Starting phenix.real_space_refine on Fri Aug 7 19:13:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yhd_39287/08_2026/8yhd_39287_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yhd_39287/08_2026/8yhd_39287.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yhd_39287/08_2026/8yhd_39287.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yhd_39287/08_2026/8yhd_39287.map" model { file = "/net/cci-nas-00/data/ceres_data/8yhd_39287/08_2026/8yhd_39287_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yhd_39287/08_2026/8yhd_39287_neut.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/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: 5.30, per 1000 atoms: 0.22 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: 1.93 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 84 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 71 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 81 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 87 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 84 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 87 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 71 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 81 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 84 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 87 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 81 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 71 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 84 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 81 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 71 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 87 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 87 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 84 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 71 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 81 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 71 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 84 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 87 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 81 " pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 88 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 85 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 70 " pdb=" ZN H 701 " pdb="ZN ZN H 701 " - pdb=" ND1 HIS H 64 " pdb="ZN ZN H 701 " - pdb=" NE2 HIS H 62 " pdb="ZN ZN H 701 " - pdb=" ND1 HIS H 148 " pdb=" ZN H 702 " pdb="ZN ZN H 702 " - pdb=" NE2 HIS H 67 " pdb=" ZN J 301 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 87 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 71 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 81 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 84 " pdb=" ZN O 301 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 84 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 87 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 81 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 71 " Number of angles added : 48 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5330 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 39 sheets defined 35.4% alpha, 22.2% beta 23 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 2.96 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: 3.96 Time building geometry restraints manager: 2.64 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: 31494 2.61 - 5.22: 1535 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: 3237 0.098 - 0.196: 569 0.196 - 0.293: 41 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 25.910 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 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= 0.546 Angle : 1.312 21.532 33368 Z= 0.821 Chirality : 0.076 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 are 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/Z covalent geometry : bond 0.00835 / 0.51 (24400) covalent geometry : angle 1.27825 / 0.82 (33320) hydrogen bonds : bond 0.14712 / 9.72 ( 1037) hydrogen bonds : angle 7.62776 / 5.29 ( 3063) metal coordination : bond 0.14314 / 7.69 ( 39) metal coordination : angle 7.89446 / 5.10 ( 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 : 0.899 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: 0.7842 (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: 0.7743 (mtm) REVERT: J 13 LYS cc_start: 0.8290 (ttmm) cc_final: 0.7837 (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: 0.6972 (tt0) REVERT: K 529 ASN cc_start: 0.8381 (t0) cc_final: 0.7461 (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: 0.6107 time to fit residues: 534.8139 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 : 0.944 ------------------------------------------------------------------------------- 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: 2.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 6.9990 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: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 162 GLN C 112 GLN D 178 ASN E 32 GLN E 119 HIS E 171 ASN E 178 ASN G 20 ASN G 81 ASN G 147 ASN H 62 HIS H 446 ASN H 479 ASN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 472 ASN I 556 ASN J 154 GLN K 469 ASN ** L 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 553 HIS O 112 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.167092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.129090 restraints weight = 28211.613| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.32 r_work: 0.3246 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.659 24439 Z= 0.216 Angle : 0.694 18.618 33368 Z= 0.356 Chirality : 0.045 0.296 3870 Planarity : 0.005 0.066 3956 Dihedral : 15.166 179.914 4382 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.82 % Allowed : 28.52 % Favored : 67.67 % 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 are not related in a simple way. whole: -1.35 (0.14), residues: 2762 helix: 0.05 (0.16), residues: 939 sheet: -0.41 (0.22), residues: 507 loop : -1.81 (0.15), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 124 TYR 0.021 0.002 TYR G 137 PHE 0.039 0.002 PHE G 74 TRP 0.013 0.001 TRP I 478 HIS 0.004 0.001 HIS H 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (24400) covalent geometry : angle 0.64685 / 0.35 (33320) hydrogen bonds : bond 0.04580 / 3.03 ( 1037) hydrogen bonds : angle 5.50823 / 3.81 ( 3063) metal coordination : bond 0.10612 / 4.26 ( 39) metal coordination : angle 6.69660 / 4.24 ( 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 545 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 456 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6697 (tpp) REVERT: A 7 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7258 (mptm) REVERT: A 51 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.7704 (t80) REVERT: A 55 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7725 (mm) REVERT: A 93 MET cc_start: 0.8143 (tpp) cc_final: 0.7893 (tpp) REVERT: A 165 LEU cc_start: 0.8248 (mt) cc_final: 0.7626 (mt) REVERT: A 169 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7249 (mp0) REVERT: A 191 GLU cc_start: 0.8219 (tt0) cc_final: 0.7932 (tp30) REVERT: A 196 ASP cc_start: 0.8031 (p0) cc_final: 0.7553 (p0) REVERT: B 76 SER cc_start: 0.8273 (t) cc_final: 0.7977 (m) REVERT: C 36 ASN cc_start: 0.8363 (m-40) cc_final: 0.7995 (m-40) REVERT: C 83 ARG cc_start: 0.8306 (mtm-85) cc_final: 0.7843 (ptp90) REVERT: C 123 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7249 (mm-30) REVERT: D 13 LYS cc_start: 0.8243 (tptt) cc_final: 0.8021 (tptm) REVERT: D 25 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7939 (ttp80) REVERT: D 29 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8330 (mt-10) REVERT: D 123 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.8015 (mt-10) REVERT: D 131 ASP cc_start: 0.7972 (t70) cc_final: 0.7681 (t0) REVERT: E 13 LYS cc_start: 0.8668 (ttpp) cc_final: 0.8334 (ttpp) REVERT: E 92 SER cc_start: 0.8866 (p) cc_final: 0.8602 (t) REVERT: E 110 LYS cc_start: 0.8176 (ptmm) cc_final: 0.7915 (ptpt) REVERT: F 123 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7841 (mt-10) REVERT: F 127 LYS cc_start: 0.8247 (mttp) cc_final: 