N 23 " model vdw 2.283 3.040 nonbonded pdb=" OG SER G 178 " pdb=" O PHE G 233 " model vdw 2.286 3.040 nonbonded pdb=" OG SER I 527 " pdb=" OP1 U N 17 " model vdw 2.287 3.040 ... (remaining 203345 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 73 or (resid 79 and (name N or name CA or name C \ or name O or name CB )) or resid 80 through 82 or (resid 83 and (name N or name \ CA or name C or name O or name CB )) or resid 84 through 94 or (resid 95 through \ 96 and (name N or name CA or name C or name O or name CB )) or resid 97 through \ 154 or (resid 155 through 156 and (name N or name CA or name C or name O or nam \ e CB )) or resid 157 through 165 or (resid 166 and (name N or name CA or name C \ or name O or name CB )) or resid 167 through 196 or resid 301)) selection = (chain 'O' and (resid 2 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 or (resid 15 and (name N or name CA or name \ C or name O or name CB )) or resid 16 through 19 or (resid 20 and (name N or na \ me CA or name C or name O or name CB )) or resid 21 through 23 or (resid 24 thro \ ugh 25 and (name N or name CA or name C or name O or name CB )) or (resid 41 thr \ ough 43 and (name N or name CA or name C or name O or name CB )) or resid 44 thr \ ough 63 or (resid 64 through 66 and (name N or name CA or name C or name O or na \ me CB )) or resid 67 through 68 or (resid 69 through 70 and (name N or name CA o \ r name C or name O or name CB )) or resid 71 through 109 or (resid 110 and (name \ N or name CA or name C or name O or name CB )) or resid 111 through 114 or (res \ id 115 through 116 and (name N or name CA or name C or name O or name CB )) or r \ esid 137 through 169 or (resid 170 and (name N or name CA or name C or name O or \ name CB )) or resid 171 through 176 or (resid 177 and (name N or name CA or nam \ e C or name O or name CB )) or resid 178 or (resid 179 and (name N or name CA or \ name C or name O or name CB )) or resid 180 or (resid 181 and (name N or name C \ A or name C or name O or name CB )) or resid 182 or (resid 183 and (name N or na \ me CA or name C or name O or name CB )) or resid 184 through 186 or (resid 187 a \ nd (name N or name CA or name C or name O or name CB )) or resid 188 or (resid 1 \ 89 and (name N or name CA or name C or name O or name CB )) or resid 190 through \ 196 or resid 301)) } ncs_group { reference = (chain 'B' and (resid 2 through 33 or (resid 34 and (name N or name CA or name C \ or name O or name CB )) or resid 35 through 94 or (resid 95 through 96 and (nam \ e N or name CA or name C or name O or name CB )) or resid 97 through 124 or (res \ id 125 and (name N or name CA or name C or name O or name CB )) or resid 126 thr \ ough 199 or (resid 200 and (name N or name CA or name C or name O or name CB )) \ or resid 301)) selection = (chain 'C' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 31 or (resid 32 through 34 and (name N or name CA \ or name C or name O or name CB )) or resid 35 through 94 or (resid 95 through 9 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 97 through 1 \ 09 or (resid 110 and (name N or name CA or name C or name O or name CB )) or res \ id 111 through 124 or (resid 125 and (name N or name CA or name C or name O or n \ ame CB )) or resid 126 through 199 or (resid 200 and (name N or name CA or name \ C or name O or name CB )) or resid 301)) selection = (chain 'D' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 31 or (resid 32 through 34 and (name N or name CA \ or name C or name O or name CB )) or resid 35 through 94 or (resid 95 through 9 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 97 through 1 \ 09 or (resid 110 and (name N or name CA or name C or name O or name CB )) or res \ id 111 through 199 or (resid 200 and (name N or name CA or name C or name O or n \ ame CB )) or resid 301)) selection = (chain 'E' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 31 or (resid 32 through 34 and (name N or name CA \ or name C or name O or name CB )) or resid 35 through 94 or (resid 95 through 9 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 97 through 1 \ 09 or (resid 110 and (name N or name CA or name C or name O or name CB )) or res \ id 111 through 124 or (resid 125 and (name N or name CA or name C or name O or n \ ame CB )) or resid 126 through 199 or (resid 200 and (name N or name CA or name \ C or name O or name CB )) or resid 301)) selection = (chain 'F' and (resid 2 through 31 or (resid 32 through 34 and (name N or name C \ A or name C or name O or name CB )) or resid 35 through 109 or (resid 110 and (n \ ame N or name CA or name C or name O or name CB )) or resid 111 through 124 or ( \ resid 125 and (name N or name CA or name C or name O or name CB )) or resid 126 \ through 200 or resid 301)) selection = (chain 'J' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 31 or (resid 32 through 34 and (name N or name CA \ or name C or name O or name CB )) or resid 35 through 94 or (resid 95 through 9 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 97 through 1 \ 09 or (resid 110 and (name N or name CA or name C or name O or name CB )) or res \ id 111 through 124 or (resid 125 and (name N or name CA or name C or name O or n \ ame CB )) or resid 126 through 199 or (resid 200 and (name N or name CA or name \ C or name O or name CB )) or resid 301)) } ncs_group { reference = (chain 'I' and (resid 435 through 479 or (resid 480 through 481 and (name N or n \ ame CA or name C or name O or name CB )) or resid 482 through 483 or (resid 484 \ through 486 and (name N or name CA or name C or name O or name CB )) or resid 48 \ 7 through 490 or resid 505 through 510 or (resid 511 and (name N or name CA or n \ ame C or name O or name CB )) or resid 512 through 577 or (resid 578 and (name N \ or name CA or name C or name O or name CB )) or resid 579 through 595 or (resid \ 596 and (name N or name CA or name C or name O or name CB )) or resid 597 throu \ gh 607 or (resid 608 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'L' and (resid 435 through 461 or (resid 462 and (name N or name CA or na \ me C or name O or name CB )) or resid 465 through 485 or (resid 486 and (name N \ or name CA or name C or name O or name CB )) or resid 487 through 489 or (resid \ 490 through 505 and (name N or name CA or name C or name O or name CB )) or resi \ d 506 through 608)) } 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 individual isotropic 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 62.570 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:10.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 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 : 0.008 0.110 24400 Z= 0.541 Angle : 1.265 13.042 33320 Z= 0.766 Chirality : 0.074 0.489 3870 Planarity : 0.012 0.233 3956 Dihedral : 18.371 179.863 9601 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.02 % Allowed : 26.80 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.64 (0.13), residues: 2762 helix: -1.59 (0.14), residues: 927 sheet: -0.81 (0.21), residues: 539 loop : -2.24 (0.14), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP L 535 HIS 0.011 0.003 HIS K 510 PHE 0.060 0.004 PHE H 100 TYR 0.043 0.003 TYR G 137 ARG 0.024 0.002 ARG H 561 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 744 time to evaluate : 2.