Starting phenix.real_space_refine on Fri Sep 19 05:35:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yhd_39287/09_2025/8yhd_39287_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yhd_39287/09_2025/8yhd_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 { model { file = "/net/cci-nas-00/data/ceres_data/8yhd_39287/09_2025/8yhd_39287_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yhd_39287/09_2025/8yhd_39287_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yhd_39287/09_2025/8yhd_39287.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yhd_39287/09_2025/8yhd_39287.map" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 3, 'TYR:plan': 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: {'ARG:plan': 1, 'GLN:plan1': 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: {'PHE:plan': 3, 'ASN:plan1': 4, 'ARG:plan': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'TYR: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: {'GLU:plan': 7, 'ASN:plan1': 6, 'ASP:plan': 1, 'TYR:plan': 3, 'ARG:plan': 4, 'GLN:plan1': 1, 'HIS:plan': 1} 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: {'ARG:plan': 1, 'GLN:plan1': 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: {'GLU:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 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: 5.46, per 1000 atoms: 0.23 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: 1.58 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 2.63 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: 4.32 Time building geometry restraints manager: 2.21 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 \ 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 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: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 25.400 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.020 ------------------------------------------------------------------------------- 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 : 0.010 0.661 24439 Z= 0.532 Angle : 1.299 21.532 33368 Z= 0.767 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 : 9.30 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.024 0.002 ARG H 561 TYR 0.043 0.003 TYR G 137 PHE 0.060 0.004 PHE H 100 TRP 0.024 0.003 TRP L 535 HIS 0.011 0.003 HIS K 510 Details of bonding type rmsd covalent geometry : bond 0.00834 (24400) covalent geometry : angle 1.26451 (33320) hydrogen bonds : bond 0.14712 ( 1037) hydrogen bonds : angle 7.62776 ( 3063) metal coordination : bond 0.14314 ( 39) metal coordination : angle 7.89446 ( 48) *********************** 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 to be fit. rotamer outliers: 47 poor density : 744 time to evaluate : 0.894 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: 0.6706 time to fit residues: 582.5016 Evaluate side-chains 408 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 403 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.0170 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- 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 E 178 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 J 178 ASN 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.167786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.129605 restraints weight = 28392.298| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.36 r_work: 0.3259 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.627 24439 Z= 0.201 Angle : 0.681 14.690 33368 Z= 0.343 Chirality : 0.045 0.289 3870 Planarity : 0.005 0.068 3956 Dihedral : 15.122 179.115 4382 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.99 % Allowed : 28.09 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.15), residues: 2762 helix: 0.14 (0.16), residues: 938 sheet: -0.41 (0.22), residues: 510 loop : -1.75 (0.15), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 77 TYR 0.023 0.001 TYR G 137 PHE 0.039 0.002 PHE G 74 TRP 0.013 0.001 TRP I 478 HIS 0.003 0.001 HIS H 67 Details of bonding type rmsd covalent geometry : bond 0.00331 (24400) covalent geometry : angle 0.63681 (33320) hydrogen bonds : bond 0.04240 ( 1037) hydrogen bonds : angle 5.30667 ( 3063) metal coordination : bond 0.10136 ( 39) metal coordination : angle 6.36922 ( 48) *********************** 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 557 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 464 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.6887 (OUTLIER) cc_final: 0.6505 (tpp) REVERT: A 51 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7520 (t80) REVERT: A 55 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7633 (mm) REVERT: A 93 MET cc_start: 0.8149 (tpp) cc_final: 0.7794 (tpp) REVERT: A 165 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7662 (mt) REVERT: A 169 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7232 (mp0) REVERT: A 191 GLU cc_start: 0.8203 (tt0) cc_final: 0.7914 (tp30) REVERT: A 196 ASP cc_start: 0.7943 (p0) cc_final: 0.7462 (p0) REVERT: B 76 SER cc_start: 0.8235 (t) cc_final: 0.7971 (m) REVERT: C 36 ASN cc_start: 0.8342 (m-40) cc_final: 0.7840 (m110) REVERT: C 83 ARG cc_start: 0.8231 (mtm-85) cc_final: 0.7798 (ptp90) REVERT: C 123 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7304 (mm-30) REVERT: D 3 LYS cc_start: 0.7992 (mtpp) cc_final: 0.7705 (mttt) REVERT: D 123 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8034 (mt-10) REVERT: D 131 ASP cc_start: 0.8006 (t70) cc_final: 0.7653 (t0) REVERT: E 13 LYS cc_start: 0.8561 (ttpp) cc_final: 0.8150 (ttpp) REVERT: E 110 LYS cc_start: 0.8077 (ptmm) cc_final: 0.7814 (ptpt) REVERT: F 123 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7769 (mt-10) REVERT: F 127 LYS cc_start: 0.8213 (mttp) cc_final: 0.7386 (mtmt) REVERT: F 145 THR cc_start: 0.8486 (m) cc_final: 0.8224 (p) REVERT: G 25 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7673 (mm) REVERT: G 56 PHE cc_start: 0.7592 (t80) cc_final: 0.7168 (t80) REVERT: G 130 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7727 (mt-10) REVERT: H 240 TYR cc_start: 0.6474 (t80) cc_final: 0.6151 (t80) REVERT: H 253 ILE cc_start: 0.7379 (mt) cc_final: 0.7037 (mm) REVERT: H 443 ASN cc_start: 0.6697 (p0) cc_final: 0.6337 (m110) REVERT: H 596 ASN cc_start: 0.7901 (m-40) cc_final: 0.7375 (p0) REVERT: I 450 TYR cc_start: 0.5646 (m-80) cc_final: 0.5185 (m-10) REVERT: I 485 MET cc_start: 0.6410 (ttm) cc_final: 0.5447 (ttp) REVERT: I 512 LYS cc_start: 0.7925 (tppt) cc_final: 0.7645 (tptp) REVERT: I 518 GLU cc_start: 0.7925 (tp30) cc_final: 0.7165 (pt0) REVERT: J 5 MET cc_start: 0.8255 (mtm) cc_final: 0.7985 (mtm) REVERT: J 13 LYS cc_start: 0.8339 (ttmm) cc_final: 0.7609 (ttpt) REVERT: J 52 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8756 (tttt) REVERT: J 137 GLU cc_start: 0.8448 (pt0) cc_final: 0.8173 (pt0) REVERT: K 166 PHE cc_start: 0.6240 (m-80) cc_final: 0.5130 (p90) REVERT: K 386 LEU cc_start: 0.7958 (mt) cc_final: 0.7666 (tt) REVERT: K 394 PHE cc_start: 0.7572 (m-80) cc_final: 0.7244 (m-80) REVERT: K 461 GLU cc_start: 0.7597 (tt0) cc_final: 0.7156 (tt0) REVERT: K 529 ASN cc_start: 0.8404 (t0) cc_final: 0.7216 (m110) REVERT: K 597 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7179 (mtmm) REVERT: L 462 LYS cc_start: 0.5981 (mmmm) cc_final: 0.5574 (mmmm) REVERT: L 467 GLU cc_start: 0.6539 (pt0) cc_final: 0.6235 (pt0) REVERT: L 479 ASN cc_start: 0.8770 (m-40) cc_final: 0.8325 (m-40) REVERT: L 593 TYR cc_start: 0.6846 (m-10) cc_final: 0.6574 (m-10) REVERT: L 603 ILE cc_start: 0.7200 (pp) cc_final: 0.6927 (pt) REVERT: O 16 SER cc_start: 0.9101 (m) cc_final: 0.8878 (p) outliers start: 93 outliers final: 20 residues processed: 526 average time/residue: 0.6804 time to fit residues: 408.8639 Evaluate side-chains 401 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 372 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET 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 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 25 LEU 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 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 K residue 597 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 7 optimal weight: 7.9990 chunk 214 optimal weight: 8.9990 chunk 140 optimal weight: 7.9990 chunk 229 optimal weight: 1.9990 chunk 275 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 267 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 251 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 107 ASN C 112 GLN D 112 GLN E 32 GLN E 178 ASN F 171 ASN F 178 ASN G 42 ASN G 81 ASN ** G 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 