0.7448 (mtmt) REVERT: F 145 THR cc_start: 0.8503 (m) cc_final: 0.8255 (p) REVERT: G 25 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7612 (mm) REVERT: G 130 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7718 (mt-10) REVERT: H 253 ILE cc_start: 0.7426 (mt) cc_final: 0.7095 (mm) REVERT: H 290 TYR cc_start: 0.7468 (p90) cc_final: 0.7249 (p90) REVERT: H 384 GLU cc_start: 0.8205 (tt0) cc_final: 0.7986 (tp30) REVERT: H 443 ASN cc_start: 0.6787 (p0) cc_final: 0.6398 (m110) REVERT: H 596 ASN cc_start: 0.7920 (m-40) cc_final: 0.7394 (p0) REVERT: I 450 TYR cc_start: 0.5787 (m-80) cc_final: 0.5252 (m-10) REVERT: I 485 MET cc_start: 0.6435 (ttm) cc_final: 0.5542 (ttp) REVERT: I 512 LYS cc_start: 0.7983 (tppt) cc_final: 0.7565 (tptp) REVERT: I 518 GLU cc_start: 0.8000 (tp30) cc_final: 0.7390 (tm-30) REVERT: J 5 MET cc_start: 0.8281 (mtm) cc_final: 0.8003 (mtm) REVERT: J 13 LYS cc_start: 0.8423 (ttmm) cc_final: 0.7761 (ttpt) REVERT: J 52 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8706 (tttt) REVERT: J 112 GLN cc_start: 0.8885 (mt0) cc_final: 0.8681 (mt0) REVERT: J 137 GLU cc_start: 0.8432 (pt0) cc_final: 0.8181 (pt0) REVERT: K 166 PHE cc_start: 0.6264 (m-80) cc_final: 0.5110 (p90) REVERT: K 386 LEU cc_start: 0.7826 (mt) cc_final: 0.7573 (tt) REVERT: K 394 PHE cc_start: 0.7709 (m-80) cc_final: 0.7360 (m-80) REVERT: K 461 GLU cc_start: 0.7646 (tt0) cc_final: 0.7222 (tt0) REVERT: K 561 ARG cc_start: 0.8641 (tpp80) cc_final: 0.8333 (ttm110) REVERT: L 462 LYS cc_start: 0.5979 (mmmm) cc_final: 0.5657 (mmmm) REVERT: L 467 GLU cc_start: 0.6659 (pt0) cc_final: 0.6344 (pt0) REVERT: L 479 ASN cc_start: 0.8838 (m-40) cc_final: 0.8356 (m-40) REVERT: L 593 TYR cc_start: 0.6993 (m-10) cc_final: 0.6732 (m-10) REVERT: L 603 ILE cc_start: 0.7325 (pp) cc_final: 0.7044 (pt) REVERT: O 16 SER cc_start: 0.9115 (m) cc_final: 0.8877 (p) REVERT: O 123 GLU cc_start: 0.8427 (mt-10) cc_final: 0.7990 (mm-30) REVERT: O 152 ASN cc_start: 0.8110 (t0) cc_final: 0.7889 (t0) outliers start: 89 outliers final: 24 residues processed: 518 average time/residue: 0.6564 time to fit residues: 391.7454 Evaluate side-chains 404 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 371 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 7 LYS 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 B residue 35 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 25 ARG 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 F residue 109 THR Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 259 SER Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 399 GLU Chi-restraints excluded: chain H residue 431 ILE Chi-restraints excluded: chain I residue 608 LYS Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain L residue 556 ASN 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: 4.9990 chunk 214 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 229 optimal weight: 0.9980 chunk 275 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 267 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 251 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 107 ASN D 178 ASN E 32 GLN F 171 ASN G 20 ASN G 42 ASN G 81 ASN ** 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 ** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.165258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.127247 restraints weight = 28240.957| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.27 r_work: 0.3214 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24439 Z= 0.156 Angle : 0.634 20.192 33368 Z= 0.322 Chirality : 0.044 0.257 3870 Planarity : 0.005 0.054 3956 Dihedral : 14.990 179.457 4375 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.16 % Allowed : 27.83 % Favored : 68.01 % 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 are not related in a simple way. whole: -0.77 (0.15), residues: 2762 helix: 0.78 (0.17), residues: 937 sheet: -0.39 (0.22), residues: 514 loop : -1.52 (0.15), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 95 TYR 0.017 0.001 TYR I 599 PHE 0.024 0.002 PHE C 133 TRP 0.012 0.001 TRP L 535 HIS 0.014 0.002 HIS H 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (24400) covalent geometry : angle 0.58637 / 0.32 (33320) hydrogen bonds : bond 0.04143 / 2.72 ( 1037) hydrogen bonds : angle 5.01875 / 3.48 ( 3063) metal coordination : bond 0.00607 / 0.36 ( 39) metal coordination : angle 6.40333 / 4.02 ( 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 508 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 411 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7018 (OUTLIER) cc_final: 0.6617 (tpp) REVERT: A 18 LEU cc_start: 0.6362 (tp) cc_final: 0.5541 (mp) REVERT: A 51 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7825 (t80) REVERT: A 55 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7763 (mm) REVERT: A 93 MET cc_start: 0.8185 (tpp) cc_final: 0.7944 (mmm) REVERT: A 154 GLN cc_start: 0.7465 (tm-30) cc_final: 0.7204 (tm-30) REVERT: A 169 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7307 (mp0) REVERT: A 191 GLU cc_start: 0.8294 (tt0) cc_final: 0.7963 (tp30) REVERT: B 76 SER cc_start: 0.8315 (t) cc_final: 0.8013 (m) REVERT: B 79 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7628 (ttp80) REVERT: C 36 ASN cc_start: 0.8322 (m-40) cc_final: 0.7960 (m110) REVERT: C 83 ARG cc_start: 0.8250 (mtm-85) cc_final: 0.7892 (ptp90) REVERT: C 85 VAL cc_start: 0.7857 (m) cc_final: 0.7576 (p) REVERT: C 111 GLU cc_start: 0.8509 (pm20) cc_final: 0.8287 (pm20) REVERT: D 13 LYS cc_start: 0.8281 (tptt) cc_final: 0.8069 (tptm) REVERT: D 123 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.8003 (mt-10) REVERT: D 131 ASP cc_start: 0.8201 (t70) cc_final: 0.7847 (t0) REVERT: E 92 SER cc_start: 0.8892 (p) cc_final: 0.8617 (t) REVERT: F 93 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.7218 (mpt) REVERT: F 123 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7863 (mt-10) REVERT: F 127 LYS cc_start: 0.8287 (mttp) cc_final: 0.7634 (mtmt) REVERT: F 145 THR cc_start: 0.8573 (m) cc_final: 0.8350 (p) REVERT: F 189 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7461 (mptt) REVERT: G 56 PHE cc_start: 0.7645 (t80) cc_final: 0.7286 (t80) REVERT: G 92 TYR cc_start: 0.7942 (t80) cc_final: 0.7636 (t80) REVERT: G 130 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7672 (mt-10) REVERT: H 99 ASP cc_start: 0.8494 (t70) cc_final: 0.8257 (t70) REVERT: H 152 SER cc_start: 0.8474 (OUTLIER) cc_final: 0.7861 (p) REVERT: H 253 ILE cc_start: 0.7386 (mt) cc_final: 0.7044 (mm) REVERT: H 384 GLU cc_start: 0.8217 (tt0) cc_final: 0.8001 (tp30) REVERT: H 409 ARG cc_start: 0.7064 (ttp80) cc_final: 0.6831 (ttp80) REVERT: H 596 ASN cc_start: 0.7941 (m-40) cc_final: 0.7419 (p0) REVERT: I 450 TYR cc_start: 0.5694 (m-80) cc_final: 0.5107 (m-10) REVERT: I 485 MET cc_start: 0.6376 (OUTLIER) cc_final: 0.5507 (ttp) REVERT: I 518 GLU cc_start: 0.7962 (tp30) cc_final: 0.7370 (tm-30) REVERT: J 13 LYS cc_start: 0.8487 (ttmm) cc_final: 0.7819 (ttpt) REVERT: J 52 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8727 (tttt) REVERT: J 116 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8126 (tp30) REVERT: J 137 GLU cc_start: 0.8503 (pt0) cc_final: 0.8259 (pt0) REVERT: K 386 LEU cc_start: 0.7952 (mt) cc_final: 0.7651 (tt) REVERT: K 394 PHE cc_start: 0.7758 (m-80) cc_final: 0.7408 (m-80) REVERT: K 461 GLU cc_start: 0.7732 (tt0) cc_final: 0.7297 (tt0) REVERT: K 561 ARG cc_start: 0.8658 (tpp80) cc_final: 0.8416 (mtm110) REVERT: L 462 LYS cc_start: 0.6099 (mmmm) cc_final: 0.5714 (mmmm) REVERT: L 467 GLU cc_start: 0.6688 (pt0) cc_final: 0.6194 (pt0) REVERT: L 469 ASN cc_start: 0.7468 (m110) cc_final: 0.6684 (m-40) REVERT: L 512 LYS cc_start: 0.8548 (tppp) cc_final: 0.8000 (tppt) REVERT: L 524 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.8038 (mttp) REVERT: L 577 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7437 (mp0) REVERT: L 593 TYR cc_start: 0.6964 (m-10) cc_final: 0.6674 (m-10) REVERT: O 16 SER cc_start: 0.9160 (m) cc_final: 0.8941 (p) REVERT: O 152 ASN cc_start: 0.8170 (t0) cc_final: 0.7899 (t0) REVERT: O 191 GLU cc_start: 0.7268 (tm-30) cc_final: 0.7041 (tm-30) outliers start: 97 outliers final: 