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 THR cc_start: 0.8491 (m) cc_final: 0.8220 (p) REVERT: A 109 THR cc_start: 0.7078 (p) cc_final: 0.6430 (m) REVERT: A 169 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7514 (mm-30) REVERT: A 196 ASP cc_start: 0.7913 (p0) cc_final: 0.7667 (p0) REVERT: B 158 LEU cc_start: 0.7648 (tp) cc_final: 0.7397 (tp) REVERT: C 83 ARG cc_start: 0.8321 (mtm-85) cc_final: 0.8096 (ptp90) REVERT: D 131 ASP cc_start: 0.7766 (t70) cc_final: 0.7549 (t0) REVERT: E 13 LYS cc_start: 0.8615 (ttpp) cc_final: 0.8196 (ttpp) REVERT: E 92 SER cc_start: 0.8919 (p) cc_final: 0.8700 (t) REVERT: F 123 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7737 (mt-10) REVERT: F 127 LYS cc_start: 0.8365 (mttp) cc_final: 0.7533 (mtmm) REVERT: G 59 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7741 (OUTLIER) REVERT: H 117 ASP cc_start: 0.7245 (m-30) cc_final: 0.7015 (m-30) REVERT: H 253 ILE cc_start: 0.8045 (mt) cc_final: 0.7841 (mm) REVERT: H 443 ASN cc_start: 0.6956 (p0) cc_final: 0.6571 (m110) REVERT: H 596 ASN cc_start: 0.7693 (m-40) cc_final: 0.7362 (p0) REVERT: I 450 TYR cc_start: 0.6456 (m-80) cc_final: 0.6109 (m-10) REVERT: I 512 LYS cc_start: 0.8054 (tppt) cc_final: 0.7846 (tptp) REVERT: I 518 GLU cc_start: 0.7849 (tp30) cc_final: 0.7559 (tm-30) REVERT: I 550 THR cc_start: 0.8536 (m) cc_final: 0.8305 (p) REVERT: J 5 MET cc_start: 0.8137 (mtm) cc_final: 0.7742 (mtm) REVERT: J 13 LYS cc_start: 0.8290 (ttmm) cc_final: 0.7838 (ttpt) REVERT: J 108 ASP cc_start: 0.8207 (m-30) cc_final: 0.7964 (m-30) REVERT: K 386 LEU cc_start: 0.8119 (mt) cc_final: 0.7557 (tt) REVERT: K 461 GLU cc_start: 0.7418 (tt0) cc_final: 0.6971 (tt0) REVERT: K 529 ASN cc_start: 0.8381 (t0) cc_final: 0.7458 (m-40) REVERT: K 584 TYR cc_start: 0.7610 (t80) cc_final: 0.7368 (t80) REVERT: L 479 ASN cc_start: 0.8776 (m-40) cc_final: 0.8503 (m-40) REVERT: L 593 TYR cc_start: 0.7230 (m-10) cc_final: 0.7025 (m-10) outliers start: 47 outliers final: 5 residues processed: 765 average time/residue: 1.4016 time to fit residues: 1221.8050 Evaluate side-chains 408 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 403 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain H residue 137 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 239 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 222 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 165 optimal weight: 20.0000 chunk 257 optimal weight: 8.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 GLN C 112 GLN E 32 GLN E 119 HIS E 171 ASN G 20 ASN G 81 ASN ** G 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 HIS H 446 ASN H 479 ASN H 551 GLN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 472 ASN I 556 ASN ** I 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 154 GLN K 469 ASN ** L 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 553 HIS O 112 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 24400 Z= 0.251 Angle : 0.643 10.075 33320 Z= 0.343 Chirality : 0.045 0.291 3870 Planarity : 0.005 0.067 3956 Dihedral : 15.088 178.859 4382 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.29 % Allowed : 27.62 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.26 (0.15), residues: 2762 helix: 0.16 (0.16), residues: 938 sheet: -0.42 (0.22), residues: 510 loop : -1.74 (0.15), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 478 HIS 0.004 0.001 HIS H 64 PHE 0.040 0.002 PHE G 74 TYR 0.022 0.001 TYR G 137 ARG 0.008 0.001 ARG B 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 459 time to evaluate : 2.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.8015 (t80) REVERT: A 55 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8308 (mm) REVERT: A 165 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7726 (mt) REVERT: A 169 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7266 (mp0) REVERT: A 196 ASP cc_start: 0.8019 (p0) cc_final: 0.7513 (p0) REVERT: B 76 SER cc_start: 0.8278 (t) cc_final: 0.8063 (m) REVERT: B 102 ASP cc_start: 0.8385 (p0) cc_final: 0.8171 (p0) REVERT: C 36 ASN cc_start: 0.8493 (m-40) cc_final: 0.8203 (m110) REVERT: C 123 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7367 (mm-30) REVERT: D 3 LYS cc_start: 0.8101 (mtpp) cc_final: 0.7877 (mttt) REVERT: D 123 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: D 131 ASP cc_start: 0.8089 (t70) cc_final: 0.7800 (t0) REVERT: E 92 SER cc_start: 0.9030 (p) cc_final: 0.8772 (t) REVERT: E 110 LYS cc_start: 0.8218 (ptmm) cc_final: 0.7988 (ptpt) REVERT: F 123 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7766 (mt-10) REVERT: F 127 LYS cc_start: 0.8276 (mttp) cc_final: 0.7579 (mtmt) REVERT: H 253 ILE cc_start: 0.7822 (mt) cc_final: 0.7556 (mm) REVERT: H 443 ASN cc_start: 0.6750 (p0) cc_final: 0.6380 (m110) REVERT: I 485 MET cc_start: 0.4654 (ttm) cc_final: 0.4417 (ttp) REVERT: I 512 LYS cc_start: 0.8201 (tppt) cc_final: 0.7966 (tptp) REVERT: I 518 GLU cc_start: 0.7903 (tp30) cc_final: 0.7385 (pt0) REVERT: J 13 LYS cc_start: 0.8399 (ttmm) cc_final: 0.7945 (ttpt) REVERT: J 52 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8714 (tttt) REVERT: J 137 GLU cc_start: 0.8358 (pt0) cc_final: 0.8147 (pt0) REVERT: K 166 PHE cc_start: 0.6247 (m-80) cc_final: 0.5182 (p90) REVERT: K 386 LEU cc_start: 0.8267 (mt) cc_final: 0.7831 (tt) REVERT: K 394 PHE cc_start: 0.8254 (m-80) cc_final: 0.7861 (m-80) REVERT: K 461 GLU cc_start: 0.7536 (tt0) cc_final: 0.7176 (tt0) REVERT: K 529 ASN cc_start: 0.8406 (t0) cc_final: 0.7387 (m110) REVERT: L 462 LYS cc_start: 0.6292 (mmmm) cc_final: 0.6057 (mmmm) REVERT: L 467 GLU cc_start: 0.6806 (pt0) cc_final: 0.6511 (pt0) REVERT: L 479 ASN cc_start: 0.8858 (m-40) cc_final: 0.8359 (m-40) REVERT: L 513 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7443 (mp) REVERT: L 593 TYR cc_start: 0.7151 (m-10) cc_final: 0.6927 (m-10) REVERT: L 603 ILE cc_start: 0.7747 (pp) cc_final: 0.7492 (pt) outliers start: 100 outliers final: 22 residues processed: 526 average time/residue: 1.3337 time to fit residues: 804.4656 Evaluate side-chains 397 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 368 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 226 LEU Chi-restraints excluded: chain H residue 259 SER Chi-restraints excluded: chain H residue 399 GLU Chi-restraints excluded: chain H residue 570 ASP Chi-restraints excluded: chain I residue 608 LYS Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain L residue 513 ILE Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 190 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 143 optimal weight: 9.9990 chunk 80 optimal weight: 0.9980 chunk 214 optimal weight: 4.9990 chunk 175 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 258 optimal weight: 4.9990 chunk 279 optimal weight: 4.9990 chunk 230 optimal weight: 10.0000 chunk 256 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 207 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 GLN C 107 ASN C 112 GLN D 112 GLN E 32 GLN F 171 ASN G 42 ASN G 81 ASN ** G 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 479 ASN H 551 GLN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 606 ASN J 119 HIS J 178 ASN ** K 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 574 ASN O 107 ASN O 112 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 24400 Z= 0.347 Angle : 0.631 9.055 33320 Z= 0.334 Chirality : 0.046 0.265 3870 Planarity : 0.005 0.056 3956 Dihedral : 14.903 179.068 4377 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.63 % Allowed : 26.97 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.76 (0.15), residues: 2762 helix: 0.79 (0.16), residues: 940 sheet: -0.49 (0.21), residues: 538 loop : -1.49 (0.15), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 125 HIS 0.007 0.001 HIS H 64 PHE 0.027 0.002 PHE G 56 TYR 0.022 0.002 TYR I 599 ARG 0.010 0.001 ARG K 409 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 414 time to evaluate : 2.