HIS ** 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 112 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.158386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.119301 restraints weight = 28378.095| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.53 r_work: 0.3077 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 24439 Z= 0.301 Angle : 0.731 20.534 33368 Z= 0.360 Chirality : 0.048 0.262 3870 Planarity : 0.005 0.057 3956 Dihedral : 14.891 178.449 4377 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 5.23 % Allowed : 26.63 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.15), residues: 2762 helix: 0.68 (0.16), residues: 935 sheet: -0.53 (0.21), residues: 534 loop : -1.51 (0.15), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 77 TYR 0.023 0.002 TYR I 599 PHE 0.023 0.002 PHE C 133 TRP 0.018 0.002 TRP H 125 HIS 0.015 0.002 HIS H 64 Details of bonding type rmsd covalent geometry : bond 0.00694 (24400) covalent geometry : angle 0.67674 (33320) hydrogen bonds : bond 0.04065 ( 1037) hydrogen bonds : angle 5.02992 ( 3063) metal coordination : bond 0.01280 ( 39) metal coordination : angle 7.33047 ( 48) *********************** 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 536 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 414 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.6862 (OUTLIER) cc_final: 0.6468 (tpp) REVERT: A 18 LEU cc_start: 0.6273 (tp) cc_final: 0.5493 (mp) REVERT: A 51 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7825 (t80) REVERT: A 55 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7688 (mm) REVERT: A 60 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6689 (tt0) REVERT: A 73 THR cc_start: 0.8572 (m) cc_final: 0.8296 (p) REVERT: A 93 MET cc_start: 0.8245 (tpp) cc_final: 0.8001 (mmm) REVERT: A 165 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7474 (mt) REVERT: A 169 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7226 (mp0) REVERT: B 79 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7805 (ttp80) REVERT: C 5 MET cc_start: 0.8570 (mtm) cc_final: 0.8026 (mtt) REVERT: C 33 LYS cc_start: 0.8557 (mptt) cc_final: 0.8221 (ptmt) REVERT: C 36 ASN cc_start: 0.8512 (m110) cc_final: 0.8183 (m110) REVERT: C 83 ARG cc_start: 0.8081 (mtm-85) cc_final: 0.7655 (mtm-85) REVERT: C 85 VAL cc_start: 0.8167 (m) cc_final: 0.7932 (p) REVERT: C 116 GLU cc_start: 0.7901 (tt0) cc_final: 0.7692 (tt0) REVERT: D 3 LYS cc_start: 0.7971 (mtpp) cc_final: 0.7601 (mttm) REVERT: D 13 LYS cc_start: 0.8592 (tptt) cc_final: 0.8199 (ttpt) REVERT: D 75 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7806 (mm-30) REVERT: D 131 ASP cc_start: 0.8491 (t70) cc_final: 0.8090 (t70) REVERT: D 179 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8484 (ptpt) REVERT: E 83 ARG cc_start: 0.8148 (mtm110) cc_final: 0.7782 (ptp90) REVERT: E 127 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8321 (mmtm) REVERT: F 112 GLN cc_start: 0.8490 (mt0) cc_final: 0.8196 (mp10) REVERT: F 123 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8104 (mt-10) REVERT: F 127 LYS cc_start: 0.8359 (mttp) cc_final: 0.7550 (mtmt) REVERT: G 56 PHE cc_start: 0.7590 (t80) cc_final: 0.7328 (t80) REVERT: G 129 ASN cc_start: 0.6580 (OUTLIER) cc_final: 0.6316 (m110) REVERT: G 130 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7872 (mt-10) REVERT: H 99 ASP cc_start: 0.8626 (t70) cc_final: 0.8353 (t70) REVERT: H 152 SER cc_start: 0.8586 (OUTLIER) cc_final: 0.8180 (p) REVERT: H 253 ILE cc_start: 0.7408 (mt) cc_final: 0.6989 (mm) REVERT: H 395 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8077 (tt) REVERT: H 409 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.5678 (ttp-170) REVERT: H 429 ILE cc_start: 0.6993 (OUTLIER) cc_final: 0.6660 (tp) REVERT: H 596 ASN cc_start: 0.7985 (m-40) cc_final: 0.7372 (p0) REVERT: I 450 TYR cc_start: 0.5703 (m-80) cc_final: 0.5023 (m-10) REVERT: I 477 ILE cc_start: 0.6260 (tp) cc_final: 0.6014 (tt) REVERT: I 518 GLU cc_start: 0.7967 (tp30) cc_final: 0.7361 (tm-30) REVERT: J 13 LYS cc_start: 0.8632 (ttmm) cc_final: 0.7911 (ttpt) REVERT: J 28 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7401 (mtmt) REVERT: J 29 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7742 (mt-10) REVERT: J 52 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8638 (tttt) REVERT: J 68 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7598 (mm-30) REVERT: J 125 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8016 (mp10) REVERT: K 191 TYR cc_start: 0.7384 (m-80) cc_final: 0.7041 (m-80) REVERT: K 394 PHE cc_start: 0.7791 (m-80) cc_final: 0.7314 (m-80) REVERT: K 411 ILE cc_start: 0.7244 (mm) cc_final: 0.7029 (mp) REVERT: K 461 GLU cc_start: 0.7734 (tt0) cc_final: 0.7253 (tt0) REVERT: L 513 ILE cc_start: 0.7033 (OUTLIER) cc_final: 0.6821 (mp) REVERT: L 577 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: O 111 GLU cc_start: 0.8443 (mp0) cc_final: 0.8132 (mp0) REVERT: O 115 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8508 (mmt90) REVERT: O 127 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.7900 (mtpt) outliers start: 122 outliers final: 36 residues processed: 506 average time/residue: 0.6959 time to fit residues: 401.3985 Evaluate side-chains 403 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 346 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 60 GLU 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 39 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 179 LYS 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 57 SER Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 129 ASN 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 190 ASP 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 H residue 429 ILE Chi-restraints excluded: chain I residue 608 LYS 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 108 ASP Chi-restraints excluded: chain J residue 125 GLN Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain K residue 410 ILE 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 127 LYS Chi-restraints excluded: chain O residue 147 THR 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 160 optimal weight: 6.9990 chunk 105 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 199 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 174 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 166 optimal weight: 4.9990 chunk 223 optimal weight: 9.9990 chunk 156 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 F 178 ASN G 42 ASN G 81 ASN ** H 62 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 K 510 HIS ** K 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 574 ASN O 32 GLN O 107 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.162818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.123892 restraints weight = 28265.597| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.29 r_work: 0.3180 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24439 Z= 0.131 Angle : 0.608 15.802 33368 Z= 0.303 Chirality : 0.043 0.299 3870 Planarity : 0.004 0.055 3956 Dihedral : 14.940 179.511 4377 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.16 % Allowed : 27.96 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.15), residues: 2762 helix: 1.22 (0.17), residues: 938 sheet: -0.21 (0.22), residues: 500 loop : -1.27 (0.16), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 102 TYR 0.012 0.001 TYR G 107 PHE 0.026 0.002 PHE C 133 TRP 0.012 0.001 TRP L 535 HIS 0.009 0.001 HIS K 510 Details of bonding type rmsd covalent geometry : bond 0.00293 (24400) covalent geometry : angle 0.56397 (33320) hydrogen bonds : bond 0.03537 ( 1037) hydrogen bonds : angle 4.69734 ( 3063) metal coordination : bond 0.00787 ( 39) metal coordination : angle 6.00699 ( 48) *********************** 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 487 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 390 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.6902 (ttm) cc_final: 0.6539 (tpp) REVERT: A 18 LEU cc_start: 0.6217 (tp) cc_final: 0.5400 (mp) REVERT: A 51 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.7800 (t80) REVERT: A 55 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7752 (mm) REVERT: A 93 MET cc_start: 0.8320 (tpp) cc_final: 0.8038 (mmm) REVERT: A 165 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7604 (mt) REVERT: A 169 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7203 (mp0) REVERT: B 22 GLU cc_start: 0.8154 (tp30) cc_final: 0.7897 (tp30) REVERT: B 28 LYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6760 (mttt) REVERT: C 5 MET cc_start: 0.8576 (mtm) cc_final: 0.8007 (mtt) REVERT: C 33 LYS cc_start: 0.8512 (mptt) cc_final: 0.8182 (ptmt) REVERT: C 36 ASN cc_start: 0.8484 (m110) cc_final: 0.8269 (m110) REVERT: C 83 ARG cc_start: 0.8122 (mtm-85) cc_final: 0.7763 (ptp90) REVERT: C 85 VAL cc_start: 0.7876 (m) cc_final: 0.7631 (p) REVERT: C 108 ASP cc_start: 0.8282 (m-30) cc_final: 0.7870 (t0) REVERT: C 111 GLU cc_start: 0.8524 (pm20) cc_final: 0.8078 (pm20) REVERT: C 112 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.7860 (mt0) REVERT: D 3 LYS cc_start: 0.8000 (mtpp) cc_final: 0.7719 (mttt) REVERT: D 13 LYS cc_start: 0.8383 (tptt) cc_final: 0.7960 (ttpp) REVERT: D 131 ASP cc_start: 0.8251 (t70) cc_final: 0.7788 (t70) REVERT: F 93 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.7212 (mpt) REVERT: F 112 GLN cc_start: 0.8479 (mt0) cc_final: 0.8095 (mp10) REVERT: F 123 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8064 (mt-10) REVERT: F 127 LYS cc_start: 0.8332 (mttp) cc_final: 0.7487 (mtmm) REVERT: F 145 THR cc_start: 0.8620 (m) cc_final: 0.8337 (p) REVERT: G 129 ASN cc_start: 0.6772 (OUTLIER) cc_final: 0.6395 (m110) REVERT: G 130 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7773 (mt-10) REVERT: G 132 GLU cc_start: 0.7262 (pp20) cc_final: 0.6998 (pp20) REVERT: G 191 PHE cc_start: 0.7670 (p90) cc_final: 0.7279 (p90) REVERT: H 99 ASP cc_start: 0.8656 (t70) cc_final: 0.8360 (t70) REVERT: H 152 SER cc_start: 0.8454 (OUTLIER) cc_final: 0.8204 (p) REVERT: H 395 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.7998 (tt) REVERT: H 409 ARG cc_start: 0.6874 (OUTLIER) cc_final: 0.5646 (ttp-170) REVERT: H 456 SER cc_start: 0.7403 (p) cc_final: 0.7200 (p) REVERT: H 596 ASN cc_start: 0.7996 (m-40) cc_final: 0.7414 (p0) REVERT: I 450 TYR cc_start: 0.5504 (m-80) cc_final: 0.5010 (m-10) REVERT: I 451 ARG cc_start: 0.7359 (mtp180) cc_final: 0.6775 (mmm-85) REVERT: I 477 ILE cc_start: 0.6271 (tp) cc_final: 0.6033 (tt) REVERT: I 518 GLU cc_start: 0.7917 (tp30) cc_final: 0.7347 (tm-30) REVERT: J 13 LYS cc_start: 0.8563 (ttmm) cc_final: 0.7845 (ttpt) REVERT: J 52 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8611 (tttt) REVERT: J 125 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8060 (mp10) REVERT: K 166 PHE cc_start: 0.6277 (m-80) cc_final: 0.5345 (p90) REVERT: K 461 GLU cc_start: 0.7673 (tt0) cc_final: 0.7196 (tt0) REVERT: K 466 ILE cc_start: 0.7246 (OUTLIER) cc_final: 0.6900 (tt) REVERT: L 512 LYS cc_start: 0.8524 (tppp) cc_final: 0.8258 (tppp) REVERT: L 513 ILE cc_start: 0.7033 (OUTLIER) cc_final: 0.6800 (mp) REVERT: L 524 LYS cc_start: 0.8332 (mttp) cc_final: 0.8096 (mmtm) REVERT: L 548 TYR cc_start: 0.8001 (t80) cc_final: 0.7789 (t80) REVERT: L 577 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7266 (mp0) REVERT: O 59 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7936 (mt) REVERT: O 93 MET cc_start: 0.8291 (tpt) cc_final: 0.8006 (mmm) REVERT: O 115 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8497 (mmt90) outliers start: 97 outliers final: 27 residues processed: 461 average time/residue: 0.6775 time to fit residues: 355.9131 Evaluate side-chains 390 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 346 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 104 LEU 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 195 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 129 ASN 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 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 52 LYS Chi-restraints excluded: chain J residue 125 GLN 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 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 59 LEU Chi-restraints excluded: chain O residue 115 ARG Chi-restraints excluded: chain O residue 147 THR 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 90 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 250 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 45 optimal weight: 0.0370 chunk 10 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 GLN C 178 ASN F 178 ASN G 42 ASN G 81 ASN G 99 ASN ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 479 ASN H 551 GLN I 438 ASN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 178 ASN ** K 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 574 ASN L 606 ASN O 32 GLN O 107 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.156642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.117447 restraints weight = 28179.414| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.47 r_work: 0.3057 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 24439 Z= 0.292 Angle : 0.697 20.391 33368 Z= 0.344 Chirality : 0.047 0.254 3870 Planarity : 0.005 0.058 3956 Dihedral : 14.880 179.938 4377 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 5.06 % Allowed : 28.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.15), residues: 2762 helix: 1.25 (0.17), residues: 936 sheet: -0.29 (0.22), residues: 501 loop : -1.23 (0.16), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 95 TYR 0.027 0.002 TYR I 599 PHE 0.033 0.002 PHE A 167 TRP 0.016 0.002 TRP H 125 HIS 0.006 0.001 HIS H 326 Details of bonding type rmsd covalent geometry : bond 0.00674 (24400) covalent geometry : angle 0.64883 (33320) hydrogen bonds : bond 0.03814 ( 1037) hydrogen bonds : angle 4.84000 ( 3063) metal coordination : bond 0.01503 ( 39) metal coordination : angle 6.76896 ( 48) *********************** 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 492 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 374 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.6905 (OUTLIER) cc_final: 0.6406 (tpp) REVERT: A 18 LEU cc_start: 0.6271 (tp) cc_final: 0.5485 (mp) REVERT: A 51 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7878 (t80) REVERT: A 55 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7785 (mm) REVERT: A 93 MET cc_start: 0.8373 (tpp) cc_final: 0.8031 (mmm) REVERT: A 157 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8342 (p0) REVERT: A 169 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7193 (mp0) REVERT: B 19 TYR cc_start: 0.8928 (t80) cc_final: 0.8724 (t80) REVERT: B 79 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7799 (ttp80) REVERT: C 5 MET cc_start: 0.8568 (mtm) cc_final: 0.8049 (mtt) REVERT: C 33 LYS cc_start: 0.8671 (mptt) cc_final: 0.8235 (ptmt) REVERT: C 76 SER cc_start: 0.8547 (p) cc_final: 0.8290 (m) REVERT: C 83 ARG cc_start: 0.8062 (mtm-85) cc_final: 0.7602 (mtm-85) REVERT: C 85 VAL cc_start: 0.8071 (m) cc_final: 0.7854 (p) REVERT: C 108 ASP cc_start: 0.8353 (m-30) cc_final: 0.7925 (t0) REVERT: C 112 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8175 (mt0) REVERT: C 156 LYS cc_start: 0.8274 (mttt) cc_final: 0.7565 (pttp) REVERT: D 3 LYS cc_start: 0.8058 (mtpp) cc_final: 0.7652 (mttm) REVERT: D 13 LYS cc_start: 0.8676 (tptt) cc_final: 0.8283 (ttpt) REVERT: D 75 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7850 (mm-30) REVERT: D 111 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7992 (mt-10) REVERT: D 123 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8066 (mt-10) REVERT: E 29 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7750 (mm-30) REVERT: E 87 CYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8465 (m) REVERT: E 110 LYS cc_start: 0.8483 (ptmm) cc_final: 0.8103 (pttt) REVERT: E 127 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8370 (mmtm) REVERT: F 112 GLN cc_start: 0.8490 (mt0) cc_final: 0.8217 (mp10) REVERT: F 123 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8183 (mt-10) REVERT: F 127 LYS cc_start: 0.8331 (mttp) cc_final: 0.7728 (mtmt) REVERT: F 187 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7416 (pp20) REVERT: G 129 ASN cc_start: 0.6714 (OUTLIER) cc_final: 0.6295 (m110) REVERT: G 130 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7748 (mt-10) REVERT: G 132 GLU cc_start: 0.7240 (pp20) cc_final: 0.6884 (pp20) REVERT: H 99 ASP cc_start: 0.8870 (t70) cc_final: 0.8558 (t0) REVERT: H 127 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7614 (pt0) REVERT: H 131 ARG cc_start: 0.7379 (mmt180) cc_final: 0.7076 (mmt180) REVERT: H 152 SER cc_start: 0.8578 (OUTLIER) cc_final: 0.8273 (p) REVERT: H 184 MET cc_start: 0.7740 (mtm) cc_final: 0.7271 (mtm) REVERT: H 409 ARG cc_start: 0.6909 (OUTLIER) cc_final: 0.5671 (ttp-170) REVERT: H 596 ASN cc_start: 0.8012 (m-40) cc_final: 0.7388 (p0) REVERT: I 450 TYR cc_start: 0.5678 (m-80) cc_final: 0.4953 (m-10) REVERT: I 451 ARG cc_start: 0.7685 (mtp180) cc_final: 0.7026 (mmm-85) REVERT: I 477 ILE cc_start: 0.6288 (tp) cc_final: 