26 residues processed: 477 average time/residue: 0.6665 time to fit residues: 365.2414 Evaluate side-chains 398 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 359 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 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 126 THR Chi-restraints excluded: chain C residue 158 LEU 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 E residue 88 SER Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 189 LYS Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 329 GLN Chi-restraints excluded: chain H residue 399 GLU Chi-restraints excluded: chain H residue 570 ASP Chi-restraints excluded: chain I residue 485 MET Chi-restraints excluded: chain I residue 608 LYS Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain K residue 603 ILE Chi-restraints excluded: chain L residue 524 LYS Chi-restraints excluded: chain L residue 577 GLU Chi-restraints excluded: chain L residue 601 ILE Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 190 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 160 optimal weight: 10.0000 chunk 105 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 199 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 174 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 223 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 162 GLN E 178 ASN G 42 ASN G 81 ASN H 443 ASN H 469 ASN H 479 ASN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 606 ASN J 119 HIS ** K 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 438 ASN L 574 ASN O 112 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.163814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.125313 restraints weight = 28241.972| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.47 r_work: 0.3181 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24439 Z= 0.154 Angle : 0.599 16.504 33368 Z= 0.306 Chirality : 0.044 0.203 3870 Planarity : 0.004 0.051 3956 Dihedral : 14.937 179.308 4375 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.12 % Allowed : 27.62 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.15), residues: 2762 helix: 1.13 (0.17), residues: 940 sheet: -0.13 (0.22), residues: 510 loop : -1.33 (0.16), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 25 TYR 0.018 0.001 TYR L 450 PHE 0.023 0.002 PHE C 133 TRP 0.018 0.001 TRP L 535 HIS 0.006 0.001 HIS H 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (24400) covalent geometry : angle 0.55694 / 0.30 (33320) hydrogen bonds : bond 0.03838 / 2.50 ( 1037) hydrogen bonds : angle 4.78351 / 3.32 ( 3063) metal coordination : bond 0.00714 / 0.44 ( 39) metal coordination : angle 5.80550 / 3.62 ( 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 494 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 398 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.6935 (ttm) cc_final: 0.6589 (tpp) REVERT: A 18 LEU cc_start: 0.6237 (tp) cc_final: 0.5417 (mp) REVERT: A 51 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7765 (t80) REVERT: A 55 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7736 (mm) REVERT: A 154 GLN cc_start: 0.7469 (tm-30) cc_final: 0.7168 (tm-30) REVERT: A 169 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7263 (mp0) REVERT: A 191 GLU cc_start: 0.8317 (tt0) cc_final: 0.7961 (tp30) REVERT: B 66 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7867 (mtpt) REVERT: B 76 SER cc_start: 0.8463 (t) cc_final: 0.8165 (m) REVERT: B 154 GLN cc_start: 0.8018 (mm110) cc_final: 0.7751 (mm110) REVERT: B 181 TYR cc_start: 0.7909 (m-80) cc_final: 0.7608 (m-80) REVERT: C 36 ASN cc_start: 0.8348 (m-40) cc_final: 0.8056 (m110) REVERT: C 83 ARG cc_start: 0.8261 (mtm-85) cc_final: 0.7910 (ptp90) REVERT: C 85 VAL cc_start: 0.7816 (m) cc_final: 0.7554 (p) REVERT: D 123 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.8010 (mt-10) REVERT: D 131 ASP cc_start: 0.8251 (t70) cc_final: 0.7821 (t70) REVERT: D 166 LYS cc_start: 0.8800 (mtpp) cc_final: 0.8437 (mtmt) REVERT: D 179 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8407 (ptpt) REVERT: E 29 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7756 (mm-30) REVERT: E 35 VAL cc_start: 0.8756 (t) cc_final: 0.8516 (p) REVERT: E 92 SER cc_start: 0.8902 (p) cc_final: 0.8593 (t) REVERT: F 123 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7893 (mt-10) REVERT: F 127 LYS cc_start: 0.8276 (mttp) cc_final: 0.7600 (mtmt) REVERT: F 145 THR cc_start: 0.8623 (m) cc_final: 0.8388 (p) REVERT: G 56 PHE cc_start: 0.7636 (t80) cc_final: 0.7303 (t80) REVERT: G 92 TYR cc_start: 0.7988 (t80) cc_final: 0.7673 (t80) REVERT: G 130 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7787 (mt-10) REVERT: G 132 GLU cc_start: 0.7347 (pp20) cc_final: 0.7086 (pp20) REVERT: H 99 ASP cc_start: 0.8534 (t70) cc_final: 0.8235 (t70) REVERT: H 127 GLU cc_start: 0.7792 (pt0) cc_final: 0.7504 (pt0) REVERT: H 130 ASP cc_start: 0.7699 (p0) cc_final: 0.7482 (p0) REVERT: H 152 SER cc_start: 0.8570 (OUTLIER) cc_final: 0.8132 (p) REVERT: H 253 ILE cc_start: 0.7252 (mt) cc_final: 0.6813 (mm) REVERT: H 395 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8053 (tt) REVERT: H 450 TYR cc_start: 0.6141 (m-80) cc_final: 0.5941 (m-80) REVERT: H 456 SER cc_start: 0.7515 (p) cc_final: 0.7235 (p) REVERT: H 596 ASN cc_start: 0.7941 (m-40) cc_final: 0.7390 (p0) REVERT: I 450 TYR cc_start: 0.5644 (m-80) cc_final: 0.5041 (m-10) REVERT: I 518 GLU cc_start: 0.7927 (tp30) cc_final: 0.7315 (tm-30) REVERT: J 13 LYS cc_start: 0.8568 (ttmm) cc_final: 0.7831 (ttpt) REVERT: J 52 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8758 (tttt) REVERT: J 68 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7615 (mt-10) REVERT: J 125 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8038 (mp10) REVERT: J 137 GLU cc_start: 0.8569 (pt0) cc_final: 0.8361 (pt0) REVERT: K 166 PHE cc_start: 0.6302 (m-80) cc_final: 0.5295 (p90) REVERT: K 386 LEU cc_start: 0.7903 (mt) cc_final: 0.7662 (tt) REVERT: K 461 GLU cc_start: 0.7769 (tt0) cc_final: 0.7319 (tt0) REVERT: L 467 GLU cc_start: 0.6685 (pt0) cc_final: 0.6160 (pt0) REVERT: L 469 ASN cc_start: 0.7437 (m110) cc_final: 0.6628 (m-40) REVERT: L 512 LYS cc_start: 0.8633 (tppp) cc_final: 0.8326 (tppp) REVERT: L 577 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: O 16 SER cc_start: 0.9247 (m) cc_final: 0.8994 (p) REVERT: O 59 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7981 (mt) REVERT: O 111 GLU cc_start: 0.8349 (mp0) cc_final: 0.8136 (mp0) REVERT: O 152 ASN cc_start: 0.8156 (t0) cc_final: 0.7879 (t0) outliers start: 96 outliers final: 30 residues processed: 462 average time/residue: 0.6680 time to fit residues: 353.4049 Evaluate side-chains 397 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 356 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 95 SER 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 137 PHE Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 239 LEU 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 549 ILE Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 125 GLN Chi-restraints excluded: chain K residue 603 ILE Chi-restraints excluded: chain L residue 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 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: 3.9990 chunk 154 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 187 optimal weight: 0.9980 chunk 250 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 162 GLN D 112 GLN E 32 GLN G 42 ASN G 81 ASN ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 479 ASN H 542 GLN H 551 GLN I 438 ASN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 119 HIS ** K 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 574 ASN O 112 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.163491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.124444 restraints weight = 28160.591| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.48 r_work: 0.3176 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3348 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= 0.148 Angle : 0.582 16.955 33368 Z= 0.297 Chirality : 0.043 0.184 3870 Planarity : 0.004 0.052 3956 Dihedral : 14.925 179.550 4375 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.86 % Allowed : 27.87 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.15), residues: 2762 helix: 1.38 (0.17), residues: 940 sheet: -0.03 (0.22), residues: 502 loop : -1.24 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 77 TYR 0.020 0.001 TYR I 599 PHE 0.025 0.002 PHE C 133 TRP 0.016 0.001 TRP L 535 HIS 0.004 0.001 HIS L 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (24400) covalent geometry : angle 0.54034 / 0.29 (33320) hydrogen bonds : bond 0.03750 / 2.44 ( 1037) hydrogen bonds : angle 4.64843 / 3.22 ( 3063) metal coordination : bond 0.00759 / 0.46 ( 39) metal coordination : angle 5.70961 / 3.58 ( 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 479 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 389 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.6911 (OUTLIER) cc_final: 0.6571 (tpp) REVERT: A 7 LYS cc_start: 0.7852 (mttm) cc_final: 0.7648 (mttm) REVERT: A 18 LEU cc_start: 0.6209 (tp) cc_final: 0.5366 (mp) REVERT: A 51 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7733 (t80) REVERT: A 55 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7743 (mm) REVERT: A 169 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7222 (mp0) REVERT: A 191 GLU cc_start: 0.8321 (tt0) cc_final: 0.7962 (tp30) REVERT: B 66 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7882 (mtpt) REVERT: B 76 SER cc_start: 0.8526 (t) cc_final: 0.8219 (m) REVERT: B 79 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7649 (ttp80) REVERT: B 154 GLN cc_start: 0.7887 (mm110) cc_final: 0.7599 (mm110) REVERT: B 181 TYR cc_start: 0.7880 (m-80) cc_final: 0.7574 (m-80) REVERT: C 36 ASN cc_start: 0.8365 (m-40) cc_final: 0.8116 (m110) REVERT: C 83 ARG cc_start: 0.8255 (mtm-85) cc_final: 0.7893 (ptp90) REVERT: C 85 VAL cc_start: 0.7806 (m) cc_final: 0.7550 (p) REVERT: D 123 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8065 (mt-10) REVERT: E 92 SER cc_start: 0.8887 (p) cc_final: 0.8570 (t) REVERT: E 127 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8242 (mmtm) REVERT: F 93 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.7272 (mpt) REVERT: F 123 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7838 (mt-10) REVERT: F 127 LYS cc_start: 0.8253 (mttp) cc_final: 0.7558 (mtmt) REVERT: F 145 THR cc_start: 0.8619 (m) cc_final: 0.8344 (p) REVERT: G 56 PHE cc_start: 0.7744 (t80) cc_final: 0.7367 (t80) REVERT: G 92 TYR cc_start: 0.8049 (t80) cc_final: 0.7719 (t80) REVERT: G 130 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7710 (mt-10) REVERT: G 132 GLU cc_start: 0.7239 (pp20) cc_final: 0.6941 (pp20) REVERT: G 191 PHE cc_start: 0.7634 (p90) cc_final: 0.7252 (p90) REVERT: H 99 ASP cc_start: 0.8540 (t70) cc_final: 0.8212 (t0) REVERT: H 127 GLU cc_start: 0.7933 (pt0) cc_final: 0.7628 (pt0) REVERT: H 152 SER cc_start: 0.8473 (OUTLIER) cc_final: 0.8121 (p) REVERT: H 253 ILE cc_start: 0.7225 (mt) cc_final: 0.6735 (mm) REVERT: H 395 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8022 (tt) REVERT: H 450 TYR cc_start: 0.6263 (m-80) cc_final: 0.6031 (m-80) REVERT: H 456 SER cc_start: 0.7409 (p) cc_final: 0.7154 (p) REVERT: H 596 ASN cc_start: 0.7947 (m-40) cc_final: 0.7358 (p0) REVERT: I 450 TYR cc_start: 0.5555 (m-80) cc_final: 0.4981 (m-10) REVERT: I 451 ARG cc_start: 0.7253 (mtp180) cc_final: 0.6678 (mmm-85) REVERT: I 518 GLU cc_start: 0.7906 (tp30) cc_final: 0.7165 (pt0) REVERT: J 13 LYS cc_start: 0.8572 (ttmm) cc_final: 0.7805 (ttpt) REVERT: J 52 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8746 (tttt) REVERT: J 125 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8048 (mp10) REVERT: K 166 PHE cc_start: 0.6204 (m-80) cc_final: 0.5192 (p90) REVERT: K 461 GLU cc_start: 0.7688 (tt0) cc_final: 0.7229 (tt0) REVERT: L 467 GLU cc_start: 0.6560 (pt0) cc_final: 0.6072 (pt0) REVERT: L 469 ASN cc_start: 0.7464 (m110) cc_final: 0.6614 (m-40) REVERT: L 512 LYS cc_start: 0.8670 (tppp) cc_final: 0.8393 (tppp) REVERT: L 524 LYS cc_start: 0.8339 (mttp) cc_final: 0.8047 (mmtm) REVERT: L 577 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7266 (mp0) REVERT: L 603 ILE cc_start: 0.7445 (pp) cc_final: 0.7136 (mm) REVERT: O 16 SER cc_start: 0.9232 (m) cc_final: 0.8968 (p) REVERT: O 59 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7918 (mt) REVERT: O 110 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7800 (ptpt) REVERT: O 111 GLU cc_start: 0.8389 (mp0) cc_final: 0.7970 (mp0) REVERT: O 152 ASN cc_start: 0.8152 (t0) cc_final: 0.7892 (t0) outliers start: 90 outliers final: 36 residues processed: 455 average time/residue: 0.5894 time to fit residues: 307.9613 Evaluate side-chains 406 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 355 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 104 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 66 LYS 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 120 LEU 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 D residue 149 THR Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 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 G residue 95 SER 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 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 J residue 52 LYS Chi-restraints excluded: chain J residue 125 GLN Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 603 ILE Chi-restraints excluded: chain L residue 556 ASN Chi-restraints excluded: chain L residue 577 GLU Chi-restraints excluded: chain L residue 601 ILE Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 110 LYS Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 190 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 176 optimal weight: 0.9980 chunk 129 optimal weight: 20.0000 chunk 175 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 277 optimal weight: 6.9990 chunk 5 optimal weight: 0.0060 chunk 153 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 197 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 162 GLN D 112 GLN E 32 GLN 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** J 119 HIS K 440 ASN K 510 HIS ** K 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 574 ASN O 112 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.162144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.123250 restraints weight = 28195.587| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.45 r_work: 0.3151 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24439 Z= 0.174 Angle : 0.599 17.074 33368 Z= 0.305 Chirality : 0.046 0.931 3870 Planarity : 0.004 0.051 3956 Dihedral : 14.888 179.941 4375 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.29 % Allowed : 27.83 % 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 are not related in a simple way. whole: -0.09 (0.15), residues: 2762 helix: 1.42 (0.17), residues: 939 sheet: 0.00 (0.22), residues: 494 loop : -1.18 (0.16), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 102 TYR 0.013 0.001 TYR G 107 PHE 0.036 0.002 PHE A 167 TRP 0.013 0.001 TRP H 125 HIS 0.008 0.001 HIS K 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (24400) covalent geometry : angle 0.55861 / 0.30 (33320) hydrogen bonds : bond 0.03737 / 2.44 ( 1037) hydrogen bonds : angle 4.62463 / 3.21 ( 3063) metal coordination : bond 0.00858 / 0.54 ( 39) metal coordination : angle 5.70941 / 3.57 ( 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 466 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 366 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.6958 (OUTLIER) cc_final: 0.6588 (tpp) REVERT: A 7 LYS cc_start: 0.7878 (mttm) cc_final: 0.7675 (mttm) REVERT: A 18 LEU cc_start: 0.6256 (tp) cc_final: 0.5428 (mp) REVERT: A 51 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7787 (t80) REVERT: A 55 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7779 (mm) REVERT: A 169 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7192 (mp0) REVERT: A 191 GLU cc_start: 0.8359 (tt0) cc_final: 0.8005 (tp30) REVERT: B 22 GLU cc_start: 0.8173 (tp30) cc_final: 0.7896 (tp30) REVERT: B 154 GLN cc_start: 0.7894 (mm110) cc_final: 0.7602 (mm110) REVERT: B 181 TYR cc_start: 0.7877 (m-80) cc_final: 0.7594 (m-80) REVERT: C 5 MET cc_start: 0.8461 (mtm) cc_final: 0.7899 (mtt) REVERT: C 33 LYS cc_start: 0.8509 (mptt) cc_final: 0.8165 (ptmt) REVERT: C 36 ASN cc_start: 0.8401 (m-40) cc_final: 0.8185 (m110) REVERT: C 83 ARG cc_start: 0.8142 (mtm-85) cc_final: 0.7804 (ptp90) REVERT: C 85 VAL cc_start: 0.7874 (m) cc_final: 0.7638 (p) REVERT: D 3 LYS cc_start: 0.8059 (mttt) cc_final: 0.7769 (mmtm) REVERT: D 13 LYS cc_start: 0.8385 (tptt) cc_final: 0.7918 (ttpp) REVERT: D 75 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7796 (mm-30) REVERT: D 123 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.8024 (mt-10) REVERT: D 179 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8483 (ptpt) REVERT: E 127 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8260 (mmtm) REVERT: F 112 GLN cc_start: 0.8470 (mt0) cc_final: 0.8108 (mp10) REVERT: F 123 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8062 (mt-10) REVERT: F 127 LYS cc_start: 0.8238 (mttp) cc_final: 0.7576 (mtmt) REVERT: F 145 THR cc_start: 0.8650 (m) cc_final: 0.8384 (p) REVERT: G 56 PHE cc_start: 0.7765 (t80) cc_final: 0.7309 (t80) REVERT: G 92 TYR cc_start: 0.8123 (t80) cc_final: 0.7910 (t80) REVERT: G 132 GLU cc_start: 0.7333 (pp20) cc_final: 0.7014 (pp20) REVERT: G 191 PHE cc_start: 0.7670 (p90) cc_final: 0.7298 (p90) REVERT: H 99 ASP cc_start: 0.8603 (t70) cc_final: 0.8289 (t0) REVERT: H 152 SER cc_start: 0.8480 (OUTLIER) cc_final: 0.8173 (p) REVERT: H 184 MET cc_start: 0.7653 (mtm) cc_final: 0.7318 (mtm) REVERT: H 253 ILE cc_start: 0.7216 (mt) cc_final: 0.6737 (mm) REVERT: H 395 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8026 (tt) REVERT: H 456 SER cc_start: 0.7406 (p) cc_final: 0.7176 (p) REVERT: H 596 ASN cc_start: 0.7980 (m-40) cc_final: 0.7380 (p0) REVERT: I 450 TYR cc_start: 0.5628 (m-80) cc_final: 0.4943 (m-10) REVERT: I 451 ARG cc_start: 0.7512 (mtp180) cc_final: 0.6916 (mmm-85) REVERT: I 518 GLU cc_start: 0.7923 (tp30) cc_final: 0.7494 (tp30) REVERT: J 13 LYS cc_start: 0.8580 (ttmm) cc_final: 0.7839 (ttpt) REVERT: J 52 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8764 (tttt) REVERT: J 72 ASP cc_start: 0.8344 (t70) cc_final: 0.8141 (t0) REVERT: J 125 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8042 (mp10) REVERT: K 461 GLU cc_start: 0.7658 (tt0) cc_final: 0.7200 (tt0) REVERT: K 465 ARG cc_start: 0.7623 (ptp-170) cc_final: 0.7294 (pmm-80) REVERT: L 467 GLU cc_start: 0.6515 (pt0) cc_final: 0.6086 (pt0) REVERT: L 469 ASN cc_start: 0.7487 (m110) cc_final: 0.6679 (m-40) REVERT: L 512 LYS cc_start: 0.8683 (tppp) cc_final: 0.8454 (tppp) REVERT: L 518 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7896 (tm-30) REVERT: L 542 GLN cc_start: 0.7863 (mt0) cc_final: 0.7469 (mt0) REVERT: L 577 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: L 603 ILE cc_start: 0.7508 (pp) cc_final: 0.7242 (mm) REVERT: O 16 SER cc_start: 0.9249 (m) cc_final: 0.8979 (p) REVERT: O 59 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7980 (mt) REVERT: O 93 MET cc_start: 0.8376 (tpt) cc_final: 0.8106 (mmm) REVERT: O 110 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7797 (ptpt) REVERT: O 111 GLU cc_start: 0.8367 (mp0) cc_final: 0.8022 (mp0) REVERT: O 152 ASN cc_start: 0.8148 (t0) cc_final: 0.7906 (t0) outliers start: 100 outliers final: 37 residues processed: 440 average time/residue: 0.5878 time to fit residues: 297.4518 Evaluate side-chains 395 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 344 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 104 LEU Chi-restraints excluded: chain A residue 147 THR 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 100 SER Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 108 ASP 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 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 J residue 52 LYS Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain J residue 125 GLN Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 603 ILE Chi-restraints excluded: chain L residue 556 ASN Chi-restraints excluded: chain L residue 577 GLU Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 110 LYS Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 187 GLU Chi-restraints excluded: chain O residue 190 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 5 optimal weight: 0.0570 chunk 57 optimal weight: 1.9990 chunk 107 optimal weight: 0.0000 chunk 240 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 218 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 63 optimal weight: 7.9990 overall best weight: 0.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 162 GLN D 112 GLN E 107 ASN E 171 ASN G 42 ASN G 81 ASN H 479 ASN H 558 ASN I 438 ASN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 119 HIS K 440 ASN K 510 HIS ** K 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 574 ASN L 606 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.164032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.125326 restraints weight = 28309.431| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.34 r_work: 0.3195 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24439 Z= 0.124 Angle : 0.568 14.981 33368 Z= 0.291 Chirality : 0.042 0.197 3870 Planarity : 0.004 0.058 3956 Dihedral : 14.912 179.632 4375 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.04 % Allowed : 28.86 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.15), residues: 2762 helix: 1.65 (0.17), residues: 935 sheet: 0.05 (0.21), residues: 504 loop : -1.14 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 102 TYR 0.013 0.001 TYR G 161 PHE 0.028 0.001 PHE A 167 TRP 0.015 0.001 TRP L 535 HIS 0.007 0.001 HIS K 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (24400) covalent geometry : angle 0.52826 / 0.29 (33320) hydrogen bonds : bond 0.03650 / 2.36 ( 1037) hydrogen bonds : angle 4.51372 / 3.13 ( 3063) metal coordination : bond 0.01074 / 0.69 ( 39) metal coordination : angle 5.56123 / 3.39 ( 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 457 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 386 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.6978 (ttm) cc_final: 0.6633 (tpp) REVERT: A 18 LEU cc_start: 0.6280 (tp) cc_final: 0.5465 (mp) REVERT: A 51 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7806 (t80) REVERT: A 55 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7869 (mm) REVERT: A 62 MET cc_start: 0.6611 (mpp) cc_final: 0.6390 (mpp) REVERT: A 85 VAL cc_start: 0.7765 (OUTLIER) cc_final: 0.7441 (p) REVERT: A 154 GLN cc_start: 0.7388 (mm-40) cc_final: 0.7149 (mm110) REVERT: A 169 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7081 (mp0) REVERT: A 191 GLU cc_start: 0.8385 (tt0) cc_final: 0.8019 (tp30) REVERT: B 22 GLU cc_start: 0.8126 (tp30) cc_final: 0.7887 (tp30) REVERT: B 66 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7796 (mtpt) REVERT: B 69 ASN cc_start: 0.8145 (t0) cc_final: 0.7744 (p0) REVERT: B 154 GLN cc_start: 0.7903 (mm110) cc_final: 0.7596 (mm110) REVERT: C 83 ARG cc_start: 0.8264 (mtm-85) cc_final: 0.7928 (ptp90) REVERT: C 85 VAL cc_start: 0.7840 (m) cc_final: 0.7625 (p) REVERT: D 3 LYS cc_start: 0.8090 (mttt) cc_final: 0.7811 (mmtm) REVERT: D 13 LYS cc_start: 0.8320 (tptt) cc_final: 0.8112 (tptm) REVERT: D 75 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7777 (mm-30) REVERT: D 179 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8446 (ptpt) REVERT: E 29 GLU cc_start: 0.8472 (mt-10) cc_final: 0.7848 (mm-30) REVERT: E 92 SER cc_start: 0.8787 (p) cc_final: 0.8480 (t) REVERT: E 127 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8251 (mmtm) REVERT: F 93 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7203 (mpt) REVERT: F 112 GLN cc_start: 0.8416 (mt0) cc_final: 0.8095 (mp10) REVERT: F 123 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7844 (mt-10) REVERT: F 127 LYS cc_start: 0.8260 (mttp) cc_final: 0.7404 (mtmm) REVERT: F 145 THR cc_start: 0.8610 (m) cc_final: 0.8370 (p) REVERT: G 56 PHE cc_start: 0.7749 (t80) cc_final: 0.7326 (t80) REVERT: G 130 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7795 (mt-10) REVERT: G 132 GLU cc_start: 0.7328 (pp20) cc_final: 0.7065 (pp20) REVERT: G 191 PHE cc_start: 0.7722 (p90) cc_final: 0.7344 (p90) REVERT: H 99 ASP cc_start: 0.8641 (t70) cc_final: 0.8303 (t0) REVERT: H 134 ILE cc_start: 0.8118 (pt) cc_final: 0.7869 (pt) REVERT: H 152 SER cc_start: 0.8472 (OUTLIER) cc_final: 0.8175 (p) REVERT: H 253 ILE cc_start: 0.7161 (mt) cc_final: 0.6650 (mm) REVERT: H 395 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8000 (tt) REVERT: H 456 SER cc_start: 0.7334 (p) cc_final: 0.7078 (p) REVERT: H 596 ASN cc_start: 0.7972 (m-40) cc_final: 0.7414 (p0) REVERT: I 450 TYR cc_start: 0.5642 (m-80) cc_final: 0.4953 (m-10) REVERT: I 451 ARG cc_start: 0.7506 (mtp180) cc_final: 0.6957 (mmm-85) REVERT: I 518 GLU cc_start: 0.7923 (tp30) cc_final: 0.7479 (tp30) REVERT: J 13 LYS cc_start: 0.8500 (ttmm) cc_final: 0.7750 (ttpt) REVERT: J 52 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8715 (tttt) REVERT: J 72 ASP cc_start: 0.8301 (t70) cc_final: 0.8088 (t0) REVERT: J 125 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7996 (mp10) REVERT: K 166 PHE cc_start: 0.6320 (m-80) cc_final: 0.5356 (p90) REVERT: K 394 PHE cc_start: 0.7929 (m-80) cc_final: 0.7585 (m-80) REVERT: K 461 GLU cc_start: 0.7607 (tt0) cc_final: 0.7145 (tt0) REVERT: K 465 ARG cc_start: 0.7592 (ptp-170) cc_final: 0.7219 (pmm-80) REVERT: L 467 GLU cc_start: 0.6472 (pt0) cc_final: 0.6115 (pt0) REVERT: L 469 ASN cc_start: 0.7510 (m110) cc_final: 0.6760 (m-40) REVERT: L 518 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7906 (tm-30) REVERT: L 524 LYS cc_start: 0.8498 (mttp) cc_final: 0.8201 (mmtm) REVERT: L 542 GLN cc_start: 0.7884 (mt0) cc_final: 0.7492 (mt0) REVERT: L 577 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: O 16 SER cc_start: 0.9200 (m) cc_final: 0.8994 (p) REVERT: O 87 CYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6763 (m) REVERT: O 93 MET cc_start: 0.8210 (tpt) cc_final: 0.7970 (mmm) REVERT: O 110 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7765 (ptpt) REVERT: O 111 GLU cc_start: 0.8315 (mp0) cc_final: 0.8000 (mp0) REVERT: O 152 ASN cc_start: 0.8069 (t0) cc_final: 0.7861 (t0) outliers start: 71 outliers final: 27 residues processed: 437 average time/residue: 0.6409 time to fit residues: 322.7772 Evaluate side-chains 391 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 349 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 B residue 39 VAL Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 179 LYS 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 93 MET Chi-restraints excluded: chain F residue 147 THR 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 137 PHE Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 399 GLU Chi-restraints excluded: chain H residue 408 LYS Chi-restraints excluded: chain H residue 549 ILE Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 125 GLN Chi-restraints excluded: chain K residue 603 ILE Chi-restraints excluded: chain L residue 556 ASN Chi-restraints excluded: chain L residue 577 GLU Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 87 CYS Chi-restraints excluded: chain O residue 110 LYS Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 187 GLU Chi-restraints excluded: chain O residue 190 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 51 optimal weight: 0.9980 chunk 227 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 195 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 chunk 233 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 240 optimal weight: 0.9990 chunk 147 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 171 ASN E 32 GLN E 171 ASN G 42 ASN G 81 ASN H 479 ASN I 438 ASN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 119 HIS K 510 HIS ** K 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 574 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.163314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.124409 restraints weight = 28105.422| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.31 r_work: 0.3186 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24439 Z= 0.138 Angle : 0.585 15.156 33368 Z= 0.296 Chirality : 0.042 0.201 3870 Planarity : 0.004 0.058 3956 Dihedral : 14.870 179.531 4375 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.00 % Allowed : 29.85 % Favored : 67.15 % 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 are not related in a simple way. whole: 0.17 (0.15), residues: 2762 helix: 1.73 (0.17), residues: 935 sheet: 0.08 (0.22), residues: 492 loop : -1.08 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 102 TYR 0.022 0.001 TYR I 599 PHE 0.028 0.001 PHE C 133 TRP 0.021 0.001 TRP L 535 HIS 0.007 0.001 HIS H 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (24400) covalent geometry : angle 0.54424 / 0.29 (33320) hydrogen bonds : bond 0.03572 / 2.32 ( 1037) hydrogen bonds : angle 4.47344 / 3.11 ( 3063) metal coordination : bond 0.00788 / 0.48 ( 39) metal coordination : angle 5.65895 / 3.48 ( 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 439 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 369 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6590 (tpp) REVERT: A 18 LEU cc_start: 0.6266 (tp) cc_final: 0.5451 (mp) REVERT: A 51 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.7757 (t80) REVERT: A 55 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7772 (mm) REVERT: A 85 VAL cc_start: 0.7731 (OUTLIER) cc_final: 0.7423 (p) REVERT: A 154 GLN cc_start: 0.7396 (mm-40) cc_final: 0.7149 (mm110) REVERT: A 169 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7060 (mp0) REVERT: A 191 GLU cc_start: 0.8388 (tt0) cc_final: 0.8027 (tp30) REVERT: B 22 GLU cc_start: 0.8149 (tp30) cc_final: 0.7896 (tp30) REVERT: B 62 MET cc_start: 0.8291 (mtp) cc_final: 0.8078 (mtm) REVERT: B 66 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7871 (mtpt) REVERT: B 69 ASN cc_start: 0.8150 (t0) cc_final: 0.7727 (p0) REVERT: B 154 GLN cc_start: 0.7899 (mm110) cc_final: 0.7576 (mm110) REVERT: C 83 ARG cc_start: 0.8304 (mtm-85) cc_final: 0.7959 (ptp90) REVERT: C 85 VAL cc_start: 0.7832 (m) cc_final: 0.7624 (p) REVERT: D 75 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7737 (mm-30) REVERT: D 123 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7951 (mt-10) REVERT: D 166 LYS cc_start: 0.8730 (mtpp) cc_final: 0.8353 (mtmt) REVERT: D 179 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8438 (ptpt) REVERT: E 29 GLU cc_start: 0.8415 (mt-10) cc_final: 0.7778 (mm-30) REVERT: E 92 SER cc_start: 0.8852 (p) cc_final: 0.8557 (t) REVERT: E 127 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8231 (mmtm) REVERT: F 112 GLN cc_start: 0.8363 (mt0) cc_final: 0.8008 (mp10) REVERT: F 123 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7868 (mt-10) REVERT: F 127 LYS cc_start: 0.8223 (mttp) cc_final: 0.7351 (mtmm) REVERT: F 145 THR cc_start: 0.8549 (m) cc_final: 0.8319 (p) REVERT: F 187 GLU cc_start: 0.7865 (pt0) cc_final: 0.7340 (pp20) REVERT: G 56 PHE cc_start: 0.7736 (t80) cc_final: 0.7310 (t80) REVERT: G 132 GLU cc_start: 0.7308 (pp20) cc_final: 0.7015 (pp20) REVERT: G 191 PHE cc_start: 0.7666 (p90) cc_final: 0.7340 (p90) REVERT: H 99 ASP cc_start: 0.8733 (t70) cc_final: 0.8427 (t0) REVERT: H 134 ILE cc_start: 0.8042 (pt) cc_final: 0.7798 (pt) REVERT: H 152 SER cc_start: 0.8438 (OUTLIER) cc_final: 0.8189 (p) REVERT: H 253 ILE cc_start: 0.7049 (mt) cc_final: 0.6603 (mm) REVERT: H 395 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7931 (tt) REVERT: H 456 SER cc_start: 0.7307 (p) cc_final: 0.7088 (m) REVERT: H 596 ASN cc_start: 0.7966 (m-40) cc_final: 0.7382 (p0) REVERT: I 450 TYR cc_start: 0.5712 (m-80) cc_final: 0.5013 (m-10) REVERT: I 451 ARG cc_start: 0.7520 (mtp180) cc_final: 0.6915 (mmm-85) REVERT: I 518 GLU cc_start: 0.7832 (tp30) cc_final: 0.7397 (tp30) REVERT: J 13 LYS cc_start: 0.8504 (ttmm) cc_final: 0.7737 (ttpt) REVERT: J 52 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8649 (tttt) REVERT: J 125 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7970 (mp10) REVERT: K 166 PHE cc_start: 0.6327 (m-80) cc_final: 0.5352 (p90) REVERT: K 186 ASP cc_start: 0.6032 (t70) cc_final: 0.5751 (p0) REVERT: K 394 PHE cc_start: 0.7892 (m-80) cc_final: 0.7583 (m-80) REVERT: K 461 GLU cc_start: 0.7568 (tt0) cc_final: 0.7097 (tt0) REVERT: K 465 ARG cc_start: 0.7606 (ptp-170) cc_final: 