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.6902 (tpp) REVERT: A 18 LEU cc_start: 0.6447 (tp) cc_final: 0.5821 (mp) REVERT: A 55 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8490 (mm) REVERT: A 154 GLN cc_start: 0.7535 (tm-30) cc_final: 0.7325 (tm-30) REVERT: A 165 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7609 (mt) REVERT: B 79 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7837 (ttp80) REVERT: C 5 MET cc_start: 0.8591 (mtm) cc_final: 0.8106 (mtt) REVERT: D 3 LYS cc_start: 0.8118 (mtpp) cc_final: 0.7843 (mttm) REVERT: D 13 LYS cc_start: 0.8463 (tptt) cc_final: 0.8214 (ttpt) REVERT: D 123 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7906 (mt-10) REVERT: D 131 ASP cc_start: 0.8336 (t70) cc_final: 0.7910 (t0) REVERT: E 127 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8357 (mmtm) REVERT: F 123 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7948 (mt-10) REVERT: F 127 LYS cc_start: 0.8339 (mttp) cc_final: 0.7615 (mtmt) REVERT: G 36 ILE cc_start: 0.8952 (tp) cc_final: 0.8697 (mt) REVERT: H 99 ASP cc_start: 0.8463 (t70) cc_final: 0.8205 (t70) REVERT: H 130 ASP cc_start: 0.7928 (p0) cc_final: 0.7714 (p0) REVERT: H 152 SER cc_start: 0.8708 (OUTLIER) cc_final: 0.8404 (p) REVERT: H 253 ILE cc_start: 0.7843 (mt) cc_final: 0.7534 (mm) REVERT: H 395 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8439 (tt) REVERT: H 409 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.6320 (ttp-170) REVERT: I 485 MET cc_start: 0.4571 (ttm) cc_final: 0.4347 (ttp) REVERT: I 518 GLU cc_start: 0.7930 (tp30) cc_final: 0.7582 (tm-30) REVERT: J 13 LYS cc_start: 0.8565 (ttmm) cc_final: 0.8065 (ttpt) REVERT: J 28 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7622 (mtmt) REVERT: J 29 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7765 (mt-10) REVERT: J 52 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8785 (tttt) REVERT: J 125 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7780 (mp10) REVERT: J 137 GLU cc_start: 0.8496 (pt0) cc_final: 0.8219 (pt0) REVERT: K 386 LEU cc_start: 0.8084 (mt) cc_final: 0.7823 (tt) REVERT: K 394 PHE cc_start: 0.8412 (m-80) cc_final: 0.7930 (m-80) REVERT: K 411 ILE cc_start: 0.8127 (mm) cc_final: 0.7904 (mp) REVERT: K 461 GLU cc_start: 0.7600 (tt0) cc_final: 0.7182 (tt0) REVERT: L 467 GLU cc_start: 0.6792 (pt0) cc_final: 0.6548 (pt0) REVERT: L 512 LYS cc_start: 0.8760 (tppp) cc_final: 0.8476 (tppp) REVERT: L 513 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7417 (mp) REVERT: L 577 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7327 (mp0) REVERT: O 111 GLU cc_start: 0.8207 (mp0) cc_final: 0.7998 (mp0) REVERT: O 115 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8615 (mmt90) outliers start: 108 outliers final: 32 residues processed: 493 average time/residue: 1.4031 time to fit residues: 791.2631 Evaluate side-chains 398 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 351 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain H residue 29 CYS Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 226 LEU Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 329 GLN Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 399 GLU Chi-restraints excluded: chain H residue 409 ARG Chi-restraints excluded: chain I residue 608 LYS Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 125 GLN Chi-restraints excluded: chain K residue 603 ILE Chi-restraints excluded: chain L residue 513 ILE Chi-restraints excluded: chain L residue 556 ASN Chi-restraints excluded: chain L residue 577 GLU Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 115 ARG Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 190 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 255 optimal weight: 9.9990 chunk 194 optimal weight: 0.0000 chunk 134 optimal weight: 0.0070 chunk 28 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 259 optimal weight: 3.9990 chunk 274 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 245 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 GLN C 112 GLN E 32 GLN G 42 ASN G 81 ASN H 443 ASN H 479 ASN H 551 GLN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 606 ASN J 119 HIS K 510 HIS ** K 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 438 ASN L 483 ASN L 574 ASN O 107 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24400 Z= 0.255 Angle : 0.581 8.276 33320 Z= 0.309 Chirality : 0.044 0.311 3870 Planarity : 0.004 0.057 3956 Dihedral : 14.926 179.525 4377 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.42 % Allowed : 27.32 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.40 (0.15), residues: 2762 helix: 1.20 (0.17), residues: 938 sheet: -0.44 (0.21), residues: 530 loop : -1.30 (0.16), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 535 HIS 0.009 0.001 HIS K 510 PHE 0.052 0.002 PHE A 51 TYR 0.012 0.001 TYR G 107 ARG 0.009 0.001 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 388 time to evaluate : 2.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.6875 (tpp) REVERT: A 18 LEU cc_start: 0.6431 (tp) cc_final: 0.5802 (mp) REVERT: A 166 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7484 (mtmt) REVERT: A 169 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7166 (mm-30) REVERT: B 28 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7350 (mttt) REVERT: B 79 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7775 (ttp80) REVERT: C 5 MET cc_start: 0.8584 (mtm) cc_final: 0.8099 (mtt) REVERT: D 3 LYS cc_start: 0.8087 (mtpp) cc_final: 0.7859 (mttt) REVERT: D 13 LYS cc_start: 0.8419 (tptt) cc_final: 0.8135 (ttpp) REVERT: D 75 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7558 (mm-30) REVERT: D 123 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: D 131 ASP cc_start: 0.8309 (t70) cc_final: 0.7883 (t70) REVERT: D 137 GLU cc_start: 0.8404 (pt0) cc_final: 0.8145 (pt0) REVERT: D 179 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8584 (ptpt) REVERT: E 66 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8440 (tttm) REVERT: E 127 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8385 (mmtm) REVERT: F 93 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.7321 (mpt) REVERT: F 123 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7927 (mt-10) REVERT: F 127 LYS cc_start: 0.8297 (mttp) cc_final: 0.7592 (mtmm) REVERT: G 191 PHE cc_start: 0.8209 (p90) cc_final: 0.7893 (p90) REVERT: H 99 ASP cc_start: 0.8515 (t70) cc_final: 0.8250 (t70) REVERT: H 130 ASP cc_start: 0.8083 (p0) cc_final: 0.7872 (p0) REVERT: H 152 SER cc_start: 0.8691 (OUTLIER) cc_final: 0.8470 (p) REVERT: H 395 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8410 (tt) REVERT: H 409 