0.6029 (tt) REVERT: I 518 GLU cc_start: 0.7923 (tp30) cc_final: 0.7504 (tp30) REVERT: I 579 LEU cc_start: 0.8222 (mt) cc_final: 0.8002 (mt) REVERT: J 13 LYS cc_start: 0.8634 (ttmm) cc_final: 0.7925 (ttpt) REVERT: J 28 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7438 (mtmt) REVERT: J 29 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7703 (mt-10) REVERT: J 52 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8689 (tttm) REVERT: K 461 GLU cc_start: 0.7695 (tt0) cc_final: 0.7224 (tt0) REVERT: K 466 ILE cc_start: 0.7361 (OUTLIER) cc_final: 0.7080 (tt) REVERT: L 512 LYS cc_start: 0.8667 (tppp) cc_final: 0.7959 (tppt) REVERT: L 513 ILE cc_start: 0.7068 (OUTLIER) cc_final: 0.6845 (mp) REVERT: L 524 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8120 (mttp) REVERT: L 542 GLN cc_start: 0.7807 (mt0) cc_final: 0.7412 (mt0) REVERT: L 548 TYR cc_start: 0.8154 (t80) cc_final: 0.7902 (t80) REVERT: L 577 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: L 603 ILE cc_start: 0.7697 (pp) cc_final: 0.7461 (mm) REVERT: O 9 TYR cc_start: 0.8386 (m-80) cc_final: 0.8156 (m-80) REVERT: O 93 MET cc_start: 0.8364 (tpt) cc_final: 0.8029 (mmm) REVERT: O 111 GLU cc_start: 0.8339 (mp0) cc_final: 0.8120 (mp0) REVERT: O 115 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8703 (mmt90) REVERT: O 127 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7931 (mtpt) outliers start: 118 outliers final: 39 residues processed: 456 average time/residue: 0.7163 time to fit residues: 370.7019 Evaluate side-chains 404 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 342 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 51 PHE Chi-restraints excluded: chain A residue 55 LEU 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 157 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 70 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 112 GLN 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 E residue 68 GLU Chi-restraints excluded: chain E residue 87 CYS 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 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 G residue 129 ASN 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 129 ASP Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 239 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 J residue 28 LYS Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 158 LEU 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 515 GLU Chi-restraints excluded: chain L residue 524 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 59 LEU Chi-restraints excluded: chain O residue 115 ARG Chi-restraints excluded: chain O residue 127 LYS Chi-restraints excluded: chain O residue 147 THR 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 176 optimal weight: 0.8980 chunk 129 optimal weight: 20.0000 chunk 175 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 277 optimal weight: 4.9990 chunk 5 optimal weight: 30.0000 chunk 153 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 overall best weight: 1.6782 ------------------------------------------------------------------------------- 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 G 42 ASN G 81 ASN ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 479 ASN H 551 GLN I 438 ASN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 178 ASN ** K 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 438 ASN L 574 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.158586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.119226 restraints weight = 28208.179| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.24 r_work: 0.3109 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 24439 Z= 0.192 Angle : 0.630 18.788 33368 Z= 0.313 Chirality : 0.044 0.289 3870 Planarity : 0.004 0.059 3956 Dihedral : 14.901 179.646 4377 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.12 % Allowed : 29.25 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.15), residues: 2762 helix: 1.43 (0.17), residues: 936 sheet: -0.24 (0.22), residues: 493 loop : -1.14 (0.16), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 102 TYR 0.018 0.001 TYR G 161 PHE 0.026 0.002 PHE A 167 TRP 0.019 0.001 TRP L 535 HIS 0.004 0.001 HIS K 510 Details of bonding type rmsd covalent geometry : bond 0.00444 (24400) covalent geometry : angle 0.58471 (33320) hydrogen bonds : bond 0.03506 ( 1037) hydrogen bonds : angle 4.70948 ( 3063) metal coordination : bond 0.00952 ( 39) metal coordination : angle 6.22711 ( 48) *********************** 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 465 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 369 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.6909 (OUTLIER) cc_final: 0.6433 (tpp) REVERT: A 18 LEU cc_start: 0.6183 (tp) cc_final: 0.5402 (mp) REVERT: A 51 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7880 (t80) REVERT: A 55 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7707 (mm) REVERT: A 93 MET cc_start: 0.8411 (tpp) cc_final: 0.8040 (mmm) REVERT: A 157 ASP cc_start: 0.8716 (OUTLIER) cc_final: 0.8401 (p0) REVERT: A 169 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7074 (mp0) REVERT: B 79 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7765 (ttp80) REVERT: C 5 MET cc_start: 0.8546 (mtm) cc_final: 0.8004 (mtt) REVERT: C 33 LYS cc_start: 0.8640 (mptt) cc_final: 0.8197 (ptmt) REVERT: C 36 ASN cc_start: 0.8534 (m110) cc_final: 0.8310 (m110) REVERT: C 76 SER cc_start: 0.8526 (p) cc_final: 0.8223 (m) REVERT: C 83 ARG cc_start: 0.8091 (mtm-85) cc_final: 0.7618 (mtm-85) REVERT: C 85 VAL cc_start: 0.7971 (m) cc_final: 0.7755 (p) REVERT: C 108 ASP cc_start: 0.8362 (m-30) cc_final: 0.7948 (t0) REVERT: C 109 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.7982 (m) REVERT: C 111 GLU cc_start: 0.8540 (pm20) cc_final: 0.7878 (pm20) REVERT: C 112 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8194 (mt0) REVERT: C 156 LYS cc_start: 0.8266 (mttt) cc_final: 0.7564 (pttp) REVERT: D 3 LYS cc_start: 0.8027 (mtpp) cc_final: 0.7626 (mttm) REVERT: D 13 LYS cc_start: 0.8532 (tptt) cc_final: 0.8111 (ttpt) REVERT: D 123 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8023 (mt-10) REVERT: E 29 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7702 (mm-30) REVERT: E 87 CYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8426 (m) REVERT: E 110 LYS cc_start: 0.8403 (ptmm) cc_final: 0.8040 (pttt) REVERT: E 127 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8341 (mmtm) REVERT: E 154 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.7558 (mm-40) REVERT: F 93 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7238 (mpt) REVERT: F 112 GLN cc_start: 0.8385 (mt0) cc_final: 0.8107 (mp10) REVERT: F 115 ARG cc_start: 0.8964 (mmt-90) cc_final: 0.8707 (mmt-90) REVERT: F 123 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8024 (mt-10) REVERT: F 127 LYS cc_start: 0.8287 (mttp) cc_final: 0.7477 (mtmm) REVERT: F 187 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7293 (pp20) REVERT: G 129 ASN cc_start: 0.6730 (OUTLIER) cc_final: 0.6332 (m110) REVERT: G 130 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7755 (mt-10) REVERT: G 132 GLU cc_start: 0.7318 (pp20) cc_final: 0.7047 (pp20) REVERT: G 191 PHE cc_start: 0.7694 (p90) cc_final: 0.7296 (p90) REVERT: H 134 ILE cc_start: 0.8100 (pt) cc_final: 0.7869 (pt) REVERT: H 152 SER cc_start: 0.8537 (OUTLIER) cc_final: 0.8260 (p) REVERT: H 395 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7841 (tt) REVERT: H 409 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.5606 (ttp-170) REVERT: H 596 ASN cc_start: 0.8001 (m-40) cc_final: 0.7386 (p0) REVERT: I 450 TYR cc_start: 0.5648 (m-80) cc_final: 0.5049 (m-10) REVERT: I 451 ARG cc_start: 0.7631 (mtp180) cc_final: 0.6953 (mmm-85) REVERT: I 477 ILE cc_start: 0.6285 (tp) cc_final: 0.6027 (tt) REVERT: I 518 GLU cc_start: 0.7797 (tp30) cc_final: 0.7392 (tp30) REVERT: I 579 LEU cc_start: 0.8248 (mt) cc_final: 0.8037 (mt) REVERT: J 13 LYS cc_start: 0.8618 (ttmm) cc_final: 0.7885 (ttpt) REVERT: J 25 ARG cc_start: 0.8409 (ttp80) cc_final: 0.7982 (ttp80) REVERT: J 28 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7373 (mtmt) REVERT: J 29 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7651 (mt-10) REVERT: J 52 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8652 (tttt) REVERT: K 461 GLU cc_start: 0.7665 (tt0) cc_final: 0.7209 (tt0) REVERT: K 466 ILE cc_start: 0.7318 (OUTLIER) cc_final: 0.7065 (tt) REVERT: L 512 LYS cc_start: 0.8690 (tppp) cc_final: 0.7972 (tppt) REVERT: L 513 ILE cc_start: 0.7129 (OUTLIER) cc_final: 