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.6356 (ttp-170) REVERT: I 451 ARG cc_start: 0.7497 (mtp180) cc_final: 0.7059 (mmm-85) REVERT: I 518 GLU cc_start: 0.7899 (tp30) cc_final: 0.7573 (tm-30) REVERT: J 13 LYS cc_start: 0.8544 (ttmm) cc_final: 0.8049 (ttpt) REVERT: J 28 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7577 (mtmt) REVERT: J 52 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8777 (tttt) REVERT: J 125 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7769 (mp10) REVERT: K 386 LEU cc_start: 0.8088 (mt) cc_final: 0.7819 (tt) REVERT: K 394 PHE cc_start: 0.8410 (m-80) cc_final: 0.7983 (m-80) REVERT: K 411 ILE cc_start: 0.8065 (mm) cc_final: 0.7834 (mp) REVERT: K 461 GLU cc_start: 0.7579 (tt0) cc_final: 0.7139 (tt0) REVERT: K 466 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7327 (tt) REVERT: L 512 LYS cc_start: 0.8847 (tppp) cc_final: 0.8615 (tppp) REVERT: L 513 ILE cc_start: 0.7716 (OUTLIER) cc_final: 0.7480 (mp) REVERT: L 515 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: L 524 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8365 (mttp) REVERT: L 548 TYR cc_start: 0.8357 (t80) cc_final: 0.8152 (t80) REVERT: L 577 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: O 115 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8537 (mmt90) outliers start: 103 outliers final: 37 residues processed: 463 average time/residue: 1.3688 time to fit residues: 723.7549 Evaluate side-chains 407 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 348 time to evaluate : 2.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain H residue 29 CYS Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 226 LEU Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 399 GLU Chi-restraints excluded: chain H residue 409 ARG Chi-restraints excluded: chain H residue 549 ILE Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 125 GLN Chi-restraints excluded: chain J residue 192 ASP Chi-restraints excluded: chain K residue 466 ILE Chi-restraints excluded: chain K residue 509 SER Chi-restraints excluded: chain K residue 603 ILE Chi-restraints excluded: chain L residue 462 LYS Chi-restraints excluded: chain L residue 513 ILE Chi-restraints excluded: chain L residue 515 GLU Chi-restraints excluded: chain L residue 524 LYS Chi-restraints excluded: chain L residue 556 ASN Chi-restraints excluded: chain L residue 577 GLU Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 115 ARG Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 190 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 228 optimal weight: 9.9990 chunk 155 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 204 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 234 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 140 optimal weight: 3.9990 chunk 246 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 GLN C 36 ASN C 178 ASN G 42 ASN G 81 ASN G 99 ASN ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 479 ASN H 542 GLN H 551 GLN I 438 ASN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 119 HIS J 178 ASN K 510 HIS ** K 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 574 ASN O 107 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 24400 Z= 0.368 Angle : 0.616 8.535 33320 Z= 0.325 Chirality : 0.045 0.260 3870 Planarity : 0.004 0.060 3956 Dihedral : 14.873 179.973 4377 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 5.02 % Allowed : 27.44 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.24 (0.15), residues: 2762 helix: 1.29 (0.17), residues: 937 sheet: -0.14 (0.22), residues: 488 loop : -1.23 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 535 HIS 0.006 0.001 HIS H 326 PHE 0.036 0.002 PHE A 167 TYR 0.025 0.002 TYR I 599 ARG 0.009 0.001 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 381 time to evaluate : 2.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7330 (OUTLIER) cc_final: 0.6947 (tpp) REVERT: A 18 LEU cc_start: 0.6490 (tp) cc_final: 0.5879 (mp) REVERT: A 167 PHE cc_start: 0.7763 (t80) cc_final: 0.7490 (t80) REVERT: A 169 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7248 (mp0) REVERT: B 68 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.6171 (mp0) REVERT: B 79 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7806 (ttp80) REVERT: C 5 MET cc_start: 0.8640 (mtm) cc_final: 0.8177 (mtt) REVERT: D 3 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7846 (mttm) REVERT: D 13 LYS cc_start: 0.8531 (tptt) cc_final: 0.8293 (ttpt) REVERT: D 75 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7591 (mm-30) REVERT: D 123 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7894 (mt-10) REVERT: D 137 GLU cc_start: 0.8494 (pt0) cc_final: 0.8270 (pt0) REVERT: E 29 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7665 (mm-30) REVERT: E 66 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8283 (tttp) REVERT: E 110 LYS cc_start: 0.8498 (ptmm) cc_final: 0.8186 (pttt) REVERT: E 127 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8332 (mmtm) REVERT: F 52 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8575 (tttt) REVERT: F 123 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7922 (mt-10) REVERT: F 127 LYS cc_start: 0.8300 (mttp) cc_final: 0.7808 (mtmt) REVERT: G 191 PHE cc_start: 0.8264 (p90) cc_final: 0.7956 (p90) REVERT: H 99 ASP cc_start: 0.8753 (t70) cc_final: 0.8460 (t0) REVERT: H 184 MET cc_start: 0.8266 (mtm) cc_final: 0.8040 (mtm) REVERT: H 395 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8394 (tt) REVERT: H 409 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.6351 (ttp-170) REVERT: I 451 ARG cc_start: 0.7645 (mtp180) cc_final: 0.7020 (mmm-85) REVERT: I 518 GLU cc_start: 0.7922 (tp30) cc_final: 0.7551 (tp30) REVERT: I 579 LEU cc_start: 0.8503 (mt) cc_final: 0.8296 (mt) REVERT: J 13 LYS cc_start: 0.8598 (ttmm) cc_final: 0.8101 (ttpt) REVERT: J 25 ARG cc_start: 0.8428 (ttp80) cc_final: 0.8004 (ttp80) REVERT: J 28 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7610 (mtmt) REVERT: J 52 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8670 (tttm) REVERT: J 125 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7796 (mp10) REVERT: K 191 TYR cc_start: 0.7585 (m-80) cc_final: 0.7299 (m-80) REVERT: K 386 LEU cc_start: 0.8106 (mt) cc_final: 0.7877 (tt) REVERT: K 411 ILE cc_start: 0.8070 (mm) cc_final: 0.7855 (mp) REVERT: K 461 GLU cc_start: 0.7584 (tt0) cc_final: 0.7149 (tt0) REVERT: K 466 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7515 (tt) REVERT: L 513 ILE cc_start: 0.7677 (OUTLIER) cc_final: 0.7468 (mp) REVERT: L 542 GLN cc_start: 0.8173 (mt0) cc_final: 0.7851 (mt0) REVERT: L 548 TYR cc_start: 0.8472 (t80) cc_final: 0.8254 (t80) REVERT: L 577 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: L 603 ILE cc_start: 0.8102 (pp) cc_final: 0.7878 (mm) REVERT: O 115 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8611 (mmt90) outliers start: 117 outliers final: 48 residues processed: 464 average time/residue: 1.4019 time to fit residues: 743.7304 Evaluate side-chains 412 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 346 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 52 LYS Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain H residue 29 CYS Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 190 ASP Chi-restraints excluded: chain H residue 226 LEU Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 399 GLU Chi-restraints excluded: chain H residue 408 LYS Chi-restraints excluded: chain H residue 409 ARG Chi-restraints excluded: chain I residue 477 ILE Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 125 GLN Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 466 ILE Chi-restraints excluded: chain K residue 509 SER Chi-restraints excluded: chain K residue 603 ILE Chi-restraints excluded: chain L residue 462 LYS Chi-restraints excluded: chain L residue 513 ILE Chi-restraints excluded: chain L residue 556 ASN Chi-restraints excluded: chain L residue 577 GLU Chi-restraints excluded: chain L residue 601 ILE Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 115 ARG Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 187 GLU Chi-restraints excluded: chain O residue 190 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 92 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 161 optimal weight: 20.0000 chunk 67 optimal weight: 0.5980 chunk 274 optimal weight: 1.9990 chunk 228 optimal weight: 6.9990 chunk 127 optimal weight: 0.0770 chunk 22 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 GLN E 32 GLN E 107 ASN F 107 ASN G 42 ASN G 81 ASN H 479 ASN I 438 ASN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 510 HIS ** K 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 574 ASN O 107 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24400 Z= 0.210 Angle : 0.557 7.443 33320 Z= 0.297 Chirality : 0.043 0.297 3870 Planarity : 0.004 0.060 3956 Dihedral : 14.925 179.778 4377 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.37 % Allowed : 28.39 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.02 (0.15), residues: 2762 helix: 1.53 (0.17), residues: 938 sheet: -0.05 (0.22), residues: 488 loop : -1.13 (0.16), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 535 HIS 0.005 0.001 HIS K 510 PHE 0.030 0.001 PHE A 51 TYR 0.019 0.001 TYR G 92 ARG 0.013 0.001 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 384 time to evaluate : 2.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.6923 (tpp) REVERT: A 18 LEU cc_start: 0.6491 (tp) cc_final: 0.5880 (mp) REVERT: A 167 PHE cc_start: 0.7807 (t80) cc_final: 0.7588 (t80) REVERT: A 169 GLU cc_start: 0.7280 (mt-10) cc_final: 0.7001 (mp0) REVERT: C 5 MET cc_start: 0.8619 (mtm) cc_final: 0.8179 (mtt) REVERT: D 3 LYS cc_start: 0.8101 (mtpp) cc_final: 0.7837 (mttm) REVERT: D 13 LYS cc_start: 0.8381 (tptt) cc_final: 0.8104 (ttpp) REVERT: D 75 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7514 (mm-30) REVERT: D 123 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7864 (mt-10) REVERT: E 29 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7733 (mm-30) REVERT: E 66 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8377 (tttm) REVERT: E 127 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8395 (mmtm) REVERT: E 154 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.7405 (mm-40) REVERT: F 93 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.7212 (mpt) REVERT: F 123 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7900 (mt-10) REVERT: F 127 LYS cc_start: 0.8332 (mttp) cc_final: 0.7616 (mtmm) REVERT: F 187 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7409 (pp20) REVERT: G 191 PHE cc_start: 0.8234 (p90) cc_final: 0.7966 (p90) REVERT: H 99 ASP cc_start: 0.8754 (t70) cc_final: 0.8489 (t0) REVERT: H 134 ILE cc_start: 0.8306 (pt) cc_final: 0.7996 (pt) REVERT: H 152 SER cc_start: 0.8686 (OUTLIER) cc_final: 0.8455 (p) REVERT: H 184 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7976 (mtm) REVERT: H 395 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8306 (tt) REVERT: H 409 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.6438 (ttp-170) REVERT: H 429 ILE cc_start: 0.6982 (OUTLIER) cc_final: 0.6436 (tp) REVERT: I 451 ARG cc_start: 0.7536 (mtp180) cc_final: 0.6963 (mmm-85) REVERT: I 477 ILE cc_start: 0.6811 (OUTLIER) cc_final: 0.6409 (mm) REVERT: I 518 GLU cc_start: 0.7822 (tp30) cc_final: 0.7459 (tp30) REVERT: I 579 LEU cc_start: 0.8488 (mt) cc_final: 0.8272 (mt) REVERT: J 13 LYS cc_start: 0.8524 (ttmm) cc_final: 0.7981 (ttpt) REVERT: J 28 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7544 (mtmt) REVERT: J 29 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7804 (mt-10) REVERT: J 52 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8546 (tttm) REVERT: K 191 TYR cc_start: 0.7575 (m-80) cc_final: 0.7266 (m-80) REVERT: K 394 PHE cc_start: 0.8437 (m-80) cc_final: 0.7997 (m-80) REVERT: K 411 ILE cc_start: 0.8108 (mm) cc_final: 0.7882 (mp) REVERT: K 461 GLU cc_start: 0.7491 (tt0) cc_final: 0.7087 (tt0) REVERT: K 466 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7382 (tt) REVERT: L 512 LYS cc_start: 0.8689 (tppp) cc_final: 0.8095 (tppt) REVERT: L 542 GLN cc_start: 0.8157 (mt0) cc_final: 0.7855 (mt0) REVERT: L 548 TYR cc_start: 0.8448 (t80) cc_final: 0.8199 (t80) REVERT: L 577 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7415 (mp0) REVERT: L 601 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7269 (pt) REVERT: O 87 CYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7258 (m) REVERT: O 115 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8530 (mmt90) outliers start: 102 outliers final: 34 residues processed: 457 average time/residue: 1.3175 time to fit residues: 694.3109 Evaluate side-chains 415 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 360 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue 29 CYS Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 184 MET Chi-restraints excluded: chain H residue 226 LEU Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 409 ARG Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain I residue 477 ILE Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain K residue 466 ILE Chi-restraints excluded: chain K residue 509 SER Chi-restraints excluded: chain K residue 603 ILE Chi-restraints excluded: chain L residue 515 GLU Chi-restraints excluded: chain L residue 556 ASN Chi-restraints excluded: chain L residue 577 GLU Chi-restraints excluded: chain L residue 601 ILE Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 87 CYS Chi-restraints excluded: chain O residue 115 ARG Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 187 GLU Chi-restraints excluded: chain O residue 190 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 264 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 156 optimal weight: 8.9990 chunk 200 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 231 optimal weight: 0.3980 chunk 153 optimal weight: 8.9990 chunk 273 optimal weight: 7.9990 chunk 171 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 GLN C 112 GLN E 32 GLN G 42 ASN G 81 ASN G 99 ASN ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 GLN H 479 ASN H 551 GLN I 438 ASN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 178 ASN K 510 HIS ** K 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 574 ASN O 107 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 24400 Z= 0.399 Angle : 0.626 9.332 33320 Z= 0.329 Chirality : 0.046 0.261 3870 Planarity : 0.004 0.061 3956 Dihedral : 14.830 179.898 4377 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.55 % Allowed : 28.52 