0.6914 (mp) REVERT: L 542 GLN cc_start: 0.7813 (mt0) cc_final: 0.7408 (mt0) REVERT: L 548 TYR cc_start: 0.8136 (t80) cc_final: 0.7884 (t80) REVERT: L 577 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7231 (mp0) REVERT: L 603 ILE cc_start: 0.7712 (pp) cc_final: 0.7470 (mm) REVERT: O 32 GLN cc_start: 0.8276 (mm110) cc_final: 0.8047 (mm110) REVERT: O 87 CYS cc_start: 0.7290 (OUTLIER) cc_final: 0.6743 (m) REVERT: O 93 MET cc_start: 0.8358 (tpt) cc_final: 0.8043 (mmm) REVERT: O 111 GLU cc_start: 0.8349 (mp0) cc_final: 0.8071 (mp0) REVERT: O 115 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8480 (mmt90) outliers start: 96 outliers final: 34 residues processed: 438 average time/residue: 0.6872 time to fit residues: 342.2050 Evaluate side-chains 408 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 350 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 51 PHE Chi-restraints excluded: chain A residue 55 LEU 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 157 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 ARG 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 109 THR Chi-restraints excluded: chain C residue 112 GLN 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 123 GLU Chi-restraints excluded: chain E residue 87 CYS 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 39 VAL 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 47 ILE Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 129 ASN 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 239 LEU 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 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 466 ILE Chi-restraints excluded: chain K residue 509 SER Chi-restraints excluded: chain K residue 603 ILE Chi-restraints excluded: chain L residue 513 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 O residue 10 VAL Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 87 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 5 optimal weight: 20.0000 chunk 57 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 240 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 chunk 218 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 G 42 ASN G 81 ASN ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 GLN H 479 ASN H 542 GLN H 551 GLN I 438 ASN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 178 ASN ** K 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 574 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.158118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.118610 restraints weight = 28268.348| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.38 r_work: 0.3091 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 24439 Z= 0.207 Angle : 0.633 18.803 33368 Z= 0.314 Chirality : 0.044 0.274 3870 Planarity : 0.004 0.059 3956 Dihedral : 14.854 179.631 4377 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.63 % Allowed : 28.56 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.15), residues: 2762 helix: 1.50 (0.17), residues: 936 sheet: -0.24 (0.22), residues: 493 loop : -1.10 (0.16), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 102 TYR 0.025 0.001 TYR I 599 PHE 0.025 0.002 PHE C 133 TRP 0.021 0.001 TRP L 535 HIS 0.004 0.001 HIS K 510 Details of bonding type rmsd covalent geometry : bond 0.00478 (24400) covalent geometry : angle 0.58837 (33320) hydrogen bonds : bond 0.03474 ( 1037) hydrogen bonds : angle 4.66775 ( 3063) metal coordination : bond 0.00979 ( 39) metal coordination : angle 6.20182 ( 48) *********************** 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 472 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 364 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.6891 (OUTLIER) cc_final: 0.6435 (tpp) REVERT: A 18 LEU cc_start: 0.6175 (tp) cc_final: 0.5390 (mp) REVERT: A 51 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.7855 (t80) REVERT: A 55 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7657 (mm) REVERT: A 93 MET cc_start: 0.8332 (tpp) cc_final: 0.7932 (mmm) REVERT: A 157 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.8414 (p0) REVERT: A 169 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7068 (mp0) REVERT: B 79 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7781 (ttp80) REVERT: B 171 ASN cc_start: 0.7732 (m-40) cc_final: 0.7077 (t0) REVERT: C 5 MET cc_start: 0.8604 (mtm) cc_final: 0.8058 (mtt) REVERT: C 33 LYS cc_start: 0.8649 (mptt) cc_final: 0.8235 (ptmt) REVERT: C 76 SER cc_start: 0.8571 (p) cc_final: 0.8342 (p) REVERT: C 83 ARG cc_start: 0.8117 (mtm-85) cc_final: 0.7648 (mtm-85) REVERT: C 85 VAL cc_start: 0.8010 (m) cc_final: 0.7793 (p) REVERT: C 108 ASP cc_start: 0.8428 (m-30) cc_final: 0.7963 (t0) REVERT: C 112 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8064 (mt0) REVERT: C 156 LYS cc_start: 0.8240 (mttt) cc_final: 0.7606 (pttp) REVERT: D 3 LYS cc_start: 0.8074 (mtpp) cc_final: 0.7679 (mttm) REVERT: D 13 LYS cc_start: 0.8561 (tptt) cc_final: 0.8056 (ttpp) REVERT: D 111 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7852 (pm20) REVERT: D 123 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8079 (mt-10) REVERT: D 137 GLU cc_start: 0.8609 (pt0) cc_final: 0.8377 (pm20) REVERT: E 29 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7709 (mm-30) REVERT: E 68 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7804 (mt-10) REVERT: E 87 CYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8452 (m) REVERT: E 110 LYS cc_start: 0.8441 (ptmm) cc_final: 0.8063 (pttt) REVERT: E 127 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8417 (mmtm) REVERT: E 154 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.7595 (mm-40) REVERT: F 93 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7271 (mpt) REVERT: F 112 GLN cc_start: 0.8406 (mt0) cc_final: 0.8115 (mp10) REVERT: F 123 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8202 (mt-10) REVERT: F 127 LYS cc_start: 0.8306 (mttp) cc_final: 0.7495 (mtmm) REVERT: F 187 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7411 (pp20) REVERT: G 129 ASN cc_start: 0.6661 (OUTLIER) cc_final: 0.6259 (m110) REVERT: G 130 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7876 (mt-10) REVERT: G 132 GLU cc_start: 0.7287 (pp20) cc_final: 0.7024 (pp20) REVERT: G 191 PHE cc_start: 0.7752 (p90) cc_final: 0.7332 (p90) REVERT: H 134 ILE cc_start: 0.8085 (pt) cc_final: 0.7859 (pt) REVERT: H 152 SER cc_start: 0.8550 (OUTLIER) cc_final: 0.8277 (p) REVERT: H 178 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.7211 (mmm) REVERT: H 395 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7796 (tt) REVERT: H 404 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7645 (mm-30) REVERT: H 409 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.5726 (ttp-170) REVERT: H 596 ASN cc_start: 0.8009 (m-40) cc_final: 0.7369 (p0) REVERT: I 450 TYR cc_start: 0.5746 (m-80) cc_final: 0.5150 (m-10) REVERT: I 451 ARG cc_start: 0.7572 (mtp180) cc_final: 0.6953 (mmm-85) REVERT: I 477 ILE cc_start: 0.6287 (tp) cc_final: 0.6028 (tt) REVERT: I 518 GLU cc_start: 0.7791 (tp30) cc_final: 0.7403 (tp30) REVERT: I 579 LEU cc_start: 0.8269 (mt) cc_final: 0.8051 (mt) REVERT: J 13 LYS cc_start: 0.8627 (ttmm) cc_final: 0.7891 (ttpt) REVERT: J 25 ARG cc_start: 0.8402 (ttp80) cc_final: 0.7922 (ttp80) REVERT: J 28 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7375 (mtmt) REVERT: J 29 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7703 (mt-10) REVERT: J 52 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8595 (tttm) REVERT: K 394 PHE cc_start: 0.7745 (m-80) cc_final: 0.7397 (m-80) REVERT: K 461 GLU cc_start: 0.7688 (tt0) cc_final: 0.7163 (tt0) REVERT: K 466 ILE cc_start: 0.7328 (OUTLIER) cc_final: 0.7051 (tt) REVERT: L 513 ILE cc_start: 0.7091 (OUTLIER) cc_final: 0.6889 (mp) REVERT: L 515 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7485 (mt-10) REVERT: L 542 GLN cc_start: 0.7808 (mt0) cc_final: 0.7411 (mt0) REVERT: L 548 TYR cc_start: 0.8198 (t80) cc_final: 0.7936 (t80) REVERT: L 577 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: L 594 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7811 (t70) REVERT: L 595 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.6872 (ttpt) REVERT: O 87 CYS cc_start: 0.7284 (OUTLIER) cc_final: 0.6717 (m) REVERT: O 93 MET cc_start: 0.8407 (tpt) cc_final: 0.8104 (mmm) REVERT: O 111 GLU cc_start: 0.8385 (mp0) cc_final: 0.8075 (mp0) REVERT: O 115 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8540 (mmt90) outliers start: 108 outliers final: 39 residues processed: 445 average time/residue: 0.6875 