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.08 (0.15), residues: 2762 helix: 1.46 (0.17), residues: 937 sheet: -0.17 (0.22), residues: 494 loop : -1.11 (0.16), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 535 HIS 0.004 0.001 HIS H 64 PHE 0.025 0.002 PHE A 51 TYR 0.026 0.002 TYR I 599 ARG 0.013 0.001 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 376 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.6798 (tpp) REVERT: A 18 LEU cc_start: 0.6513 (tp) cc_final: 0.5903 (mp) REVERT: A 167 PHE cc_start: 0.7794 (t80) cc_final: 0.7532 (t80) REVERT: A 169 GLU cc_start: 0.7280 (mt-10) cc_final: 0.7003 (mp0) REVERT: C 5 MET cc_start: 0.8629 (mtm) cc_final: 0.8211 (mtt) REVERT: C 76 SER cc_start: 0.8674 (p) cc_final: 0.8466 (t) REVERT: C 108 ASP cc_start: 0.8327 (t0) cc_final: 0.8124 (t0) REVERT: C 112 GLN cc_start: 0.8652 (mt0) cc_final: 0.8385 (mt0) REVERT: C 115 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.6610 (mtp85) REVERT: C 134 LYS cc_start: 0.8070 (tttp) cc_final: 0.7541 (mptt) REVERT: D 3 LYS cc_start: 0.8147 (mtpp) cc_final: 0.7839 (mttm) REVERT: D 13 LYS cc_start: 0.8491 (tptt) cc_final: 0.8260 (ttpt) REVERT: D 75 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7570 (mm-30) REVERT: D 123 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7951 (mt-10) REVERT: E 29 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7653 (mm-30) REVERT: E 110 LYS cc_start: 0.8533 (ptmm) cc_final: 0.8225 (pttt) REVERT: E 127 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8436 (mmtm) REVERT: E 154 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.7506 (mt0) REVERT: F 46 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8051 (mtpm) REVERT: F 52 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8631 (tttt) REVERT: F 123 GLU cc_start: 0.8243 (mt-10) cc_final: 0.8029 (mt-10) REVERT: F 127 LYS cc_start: 0.8297 (mttp) cc_final: 0.7853 (mtmt) REVERT: G 191 PHE cc_start: 0.8301 (p90) cc_final: 0.7997 (p90) REVERT: H 127 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7473 (pt0) REVERT: H 134 ILE cc_start: 0.8292 (pt) cc_final: 0.8019 (pt) REVERT: H 152 SER cc_start: 0.8705 (OUTLIER) cc_final: 0.8483 (p) REVERT: H 178 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7458 (mmm) REVERT: H 184 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7969 (mtm) REVERT: H 395 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8344 (tt) REVERT: H 409 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.6363 (ttp-170) REVERT: I 451 ARG cc_start: 0.7530 (mtp180) cc_final: 0.6970 (mmm-85) REVERT: I 518 GLU cc_start: 0.7842 (tp30) cc_final: 0.7483 (tp30) REVERT: I 579 LEU cc_start: 0.8500 (mt) cc_final: 0.8272 (mt) REVERT: J 13 LYS cc_start: 0.8609 (ttmm) cc_final: 0.8102 (ttpt) REVERT: J 28 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7554 (mtmt) REVERT: J 29 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7701 (mt-10) REVERT: J 52 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8677 (tttm) REVERT: K 191 TYR cc_start: 0.7599 (m-80) cc_final: 0.7323 (m-80) REVERT: K 411 ILE cc_start: 0.8083 (mm) cc_final: 0.7858 (mp) REVERT: K 461 GLU cc_start: 0.7615 (tt0) cc_final: 0.7173 (tt0) REVERT: K 466 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7507 (tt) REVERT: L 512 LYS cc_start: 0.8726 (tppp) cc_final: 0.7989 (tppt) REVERT: L 542 GLN cc_start: 0.8168 (mt0) cc_final: 0.7865 (mt0) REVERT: L 577 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7361 (mp0) REVERT: O 87 CYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7186 (m) REVERT: O 115 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8620 (mmt90) outliers start: 106 outliers final: 39 residues processed: 455 average time/residue: 1.3976 time to fit residues: 731.8533 Evaluate side-chains 400 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 341 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 46 LYS Chi-restraints excluded: chain F residue 52 LYS Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain H residue 29 CYS Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain H residue 184 MET Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 409 ARG Chi-restraints excluded: chain I residue 477 ILE Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 466 ILE Chi-restraints excluded: chain K residue 509 SER Chi-restraints excluded: chain K residue 603 ILE Chi-restraints excluded: chain L residue 462 LYS Chi-restraints excluded: chain L residue 577 GLU Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 87 CYS Chi-restraints excluded: chain O residue 115 ARG Chi-restraints excluded: chain O residue 190 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 169 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 chunk 163 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 174 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 215 optimal weight: 0.6980 chunk 249 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 GLN G 42 ASN G 81 ASN H 479 ASN I 438 ASN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 178 ASN K 510 HIS ** K 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 574 ASN L 606 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 24400 Z= 0.294 Angle : 0.597 7.932 33320 Z= 0.316 Chirality : 0.044 0.285 3870 Planarity : 0.004 0.062 3956 Dihedral : 14.868 179.718 4375 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.86 % Allowed : 29.72 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.01 (0.15), residues: 2762 helix: 1.55 (0.17), residues: 937 sheet: -0.18 (0.22), residues: 494 loop : -1.08 (0.16), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP L 535 HIS 0.004 0.001 HIS H 64 PHE 0.026 0.002 PHE A 51 TYR 0.019 0.001 TYR L 548 ARG 0.016 0.001 ARG H 131 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 361 time to evaluate : 2.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.6866 (tpp) REVERT: A 18 LEU cc_start: 0.6351 (tp) cc_final: 0.5777 (mp) REVERT: A 167 PHE cc_start: 0.7778 (t80) cc_final: 0.7479 (t80) REVERT: A 169 GLU cc_start: 0.7297 (mt-10) cc_final: 0.7027 (mp0) REVERT: B 79 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7823 (ttp80) REVERT: B 171 ASN cc_start: 0.7706 (m-40) cc_final: 0.7300 (t0) REVERT: C 5 MET cc_start: 0.8647 (mtm) cc_final: 0.8221 (mtt) REVERT: C 76 SER cc_start: 0.8652 (p) cc_final: 0.8434 (p) REVERT: C 112 GLN cc_start: 0.8614 (mt0) cc_final: 0.8350 (mt0) REVERT: C 116 GLU cc_start: 0.7900 (tt0) cc_final: 0.7651 (tm-30) REVERT: C 134 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7507 (mptt) REVERT: D 3 LYS cc_start: 0.8127 (mtpp) cc_final: 0.7827 (mttm) REVERT: D 13 LYS cc_start: 0.8442 (tptt) cc_final: 0.8199 (ttpt) REVERT: D 123 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7979 (mt-10) REVERT: D 137 GLU cc_start: 0.8566 (pt0) cc_final: 0.8321 (pm20) REVERT: E 29 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7672 (mm-30) REVERT: E 110 LYS cc_start: 0.8488 (ptmm) cc_final: 0.8189 (pttt) REVERT: E 127 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8455 (mmtm) REVERT: E 154 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.7512 (mm-40) REVERT: F 123 GLU cc_start: 0.8242 (mt-10) cc_final: 0.8025 (mt-10) REVERT: F 127 LYS cc_start: 0.8290 (mttp) cc_final: 0.7640 (mtmm) REVERT: F 187 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7410 (pp20) REVERT: G 191 PHE cc_start: 0.8283 (p90) cc_final: 0.8006 (p90) REVERT: H 134 ILE cc_start: 0.8233 (pt) cc_final: 0.7922 (pt) REVERT: H 152 SER cc_start: 0.8741 (OUTLIER) cc_final: 0.8509 (p) REVERT: H 395 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8232 (tt) REVERT: H 409 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.6471 (ttp-170) REVERT: I 451 ARG cc_start: 0.7504 (mtp180) cc_final: 0.7005 (mmm-85) REVERT: I 518 GLU cc_start: 0.7824 (tp30) cc_final: 0.7469 (tp30) REVERT: I 579 LEU cc_start: 0.8507 (mt) cc_final: 0.8293 (mt) REVERT: J 13 LYS cc_start: 0.8550 (ttmm) cc_final: 0.8026 (ttpt) REVERT: J 28 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7558 (mtmt) REVERT: J 52 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8592 (tttm) REVERT: K 191 TYR cc_start: 0.7643 (m-80) cc_final: 0.7418 (m-80) REVERT: K 411 ILE cc_start: 0.8080 (mm) cc_final: 0.7853 (mp) REVERT: K 461 GLU cc_start: 0.7608 (tt0) cc_final: 0.7164 (tt0) REVERT: K 466 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7523 (tt) REVERT: L 512 LYS cc_start: 0.8743 (tppp) cc_final: 0.7884 (tppt) REVERT: L 515 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7403 (mt-10) REVERT: L 542 GLN cc_start: 0.8168 (mt0) cc_final: 0.7873 (mt0) REVERT: L 577 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7395 (mp0) REVERT: O 87 CYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7241 (m) REVERT: O 115 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8561 (mmt90) outliers start: 90 outliers final: 38 residues processed: 424 average time/residue: 1.3520 time to fit residues: 657.8585 Evaluate side-chains 403 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 348 time to evaluate : 2.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue 29 CYS Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 190 ASP Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 408 LYS Chi-restraints excluded: chain H residue 409 ARG Chi-restraints excluded: chain I residue 477 ILE Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain K residue 466 ILE Chi-restraints excluded: chain K residue 509 SER Chi-restraints excluded: chain K residue 603 ILE Chi-restraints excluded: chain L residue 515 GLU Chi-restraints excluded: chain L residue 577 GLU Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 87 CYS Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain O residue 115 ARG Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 187 GLU Chi-restraints excluded: chain O residue 190 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 262 optimal weight: 5.9990 chunk 239 optimal weight: 5.9990 chunk 255 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 200 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 230 optimal weight: 10.0000 chunk 241 optimal weight: 6.9990 chunk 254 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 GLN B 178 ASN E 32 GLN G 42 ASN G 81 ASN G 99 ASN H 298 GLN H 479 ASN H 551 GLN I 438 ASN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 178 ASN K 510 HIS ** K 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 574 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 24400 Z= 0.367 Angle : 0.631 8.658 33320 Z= 0.333 Chirality : 0.046 0.268 3870 Planarity : 0.005 0.062 3956 Dihedral : 14.832 179.862 4375 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.73 % Allowed : 30.32 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.06 (0.15), residues: 2762 helix: 1.50 (0.17), residues: 939 sheet: -0.21 (0.22), residues: 495 loop : -1.11 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP L 535 HIS 0.004 0.001 HIS H 64 PHE 0.024 0.002 PHE A 51 TYR 0.028 0.002 TYR G 161 ARG 0.014 0.001 ARG K 409 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 371 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.6845 (tpp) REVERT: A 18 LEU cc_start: 0.6353 (tp) cc_final: 0.5789 (mp) REVERT: A 167 PHE cc_start: 0.7783 (t80) cc_final: 0.7523 (t80) REVERT: A 169 GLU cc_start: 0.7297 (mt-10) cc_final: 0.7019 (mp0) REVERT: B 79 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7787 (ttp80) REVERT: B 171 ASN cc_start: 0.7651 (m-40) cc_final: 0.7340 (t0) REVERT: C 5 MET cc_start: 0.8630 (mtm) cc_final: 0.8154 (mtt) REVERT: C 76 SER cc_start: 0.8682 (p) cc_final: 0.8469 (p) REVERT: C 112 GLN cc_start: 0.8609 (mt0) cc_final: 0.8349 (mt0) REVERT: C 115 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.6608 (mtp85) REVERT: C 116 GLU cc_start: 0.7971 (tt0) cc_final: 0.7157 (tm-30) REVERT: C 134 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7815 (mttm) REVERT: D 3 LYS cc_start: 0.8144 (mtpp) cc_final: 0.7832 (mttm) REVERT: D 13 LYS cc_start: 0.8496 (tptt) cc_final: 0.8255 (ttpt) REVERT: D 75 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7508 (mm-30) REVERT: D 123 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7951 (mm-30) REVERT: D 137 GLU cc_start: 0.8576 (pt0) cc_final: 0.8172 (pm20) REVERT: E 29 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7646 (mm-30) REVERT: E 110 LYS cc_start: 0.8546 (ptmm) cc_final: 0.8260 (pttt) REVERT: E 127 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8463 (mmtm) REVERT: E 154 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.7537 (mt0) REVERT: F 123 GLU cc_start: 0.8267 (mt-10) cc_final: 0.8055 (mt-10) REVERT: F 127 LYS cc_start: 0.8308 (mttp) cc_final: 0.7655 (mtmm) REVERT: F 187 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7435 (pp20) REVERT: G 191 PHE cc_start: 0.8298 (p90) cc_final: 0.8022 (p90) REVERT: H 102 ARG cc_start: 0.8091 (mtp-110) cc_final: 0.7646 (ttt90) REVERT: H 134 ILE cc_start: 0.8232 (pt) cc_final: 0.7949 (pt) REVERT: H 152 SER cc_start: 0.8803 (OUTLIER) cc_final: 0.8575 (p) REVERT: H 178 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7456 (mmm) REVERT: H 291 ILE cc_start: 0.7016 (OUTLIER) cc_final: 0.6642 (mm) REVERT: H 395 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8216 (tt) REVERT: H 409 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.6432 (ttp-170) REVERT: H 475 ASP cc_start: 0.6286 (m-30) cc_final: 0.5947 (t0) REVERT: I 451 ARG cc_start: 0.7483 (mtp180) cc_final: 0.6908 (mmm-85) REVERT: I 518 GLU cc_start: 0.7822 (tp30) cc_final: 0.7472 (tp30) REVERT: I 579 LEU cc_start: 0.8507 (mt) cc_final: 0.8302 (mt) REVERT: J 13 LYS cc_start: 0.8605 (ttmm) cc_final: 0.8093 (ttpt) REVERT: J 28 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7496 (mtmt) REVERT: J 29 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7945 (mt-10) REVERT: J 52 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8654 (tttm) REVERT: K 411 ILE cc_start: 0.8063 (mm) cc_final: 0.7823 (mp) REVERT: K 461 GLU cc_start: 0.7614 (tt0) cc_final: 0.7163 (tt0) REVERT: K 466 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7540 (tt) REVERT: L 512 LYS cc_start: 0.8710 (tppp) cc_final: 0.8002 (tppt) REVERT: L 542 GLN cc_start: 0.8195 (mt0) cc_final: 0.7893 (mt0) REVERT: L 577 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7394 (mp0) REVERT: O 87 CYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7212 (m) REVERT: O 115 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8609 (mmt90) outliers start: 87 outliers final: 40 residues processed: 432 average time/residue: 1.3646 time to fit residues: 674.7133 Evaluate side-chains 410 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 350 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain H residue 29 CYS Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 408 LYS Chi-restraints excluded: chain H residue 409 ARG Chi-restraints excluded: chain I residue 477 ILE Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 108 ASP Chi-restraints excluded: chain K residue 466 ILE Chi-restraints excluded: chain K residue 509 SER Chi-restraints excluded: chain K residue 603 ILE Chi-restraints excluded: chain L residue 556 ASN Chi-restraints excluded: chain L residue 577 GLU Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 87 CYS Chi-restraints excluded: chain O residue 115 ARG Chi-restraints excluded: chain O residue 190 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 269 optimal weight: 0.0170 chunk 164 optimal weight: 9.9990 chunk 127 optimal weight: 8.9990 chunk 187 optimal weight: 0.0020 chunk 282 optimal weight: 2.9990 chunk 260 optimal weight: 3.9990 chunk 225 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 174 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 178 optimal weight: 0.9990 overall best weight: 1.0030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 ASN E 32 GLN G 42 ASN G 81 ASN H 298 GLN H 479 ASN H 551 GLN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 178 ASN K 510 HIS ** K 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 574 ASN O 107 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24400 Z= 0.232 Angle : 0.599 9.415 33320 Z= 0.317 Chirality : 0.044 0.293 3870 Planarity : 0.004 0.063 3956 Dihedral : 14.896 179.377 4375 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.74 % Allowed : 31.43 % Favored : 65.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.08 (0.16), residues: 2762 helix: 1.68 (0.17), residues: 938 sheet: -0.19 (0.22), residues: 493 loop : -1.04 (0.16), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP L 535 HIS 0.004 0.001 HIS K 510 PHE 0.027 0.002 PHE G 74 TYR 0.023 0.001 TYR G 92 ARG 0.014 0.001 ARG H 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 364 time to evaluate : 2.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7209 (OUTLIER) cc_final: 0.6825 (tpp) REVERT: A 18 LEU cc_start: 0.6316 (tp) cc_final: 0.5738 (mp) REVERT: A 23 VAL cc_start: 0.6472 (OUTLIER) cc_final: 0.6261 (p) REVERT: A 85 VAL cc_start: 0.7699 (OUTLIER) cc_final: 0.7444 (p) REVERT: A 167 PHE cc_start: 0.7787 (t80) cc_final: 0.7511 (t80) REVERT: A 169 GLU cc_start: 0.7274 (mt-10) cc_final: 0.7000 (mp0) REVERT: B 171 ASN cc_start: 0.7615 (m-40) cc_final: 0.7358 (t0) REVERT: C 5 MET cc_start: 0.8630 (mtm) cc_final: 0.8194 (mtt) REVERT: C 111 GLU cc_start: 0.8303 (pm20) cc_final: 0.8016 (pm20) REVERT: C 112 GLN cc_start: 0.8609 (mt0) cc_final: 0.8372 (mt0) REVERT: C 116 GLU cc_start: 0.7941 (tt0) cc_final: 0.7638 (tm-30) REVERT: C 134 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7425 (mptt) REVERT: D 3 LYS cc_start: 0.8139 (mtpp) cc_final: 0.7860 (mttm) REVERT: D 13 LYS cc_start: 0.8411 (tptt) cc_final: 0.8117 (ttpp) REVERT: D 123 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7895 (mt-10) REVERT: D 137 GLU cc_start: 0.8477 (pt0) cc_final: 0.7951 (pm20) REVERT: E 29 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7666 (mm-30) REVERT: E 110 LYS cc_start: 0.8448 (ptmm) cc_final: 0.8157 (pttt) REVERT: E 127 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8571 (mmpt) REVERT: E 154 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.7481 (mm-40) REVERT: F 123 GLU cc_start: 0.8265 (mt-10) cc_final: 0.8035 (mt-10) REVERT: F 127 LYS cc_start: 0.8286 (mttp) cc_final: 0.7620 (mtmm) REVERT: F 187 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7402 (pp20) REVERT: G 191 PHE cc_start: 0.8268 (p90) cc_final: 0.8009 (p90) REVERT: H 102 ARG cc_start: 0.8070 (mtp-110) cc_final: 0.7649 (ttt90) REVERT: H 134 ILE cc_start: 0.8156 (pt) cc_final: 0.7843 (pt) REVERT: H 152 SER cc_start: 0.8735 (OUTLIER) cc_final: 0.8515 (p) REVERT: H 178 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7399 (mmm) REVERT: H 395 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8174 (tt) REVERT: H 475 ASP cc_start: 0.6282 (m-30) cc_final: 0.5927 (t0) REVERT: I 451 ARG cc_start: 0.7450 (mtp180) cc_final: 0.6955 (mmm-85) REVERT: I 518 GLU cc_start: 0.7796 (tp30) cc_final: 0.7450 (tp30) REVERT: I 579 LEU cc_start: 0.8508 (mt) cc_final: 0.8298 (mt) REVERT: J 13 LYS cc_start: 0.8527 (ttmm) cc_final: 0.7997 (ttpt) REVERT: J 28 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7572 (mtmt) REVERT: J 52 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8760 (tttt) REVERT: K 411 ILE cc_start: 0.8083 (mm) cc_final: 0.7881 (mp) REVERT: K 461 GLU cc_start: 0.7541 (tt0) cc_final: 0.7081 (tt0) REVERT: K 466 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7527 (tt) REVERT: L 542 GLN cc_start: 0.8187 (mt0) cc_final: 0.7878 (mt0) REVERT: L 577 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: O 87 CYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7264 (m) REVERT: O 115 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8535 (mmt90) outliers start: 64 outliers final: 34 residues processed: 408 average time/residue: 1.3552 time to fit residues: 633.4069 Evaluate side-chains 396 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 345 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain H residue 29 CYS Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 408 LYS Chi-restraints excluded: chain I residue 477 ILE Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 108 ASP Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain K residue 466 ILE Chi-restraints excluded: chain K residue 509 SER Chi-restraints excluded: chain K residue 603 ILE Chi-restraints excluded: chain L residue 577 GLU Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 87 CYS Chi-restraints excluded: chain O residue 115 ARG Chi-restraints excluded: chain O residue 187 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 240 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 231 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 GLN G 42 ASN G 81 ASN H 298 GLN H 479 ASN H 551 GLN I 438 ASN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 178 ASN K 510 HIS ** K 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 574 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.157761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.118278 restraints weight = 28147.945| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.32 r_work: 0.3089 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 24400 Z= 0.349 Angle : 0.631 8.711 33320 Z= 0.332 Chirality : 0.045 0.268 3870 Planarity : 0.005 0.063 3956 Dihedral : 14.835 179.649 4375 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.87 % Allowed : 31.65 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.04 (0.16), residues: 2762 helix: 1.62 (0.17), residues: 939 sheet: -0.19 (0.22), residues: 497 loop : -1.06 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP L 535 HIS 0.004 0.001 HIS H 64 PHE 0.025 0.002 PHE C 133 TYR 0.025 0.001 TYR L 548 ARG 0.015 0.001 ARG K 409 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10960.42 seconds wall clock time: 191 minutes 13.86 seconds (11473.86 seconds total)