time to fit residues: 347.2548 Evaluate side-chains 407 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 340 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 51 PHE Chi-restraints excluded: chain A residue 55 LEU 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 157 ASP Chi-restraints excluded: chain B residue 39 VAL 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 147 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 126 THR 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 123 GLU Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 87 CYS 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 93 MET 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 47 ILE Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain H residue 29 CYS Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 128 ILE 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 409 ARG Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 52 LYS 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 436 VAL Chi-restraints excluded: chain L residue 513 ILE Chi-restraints excluded: chain L residue 515 GLU Chi-restraints excluded: chain L residue 577 GLU Chi-restraints excluded: chain L residue 594 ASP Chi-restraints excluded: chain L residue 595 LYS Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 87 CYS Chi-restraints excluded: chain O residue 115 ARG Chi-restraints excluded: chain O residue 147 THR 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 51 optimal weight: 0.8980 chunk 227 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 195 optimal weight: 0.0370 chunk 212 optimal weight: 0.8980 chunk 233 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 240 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 GLN F 178 ASN G 42 ASN G 81 ASN G 99 ASN ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 479 ASN I 438 ASN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 574 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.161800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.122734 restraints weight = 28093.001| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.18 r_work: 0.3166 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24439 Z= 0.129 Angle : 0.600 15.962 33368 Z= 0.300 Chirality : 0.043 0.299 3870 Planarity : 0.004 0.059 3956 Dihedral : 14.901 179.020 4375 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.47 % Allowed : 29.76 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.15), residues: 2762 helix: 1.70 (0.17), residues: 935 sheet: -0.20 (0.22), residues: 496 loop : -1.04 (0.16), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 409 TYR 0.025 0.001 TYR G 92 PHE 0.030 0.002 PHE A 167 TRP 0.027 0.001 TRP L 535 HIS 0.004 0.001 HIS K 510 Details of bonding type rmsd covalent geometry : bond 0.00288 (24400) covalent geometry : angle 0.56350 (33320) hydrogen bonds : bond 0.03342 ( 1037) hydrogen bonds : angle 4.54120 ( 3063) metal coordination : bond 0.00635 ( 39) metal coordination : angle 5.46301 ( 48) *********************** 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 465 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 384 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8301 (mptt) cc_final: 0.8046 (mmtm) REVERT: A 5 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6505 (tpp) REVERT: A 18 LEU cc_start: 0.6254 (tp) cc_final: 0.5477 (mp) REVERT: A 51 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7870 (t80) REVERT: A 55 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7669 (mm) REVERT: A 62 MET cc_start: 0.6626 (mpp) cc_final: 0.6168 (mpt) REVERT: A 85 VAL cc_start: 0.7745 (OUTLIER) cc_final: 0.7447 (p) REVERT: A 93 MET cc_start: 0.8264 (tpp) cc_final: 0.7804 (mmm) REVERT: A 157 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.8359 (p0) REVERT: A 169 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7053 (mp0) REVERT: B 69 ASN cc_start: 0.7997 (t0) cc_final: 0.7663 (p0) REVERT: B 171 ASN cc_start: 0.7647 (m-40) cc_final: 0.7199 (t0) REVERT: C 33 LYS cc_start: 0.8552 (mptt) cc_final: 0.8171 (ptmt) REVERT: C 83 ARG cc_start: 0.8159 (mtm-85) cc_final: 0.7747 (ptp90) REVERT: C 108 ASP cc_start: 0.8248 (m-30) cc_final: 0.7862 (t0) REVERT: C 111 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7869 (pm20) REVERT: C 112 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8088 (mt0) REVERT: C 156 LYS cc_start: 0.8213 (mttt) cc_final: 0.7576 (pttp) REVERT: D 3 LYS cc_start: 0.8094 (mtpp) cc_final: 0.7750 (mttm) REVERT: D 13 LYS cc_start: 0.8391 (tptt) cc_final: 0.7910 (ttpp) REVERT: D 137 GLU cc_start: 0.8486 (pt0) cc_final: 0.7969 (pm20) REVERT: E 29 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7831 (mm-30) REVERT: E 87 CYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8456 (m) REVERT: E 127 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8458 (mmpt) REVERT: E 154 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7496 (mm-40) REVERT: F 112 GLN cc_start: 0.8329 (mt0) cc_final: 0.8023 (mp10) REVERT: F 123 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8065 (mt-10) REVERT: F 127 LYS cc_start: 0.8295 (mttp) cc_final: 0.7436 (mtmm) REVERT: F 187 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7389 (pp20) REVERT: G 92 TYR cc_start: 0.8119 (t80) cc_final: 0.7893 (t80) REVERT: G 129 ASN cc_start: 0.6747 (OUTLIER) cc_final: 0.6297 (m110) REVERT: G 132 GLU cc_start: 0.7281 (pp20) cc_final: 0.7004 (pp20) REVERT: G 191 PHE cc_start: 0.7721 (p90) cc_final: 0.7368 (p90) REVERT: H 102 ARG cc_start: 0.8174 (mtp-110) cc_final: 0.7775 (ttt90) REVERT: H 134 ILE cc_start: 0.7985 (pt) cc_final: 0.7775 (pt) REVERT: H 152 SER cc_start: 0.8448 (OUTLIER) cc_final: 0.8148 (p) REVERT: H 178 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7150 (mmm) REVERT: H 395 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7698 (tt) REVERT: H 404 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7691 (mm-30) REVERT: H 409 ARG cc_start: 0.6814 (OUTLIER) cc_final: 0.5713 (ttp-170) REVERT: H 596 ASN cc_start: 0.8018 (m-40) cc_final: 0.7411 (p0) REVERT: I 450 TYR cc_start: 0.5603 (m-80) cc_final: 0.5078 (m-10) REVERT: I 451 ARG cc_start: 0.7533 (mtp180) cc_final: 0.6935 (mmm-85) REVERT: I 477 ILE cc_start: 0.6266 (tp) cc_final: 0.6022 (tt) REVERT: I 518 GLU cc_start: 0.7782 (tp30) cc_final: 0.7378 (tp30) REVERT: I 579 LEU cc_start: 0.8265 (mt) cc_final: 0.8047 (mt) REVERT: J 13 LYS cc_start: 0.8513 (ttmm) cc_final: 0.7719 (ttpt) REVERT: J 25 ARG cc_start: 0.8397 (ttp80) cc_final: 0.8095 (ttp80) REVERT: J 52 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8698 (tttt) REVERT: K 394 PHE cc_start: 0.7756 (m-80) cc_final: 0.7436 (m-80) REVERT: K 461 GLU cc_start: 0.7557 (tt0) cc_final: 0.7045 (tt0) REVERT: L 512 LYS cc_start: 0.8532 (tppp) cc_final: 0.7565 (tppt) REVERT: L 515 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7157 (mt-10) REVERT: L 542 GLN cc_start: 0.7836 (mt0) cc_final: 0.7464 (mt0) REVERT: L 548 TYR cc_start: 0.8161 (t80) cc_final: 0.7856 (t80) REVERT: L 577 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7291 (mp0) REVERT: L 594 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7780 (t70) REVERT: O 59 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7920 (mm) REVERT: O 87 CYS cc_start: 0.7341 (OUTLIER) cc_final: 0.6795 (m) REVERT: O 93 MET cc_start: 0.8433 (tpt) cc_final: 0.8162 (mmm) REVERT: O 111 GLU cc_start: 0.8344 (mp0) cc_final: 0.8010 (mp0) REVERT: O 115 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8456 (mmt90) outliers start: 81 outliers final: 25 residues processed: 439 average time/residue: 0.6640 time to fit residues: 333.2871 Evaluate side-chains 400 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 352 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 51 PHE Chi-restraints excluded: chain A residue 55 LEU 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 157 ASP 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 147 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 112 GLN 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 E residue 87 CYS 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 187 GLU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain H residue 64 HIS 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 H residue 409 ARG Chi-restraints excluded: chain H residue 549 ILE Chi-restraints excluded: chain J residue 52 LYS 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 L residue 594 ASP Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 87 CYS Chi-restraints excluded: chain O residue 115 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 228 optimal weight: 9.9990 chunk 246 optimal weight: 20.0000 chunk 272 optimal weight: 0.9990 chunk 208 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 163 optimal weight: 20.0000 chunk 169 optimal weight: 10.0000 chunk 227 optimal weight: 2.9990 chunk 173 optimal weight: 10.0000 chunk 127 optimal weight: 0.9980 chunk 164 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 178 ASN ** K 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 574 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.157102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.117519 restraints weight = 28238.584| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.32 r_work: 0.3077 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 24439 Z= 0.262 Angle : 0.677 19.784 33368 Z= 0.334 Chirality : 0.046 0.260 3870 Planarity : 0.005 0.058 3956 Dihedral : 14.811 179.928 4375 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.82 % Allowed : 30.32 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.15), residues: 2762 helix: 1.57 (0.17), residues: 938 sheet: -0.21 (0.22), residues: 493 loop : -1.10 (0.16), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 409 TYR 0.030 0.002 TYR G 161 PHE 0.023 0.002 PHE C 133 TRP 0.029 0.002 TRP L 535 HIS 0.005 0.001 HIS H 326 Details of bonding type rmsd covalent geometry : bond 0.00610 (24400) covalent geometry : angle 0.63271 (33320) hydrogen bonds : bond 0.03563 ( 1037) hydrogen bonds : angle 4.69941 ( 3063) metal coordination : bond 0.01224 ( 39) metal coordination : angle 6.41026 ( 48) *********************** 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 459 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 370 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8207 (mptt) cc_final: 0.7927 (mmtm) REVERT: A 5 MET cc_start: 0.6965 (ttm) cc_final: 0.6521 (tpp) REVERT: A 18 LEU cc_start: 0.6164 (tp) cc_final: 0.5398 (mp) REVERT: A 51 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.7820 (t80) REVERT: A 55 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7671 (mm) REVERT: A 85 VAL cc_start: 0.7775 (OUTLIER) cc_final: 0.7468 (p) REVERT: A 93 MET cc_start: 0.8174 (tpp) cc_final: 0.7716 (mmm) REVERT: A 157 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8399 (p0) REVERT: A 169 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7014 (mp0) REVERT: B 41 LYS cc_start: 0.7874 (mtmp) cc_final: 0.7549 (mttt) REVERT: B 70 VAL cc_start: 0.7791 (OUTLIER) cc_final: 0.7538 (p) REVERT: B 171 ASN cc_start: 0.7713 (m-40) cc_final: 0.6996 (t0) REVERT: C 5 MET cc_start: 0.8528 (mtm) cc_final: 0.7964 (mtt) REVERT: C 33 LYS cc_start: 0.8620 (mptt) cc_final: 0.8211 (ptmt) REVERT: C 76 SER cc_start: 0.8612 (p) cc_final: 0.8349 (t) REVERT: C 83 ARG cc_start: 0.8117 (mtm-85) cc_final: 0.7655 (mtm-85) REVERT: C 108 ASP cc_start: 0.8289 (m-30) cc_final: 0.7858 (t0) REVERT: C 111 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8019 (pm20) REVERT: C 112 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8208 (mt0) REVERT: C 156 LYS cc_start: 0.8240 (mttt) cc_final: 0.7627 (pttp) REVERT: D 3 LYS cc_start: 0.8075 (mtpp) cc_final: 0.7669 (mttm) REVERT: D 13 LYS cc_start: 0.8586 (tptt) cc_final: 0.8162 (ttpt) REVERT: D 108 ASP cc_start: 0.8271 (m-30) cc_final: 0.8063 (m-30) REVERT: D 111 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7884 (pm20) REVERT: D 123 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.8063 (mt-10) REVERT: D 137 GLU cc_start: 0.8558 (pt0) cc_final: 0.8257 (pm20) REVERT: E 29 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7703 (mm-30) REVERT: E 87 CYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8444 (m) REVERT: E 110 LYS cc_start: 0.8460 (ptmm) cc_final: 0.8094 (pttt) REVERT: E 127 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8626 (mmpt) REVERT: E 154 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.7506 (mt0) REVERT: F 112 GLN cc_start: 0.8400 (mt0) cc_final: 0.8123 (mp10) REVERT: F 123 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8186 (mt-10) REVERT: F 127 LYS cc_start: 0.8311 (mttp) cc_final: 0.7498 (mtmm) REVERT: F 187 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7439 (pp20) REVERT: F 189 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7515 (mptt) REVERT: G 92 TYR cc_start: 0.8177 (t80) cc_final: 0.7926 (t80) REVERT: G 101 MET cc_start: 0.8079 (tpt) cc_final: 0.7752 (tpp) REVERT: G 129 ASN cc_start: 0.6633 (OUTLIER) cc_final: 0.6146 (m110) REVERT: G 132 GLU cc_start: 0.7300 (pp20) cc_final: 0.7006 (pp20) REVERT: G 191 PHE cc_start: 0.7764 (p90) cc_final: 0.7389 (p90) REVERT: H 101 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7587 (OUTLIER) REVERT: H 134 ILE cc_start: 0.8044 (pt) cc_final: 0.7832 (pt) REVERT: H 152 SER cc_start: 0.8523 (OUTLIER) cc_final: 0.8192 (p) REVERT: H 178 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.7183 (mmm) REVERT: H 257 MET cc_start: 0.7493 (ttp) cc_final: 0.7257 (ttm) REVERT: H 395 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7783 (tt) REVERT: H 402 GLN cc_start: 0.6786 (mt0) cc_final: 0.6512 (tt0) REVERT: H 409 ARG cc_start: 0.6844 (OUTLIER) cc_final: 0.5717 (ttp-170) REVERT: H 475 ASP cc_start: 0.6502 (m-30) cc_final: 0.6094 (t0) REVERT: H 596 ASN cc_start: 0.7971 (m-40) cc_final: 0.7320 (p0) REVERT: I 450 TYR cc_start: 0.5904 (m-80) cc_final: 0.5259 (m-10) REVERT: I 451 ARG cc_start: 0.7635 (mtp180) cc_final: 0.7024 (mmm-85) REVERT: I 477 ILE cc_start: 0.6402 (tp) cc_final: 0.6139 (tt) REVERT: I 518 GLU cc_start: 0.7785 (tp30) cc_final: 0.7383 (tp30) REVERT: I 579 LEU cc_start: 0.8245 (mt) cc_final: 0.8041 (mt) REVERT: J 13 LYS cc_start: 0.8653 (ttmm) cc_final: 0.7913 (ttpt) REVERT: J 28 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7422 (mtmt) REVERT: J 52 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8732 (tttt) REVERT: K 394 PHE cc_start: 0.7770 (m-80) cc_final: 0.7306 (m-80) REVERT: K 461 GLU cc_start: 0.7581 (tt0) cc_final: 0.7103 (tt0) REVERT: K 466 ILE cc_start: 0.7223 (OUTLIER) cc_final: 0.6960 (tt) REVERT: L 515 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7481 (mt-10) REVERT: L 542 GLN cc_start: 0.7784 (mt0) cc_final: 0.7415 (mt0) REVERT: L 548 TYR cc_start: 0.8231 (t80) cc_final: 0.7944 (t80) REVERT: L 577 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7244 (mp0) REVERT: O 9 TYR cc_start: 0.8489 (m-80) cc_final: 0.8220 (m-80) REVERT: O 59 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7853 (mm) REVERT: O 87 CYS cc_start: 0.7344 (OUTLIER) cc_final: 0.6824 (m) REVERT: O 93 MET cc_start: 0.8415 (tpt) cc_final: 0.8112 (mmm) REVERT: O 111 GLU cc_start: 0.8338 (mp0) cc_final: 0.8017 (mp0) REVERT: O 115 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8533 (mmt90) outliers start: 89 outliers final: 33 residues processed: 434 average time/residue: 0.6894 time to fit residues: 341.1843 Evaluate side-chains 419 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 360 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL 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 104 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 87 CYS 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 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 F residue 189 LYS 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 G residue 129 ASN 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 395 LEU Chi-restraints excluded: chain H residue 408 LYS Chi-restraints excluded: chain H residue 409 ARG Chi-restraints excluded: chain H residue 468 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 411 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 436 VAL 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 59 LEU Chi-restraints excluded: chain O residue 87 CYS Chi-restraints excluded: chain O residue 115 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 53 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 252 optimal weight: 0.5980 chunk 129 optimal weight: 20.0000 chunk 80 optimal weight: 0.3980 chunk 184 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 13 optimal weight: 8.9990 chunk 102 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 G 147 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 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 574 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.160294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.120797 restraints weight = 28286.928| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.29 r_work: 0.3133 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24439 Z= 0.138 Angle : 0.622 17.185 33368 Z= 0.310 Chirality : 0.043 0.287 3870 Planarity : 0.004 0.063 3956 Dihedral : 14.877 179.409 4375 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.92 % Allowed : 31.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.16), residues: 2762 helix: 1.72 (0.17), residues: 936 sheet: -0.21 (0.22), residues: 496 loop : -1.03 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 409 TYR 0.024 0.001 TYR I 599 PHE 0.031 0.002 PHE A 167 TRP 0.033 0.001 TRP L 535 HIS 0.004 0.001 HIS H 326 Details of bonding type rmsd covalent geometry : bond 0.00315 (24400) covalent geometry : angle 0.58182 (33320) hydrogen bonds : bond 0.03337 ( 1037) hydrogen bonds : angle 4.59130 ( 3063) metal coordination : bond 0.00724 ( 39) metal coordination : angle 5.80572 ( 48) ********************** 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 430 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 362 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.8323 (mptt) cc_final: 0.8042 (mmtm) REVERT: A 5 MET cc_start: 0.6964 (OUTLIER) cc_final: 0.6534 (tpp) REVERT: A 18 LEU cc_start: 0.6171 (tp) cc_final: 0.5401 (mp) REVERT: A 23 VAL cc_start: 0.6102 (OUTLIER) cc_final: 0.5865 (p) REVERT: A 51 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.7849 (t80) REVERT: A 55 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7664 (mm) REVERT: A 85 VAL cc_start: 0.7692 (OUTLIER) cc_final: 0.7417 (p) REVERT: A 93 MET cc_start: 0.8240 (tpp) cc_final: 0.7840 (mmm) REVERT: A 157 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8366 (p0) REVERT: A 169 GLU cc_start: 0.7622 (mt-10) cc_final: 0.6998 (mp0) REVERT: B 41 LYS cc_start: 0.7749 (mtmp) cc_final: 0.7434 (mttt) REVERT: B 69 ASN cc_start: 0.7987 (t0) cc_final: 0.7540 (p0) REVERT: B 70 VAL cc_start: 0.7757 (OUTLIER) cc_final: 0.7455 (p) REVERT: B 171 ASN cc_start: 0.7610 (m-40) cc_final: 0.7180 (t0) REVERT: C 5 MET cc_start: 0.8539 (mtm) cc_final: 0.7962 (mtt) REVERT: C 83 ARG cc_start: 0.8208 (mtm-85) cc_final: 0.7917 (ptp90) REVERT: C 108 ASP cc_start: 0.8211 (m-30) cc_final: 0.7842 (t0) REVERT: C 111 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8013 (pm20) REVERT: C 112 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8253 (mt0) REVERT: C 156 LYS cc_start: 0.8236 (mttt) cc_final: 0.7621 (pttp) REVERT: D 3 LYS cc_start: 0.8096 (mtpp) cc_final: 0.7739 (mttm) REVERT: D 13 LYS cc_start: 0.8443 (tptt) cc_final: 0.7956 (ttpp) REVERT: D 108 ASP cc_start: 0.8215 (m-30) cc_final: 0.7979 (m-30) REVERT: D 111 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7977 (pm20) REVERT: D 137 GLU cc_start: 0.8537 (pt0) cc_final: 0.7989 (pm20) REVERT: E 29 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7764 (mm-30) REVERT: E 87 CYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8469 (m) REVERT: E 110 LYS cc_start: 0.8340 (ptmm) cc_final: 0.7961 (ptpt) REVERT: E 127 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8492 (mmpt) REVERT: E 154 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7495 (mm-40) REVERT: F 112 GLN cc_start: 0.8377 (mt0) cc_final: 0.8081 (mp10) REVERT: F 123 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8178 (mt-10) REVERT: F 127 LYS cc_start: 0.8297 (mttp) cc_final: 0.7465 (mtmm) REVERT: F 187 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7454 (pp20) REVERT: F 189 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7467 (mptt) REVERT: G 191 PHE cc_start: 0.7720 (p90) cc_final: 0.7411 (p90) REVERT: H 95 LEU cc_start: 0.7444 (mp) cc_final: 0.7221 (mp) REVERT: H 102 ARG cc_start: 0.8117 (mtp-110) cc_final: 0.7739 (ttt90) REVERT: H 134 ILE cc_start: 0.7934 (pt) cc_final: 0.7705 (pt) REVERT: H 152 SER cc_start: 0.8459 (OUTLIER) cc_final: 0.8141 (p) REVERT: H 178 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7130 (mmm) REVERT: H 257 MET cc_start: 0.7460 (ttp) cc_final: 0.7047 (ttt) REVERT: H 395 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7722 (tt) REVERT: H 402 GLN cc_start: 0.6776 (mt0) cc_final: 0.6564 (tt0) REVERT: H 475 ASP cc_start: 0.6488 (m-30) cc_final: 0.6074 (t0) REVERT: H 596 ASN cc_start: 0.7921 (m-40) cc_final: 0.7310 (p0) REVERT: I 438 ASN cc_start: 0.8299 (t0) cc_final: 0.8060 (t0) REVERT: I 450 TYR cc_start: 0.5758 (m-80) cc_final: 0.5203 (m-10) REVERT: I 451 ARG cc_start: 0.7583 (mtp180) cc_final: 0.6942 (mmm-85) REVERT: I 477 ILE cc_start: 0.6263 (tp) cc_final: 0.6014 (tt) REVERT: I 518 GLU cc_start: 0.7758 (tp30) cc_final: 0.7361 (tp30) REVERT: I 579 LEU cc_start: 0.8262 (mt) cc_final: 0.8054 (mt) REVERT: J 13 LYS cc_start: 0.8563 (ttmm) cc_final: 0.7794 (ttpt) REVERT: J 28 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7403 (mtmt) REVERT: J 52 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8715 (tttt) REVERT: K 394 PHE cc_start: 0.7772 (m-80) cc_final: 0.7479 (m-80) REVERT: K 461 GLU cc_start: 0.7571 (tt0) cc_final: 0.7078 (tt0) REVERT: L 515 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7489 (mt-10) REVERT: L 548 TYR cc_start: 0.8199 (t80) cc_final: 0.7936 (t80) REVERT: L 577 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: O 59 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7988 (mt) REVERT: O 87 CYS cc_start: 0.7392 (OUTLIER) cc_final: 0.6847 (m) REVERT: O 93 MET cc_start: 0.8442 (tpt) cc_final: 0.8174 (mmm) REVERT: O 111 GLU cc_start: 0.8352 (mp0) cc_final: 0.8055 (mp0) REVERT: O 115 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8463 (mmt90) outliers start: 68 outliers final: 29 residues processed: 407 average time/residue: 0.6816 time to fit residues: 316.6466 Evaluate side-chains 403 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 350 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 51 PHE Chi-restraints excluded: chain A residue 55 LEU 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 157 ASP 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 120 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 112 GLN 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 E residue 87 CYS 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 147 THR Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 189 LYS 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 64 HIS Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 408 LYS Chi-restraints excluded: chain H residue 468 ILE 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 108 ASP Chi-restraints excluded: chain K residue 509 SER Chi-restraints excluded: chain K residue 603 ILE Chi-restraints excluded: chain L residue 436 VAL 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 59 LEU Chi-restraints excluded: chain O residue 87 CYS Chi-restraints excluded: chain O residue 115 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 85 optimal weight: 0.0050 chunk 272 optimal weight: 0.0870 chunk 2 optimal weight: 20.0000 chunk 110 optimal weight: 4.9990 chunk 226 optimal weight: 5.9990 chunk 266 optimal weight: 6.9990 chunk 162 optimal weight: 30.0000 chunk 219 optimal weight: 3.9990 chunk 247 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.6178 ------------------------------------------------------------------------------- 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 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 178 ASN ** K 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 483 ASN L 574 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.158907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.120429 restraints weight = 28068.848| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.21 r_work: 0.3123 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 24439 Z= 0.189 Angle : 0.637 17.784 33368 Z= 0.315 Chirality : 0.044 0.275 3870 Planarity : 0.004 0.059 3956 Dihedral : 14.837 179.538 4375 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.00 % Allowed : 31.43 % Favored : 65.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.16), residues: 2762 helix: 1.68 (0.17), residues: 937 sheet: -0.20 (0.22), residues: 498 loop : -1.00 (0.16), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 102 TYR 0.025 0.001 TYR I 599 PHE 0.025 0.002 PHE C 133 TRP 0.034 0.001 TRP L 535 HIS 0.004 0.001 HIS K 510 Details of bonding type rmsd covalent geometry : bond 0.00441 (24400) covalent geometry : angle 0.59695 (33320) hydrogen bonds : bond 0.03366 ( 1037) hydrogen bonds : angle 4.62312 ( 3063) metal coordination : bond 0.00939 ( 39) metal coordination : angle 5.88842 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10365.93 seconds wall clock time: 176 minutes 50.76 seconds (10610.76 seconds total)