0.7235 (pmm-80) REVERT: L 467 GLU cc_start: 0.6456 (pt0) cc_final: 0.6094 (pt0) REVERT: L 469 ASN cc_start: 0.7751 (m110) cc_final: 0.6997 (m-40) REVERT: L 512 LYS cc_start: 0.8375 (tppp) cc_final: 0.7587 (tppt) REVERT: L 518 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7871 (tm-30) REVERT: L 524 LYS cc_start: 0.8450 (mttp) cc_final: 0.8160 (mmtm) REVERT: L 537 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8035 (mm-30) REVERT: L 542 GLN cc_start: 0.7844 (mt0) cc_final: 0.7449 (mt0) REVERT: L 575 GLU cc_start: 0.7049 (tp30) cc_final: 0.6644 (tp30) REVERT: L 577 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7352 (mp0) REVERT: O 16 SER cc_start: 0.9203 (m) cc_final: 0.8980 (p) REVERT: O 87 CYS cc_start: 0.7328 (OUTLIER) cc_final: 0.6800 (m) REVERT: O 93 MET cc_start: 0.8180 (tpt) cc_final: 0.7933 (mmm) REVERT: O 110 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7722 (ptpt) REVERT: O 111 GLU cc_start: 0.8323 (mp0) cc_final: 0.7992 (mp0) REVERT: O 152 ASN cc_start: 0.8083 (t0) cc_final: 0.7883 (t0) outliers start: 70 outliers final: 27 residues processed: 418 average time/residue: 0.6123 time to fit residues: 294.9761 Evaluate side-chains 402 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 359 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 104 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 66 LYS 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 120 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 147 THR 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 137 PHE Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 549 ILE Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain J residue 125 GLN Chi-restraints excluded: chain K residue 603 ILE Chi-restraints excluded: chain L residue 556 ASN Chi-restraints excluded: chain L residue 577 GLU Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 87 CYS Chi-restraints excluded: chain O residue 110 LYS Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 187 GLU Chi-restraints excluded: chain O residue 190 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 228 optimal weight: 9.9990 chunk 246 optimal weight: 30.0000 chunk 272 optimal weight: 0.0000 chunk 208 optimal weight: 0.8980 chunk 144 optimal weight: 0.5980 chunk 163 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 227 optimal weight: 7.9990 chunk 173 optimal weight: 1.9990 chunk 127 optimal weight: 0.0980 chunk 164 optimal weight: 9.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 171 ASN E 32 GLN E 171 ASN G 42 ASN G 81 ASN H 479 ASN H 551 GLN I 438 ASN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 574 ASN O 107 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.164389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.125517 restraints weight = 28354.602| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.26 r_work: 0.3209 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24439 Z= 0.123 Angle : 0.569 14.469 33368 Z= 0.290 Chirality : 0.042 0.205 3870 Planarity : 0.004 0.061 3956 Dihedral : 14.867 179.348 4375 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.57 % Allowed : 30.23 % Favored : 67.20 % 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 are not related in a simple way. whole: 0.24 (0.15), residues: 2762 helix: 1.81 (0.17), residues: 936 sheet: 0.04 (0.21), residues: 507 loop : -1.02 (0.16), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 409 TYR 0.017 0.001 TYR L 599 PHE 0.029 0.001 PHE C 133 TRP 0.026 0.001 TRP L 535 HIS 0.005 0.001 HIS K 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (24400) covalent geometry : angle 0.53187 / 0.29 (33320) hydrogen bonds : bond 0.03545 / 2.28 ( 1037) hydrogen bonds : angle 4.41348 / 3.06 ( 3063) metal coordination : bond 0.00641 / 0.39 ( 39) metal coordination : angle 5.33897 / 3.30 ( 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 435 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 375 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.6944 (OUTLIER) cc_final: 0.6482 (tpp) REVERT: A 18 LEU cc_start: 0.6186 (tp) cc_final: 0.5370 (mp) REVERT: A 51 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7779 (t80) REVERT: A 55 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7801 (mm) REVERT: A 85 VAL cc_start: 0.7653 (OUTLIER) cc_final: 0.7383 (p) REVERT: A 154 GLN cc_start: 0.7437 (mm-40) cc_final: 0.7229 (mm110) REVERT: A 166 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7472 (tmmt) REVERT: A 169 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7091 (mp0) REVERT: A 191 GLU cc_start: 0.8326 (tt0) cc_final: 0.7978 (tp30) REVERT: B 66 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7955 (mtpt) REVERT: B 69 ASN cc_start: 0.8092 (t0) cc_final: 0.7662 (p0) REVERT: B 154 GLN cc_start: 0.7924 (mm110) cc_final: 0.7628 (mm110) REVERT: C 83 ARG cc_start: 0.8275 (mtm-85) cc_final: 0.7918 (ptp90) REVERT: C 85 VAL cc_start: 0.7823 (m) cc_final: 0.7621 (p) REVERT: C 108 ASP cc_start: 0.7877 (m-30) cc_final: 0.7629 (t0) REVERT: C 111 GLU cc_start: 0.8432 (pm20) cc_final: 0.8116 (pm20) REVERT: D 75 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7687 (mm-30) REVERT: D 166 LYS cc_start: 0.8717 (mtpp) cc_final: 0.8345 (mtmt) REVERT: D 179 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8423 (ptpt) REVERT: E 29 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7715 (mm-30) REVERT: E 92 SER cc_start: 0.8815 (p) cc_final: 0.8559 (t) REVERT: E 127 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8305 (mmtm) REVERT: F 93 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7063 (mpt) REVERT: F 112 GLN cc_start: 0.8327 (mt0) cc_final: 0.7949 (mp10) REVERT: F 123 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7783 (mt-10) REVERT: F 127 LYS cc_start: 0.8209 (mttp) cc_final: 0.7335 (mtmm) REVERT: F 145 THR cc_start: 0.8540 (m) cc_final: 0.8325 (p) REVERT: F 187 GLU cc_start: 0.7891 (pt0) cc_final: 0.7369 (pp20) REVERT: G 41 PHE cc_start: 0.7596 (t80) cc_final: 0.7367 (t80) REVERT: G 56 PHE cc_start: 0.7746 (t80) cc_final: 0.7285 (t80) REVERT: G 191 PHE cc_start: 0.7654 (p90) cc_final: 0.7342 (p90) REVERT: H 99 ASP cc_start: 0.8777 (t70) cc_final: 0.8468 (t0) REVERT: H 102 ARG cc_start: 0.8161 (mtp-110) cc_final: 0.7721 (ttt90) REVERT: H 134 ILE cc_start: 0.7996 (pt) cc_final: 0.7745 (pt) REVERT: H 152 SER cc_start: 0.8368 (OUTLIER) cc_final: 0.8145 (p) REVERT: H 253 ILE cc_start: 0.7172 (mt) cc_final: 0.6711 (mm) REVERT: H 395 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7807 (tt) REVERT: H 456 SER cc_start: 0.7312 (p) cc_final: 0.7102 (m) REVERT: H 475 ASP cc_start: 0.6407 (m-30) cc_final: 0.5909 (t0) REVERT: H 596 ASN cc_start: 0.7952 (m-40) cc_final: 0.7370 (p0) REVERT: I 450 TYR cc_start: 0.5569 (m-80) cc_final: 0.4919 (m-10) REVERT: I 451 ARG cc_start: 0.7477 (mtp180) cc_final: 0.6883 (mmm-85) REVERT: I 518 GLU cc_start: 0.7737 (tp30) cc_final: 0.7304 (tp30) REVERT: J 13 LYS cc_start: 0.8460 (ttmm) cc_final: 0.7658 (ttpt) REVERT: J 52 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8712 (tttt) REVERT: J 125 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7918 (mp10) REVERT: K 166 PHE cc_start: 0.6234 (m-80) cc_final: 0.5395 (p90) REVERT: K 186 ASP cc_start: 0.6137 (t70) cc_final: 0.5858 (p0) REVERT: K 394 PHE cc_start: 0.7859 (m-80) cc_final: 0.7581 (m-80) REVERT: K 461 GLU cc_start: 0.7633 (tt0) cc_final: 0.7141 (tt0) REVERT: K 465 ARG cc_start: 0.7449 (ptp-170) cc_final: 0.7074 (pmm-80) REVERT: L 467 GLU cc_start: 0.6425 (pt0) cc_final: 0.6165 (pt0) REVERT: L 469 ASN cc_start: 0.7810 (m110) cc_final: 0.7033 (m-40) REVERT: L 512 LYS cc_start: 0.8343 (tppp) cc_final: 0.7506 (tppt) REVERT: L 518 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7858 (tm-30) REVERT: L 524 LYS cc_start: 0.8416 (mttp) cc_final: 0.8138 (mmtm) REVERT: L 577 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: O 16 SER cc_start: 0.9186 (m) cc_final: 0.8963 (p) REVERT: O 87 CYS cc_start: 0.7272 (OUTLIER) cc_final: 0.6733 (m) REVERT: O 93 MET cc_start: 0.8243 (tpt) cc_final: 0.8005 (mmm) REVERT: O 110 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7701 (ptpt) REVERT: O 111 GLU cc_start: 0.8304 (mp0) cc_final: 0.7967 (mp0) outliers start: 60 outliers final: 27 residues processed: 419 average time/residue: 0.5760 time to fit residues: 278.3356 Evaluate side-chains 397 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 353 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 104 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 126 THR 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 75 GLU Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 147 THR 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 395 LEU Chi-restraints excluded: chain H residue 408 LYS 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 K residue 603 ILE Chi-restraints excluded: chain L residue 556 ASN Chi-restraints excluded: chain L residue 577 GLU Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 87 CYS Chi-restraints excluded: chain O residue 110 LYS Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 187 GLU Chi-restraints excluded: chain O residue 190 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 53 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 252 optimal weight: 0.5980 chunk 129 optimal weight: 20.0000 chunk 80 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 178 ASN E 32 GLN 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** K 510 HIS ** K 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 438 ASN L 542 GLN O 107 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.158339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.119012 restraints weight = 28433.344| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.52 r_work: 0.3084 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 24439 Z= 0.260 Angle : 0.699 19.080 33368 Z= 0.346 Chirality : 0.047 0.190 3870 Planarity : 0.005 0.058 3956 Dihedral : 14.753 179.774 4373 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.70 % Allowed : 30.57 % Favored : 66.72 % 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 are not related in a simple way. whole: 0.08 (0.15), residues: 2762 helix: 1.60 (0.17), residues: 939 sheet: -0.01 (0.22), residues: 492 loop : -1.06 (0.16), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 409 TYR 0.031 0.002 TYR G 161 PHE 0.032 0.002 PHE A 167 TRP 0.036 0.002 TRP L 535 HIS 0.008 0.001 HIS K 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.26 (24400) covalent geometry : angle 0.65145 / 0.34 (33320) hydrogen bonds : bond 0.03870 / 2.51 ( 1037) hydrogen bonds : angle 4.68322 / 3.24 ( 3063) metal coordination : bond 0.01295 / 0.82 ( 39) metal coordination : angle 6.71625 / 4.18 ( 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 434 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 371 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7022 (ttm) cc_final: 0.6613 (tpp) REVERT: A 18 LEU cc_start: 0.6187 (tp) cc_final: 0.5406 (mp) REVERT: A 51 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7823 (t80) REVERT: A 55 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7805 (mm) REVERT: A 62 MET cc_start: 0.6457 (mpp) cc_final: 0.6123 (mpt) REVERT: A 85 VAL cc_start: 0.7704 (OUTLIER) cc_final: 0.7427 (p) REVERT: A 154 GLN cc_start: 0.7556 (mm-40) cc_final: 0.7331 (mm110) REVERT: A 166 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7448 (tmmt) REVERT: A 169 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7243 (mp0) REVERT: B 69 ASN cc_start: 0.8084 (t0) cc_final: 0.7607 (p0) REVERT: B 70 VAL cc_start: 0.7604 (OUTLIER) cc_final: 0.7347 (p) REVERT: B 154 GLN cc_start: 0.7941 (mm110) cc_final: 0.7662 (mm110) REVERT: C 5 MET cc_start: 0.8498 (mtm) cc_final: 0.7955 (mtt) REVERT: C 33 LYS cc_start: 0.8640 (mptt) cc_final: 0.8209 (ptmt) REVERT: C 83 ARG cc_start: 0.8164 (mtm-85) cc_final: 0.7731 (mtm-85) REVERT: C 108 ASP cc_start: 0.8164 (m-30) cc_final: 0.7865 (t0) REVERT: C 111 GLU cc_start: 0.8458 (pm20) cc_final: 0.8211 (pm20) REVERT: C 156 LYS cc_start: 0.8227 (mttt) cc_final: 0.7537 (pttp) REVERT: D 13 LYS cc_start: 0.8594 (tptt) cc_final: 0.8171 (ttpt) REVERT: D 179 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8568 (ptpt) REVERT: E 29 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7815 (mm-30) REVERT: E 110 LYS cc_start: 0.8525 (ptmm) cc_final: 0.8169 (ptpt) REVERT: E 127 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8390 (mmtm) REVERT: F 112 GLN cc_start: 0.8468 (mt0) cc_final: 0.8213 (mp10) REVERT: F 123 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8173 (mt-10) REVERT: F 127 LYS cc_start: 0.8361 (mttp) cc_final: 0.7695 (mtmt) REVERT: F 187 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7455 (pp20) REVERT: G 56 PHE cc_start: 0.7751 (t80) cc_final: 0.7281 (t80) REVERT: G 132 GLU cc_start: 0.6950 (pp20) cc_final: 0.6687 (pp20) REVERT: G 191 PHE cc_start: 0.7748 (p90) cc_final: 0.7415 (p90) REVERT: H 99 ASP cc_start: 0.8826 (t70) cc_final: 0.8610 (t0) REVERT: H 127 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7483 (pt0) REVERT: H 134 ILE cc_start: 0.8075 (pt) cc_final: 0.7841 (pt) REVERT: H 152 SER cc_start: 0.8608 (OUTLIER) cc_final: 0.8339 (p) REVERT: H 253 ILE cc_start: 0.7358 (mt) cc_final: 0.6884 (mm) REVERT: H 395 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7931 (tt) REVERT: H 456 SER cc_start: 0.7440 (p) cc_final: 0.7234 (m) REVERT: H 475 ASP cc_start: 0.6410 (m-30) cc_final: 0.5872 (t0) REVERT: H 596 ASN cc_start: 0.7985 (m-40) cc_final: 0.7380 (p0) REVERT: I 450 TYR cc_start: 0.5875 (m-80) cc_final: 0.4998 (m-10) REVERT: I 451 ARG cc_start: 0.7646 (mtp180) cc_final: 0.6909 (mmm-85) REVERT: I 518 GLU cc_start: 0.7824 (tp30) cc_final: 0.7413 (tp30) REVERT: I 579 LEU cc_start: 0.8260 (mt) cc_final: 0.8049 (mt) REVERT: J 13 LYS cc_start: 0.8651 (ttmm) cc_final: 0.7971 (ttpt) REVERT: J 52 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8758 (tttt) REVERT: K 191 TYR cc_start: 0.7300 (m-80) cc_final: 0.7009 (m-80) REVERT: K 394 PHE cc_start: 0.7924 (m-80) cc_final: 0.7413 (m-80) REVERT: K 461 GLU cc_start: 0.7592 (tt0) cc_final: 0.7136 (tt0) REVERT: K 465 ARG cc_start: 0.7581 (ptp-170) cc_final: 0.7194 (pmm-80) REVERT: L 467 GLU cc_start: 0.6473 (pt0) cc_final: 0.6032 (pt0) REVERT: L 512 LYS cc_start: 0.8479 (tppp) cc_final: 0.7535 (tppt) REVERT: L 518 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7925 (tm-30) REVERT: L 577 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: O 25 ARG cc_start: 0.8250 (ttm-80) cc_final: 0.7915 (mtm110) REVERT: O 26 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8284 (mm-30) REVERT: O 87 CYS cc_start: 0.7504 (OUTLIER) cc_final: 0.6972 (m) REVERT: O 93 MET cc_start: 0.8360 (tpt) cc_final: 0.8049 (mmm) REVERT: O 110 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7957 (ptpt) REVERT: O 111 GLU cc_start: 0.8421 (mp0) cc_final: 0.8036 (mp0) outliers start: 63 outliers final: 27 residues processed: 416 average time/residue: 0.5794 time to fit residues: 278.5961 Evaluate side-chains 391 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 348 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 166 LYS 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 B residue 195 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain H residue 29 CYS Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 408 LYS Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 603 ILE Chi-restraints excluded: chain L residue 556 ASN Chi-restraints excluded: chain L residue 577 GLU Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 87 CYS Chi-restraints excluded: chain O residue 110 LYS Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 190 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 85 optimal weight: 2.9990 chunk 272 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 110 optimal weight: 0.5980 chunk 226 optimal weight: 9.9990 chunk 266 optimal weight: 0.9990 chunk 162 optimal weight: 10.0000 chunk 219 optimal weight: 0.6980 chunk 247 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 171 ASN E 32 GLN G 42 ASN H 479 ASN H 551 GLN I 438 ASN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.161378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.122443 restraints weight = 28116.010| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.34 r_work: 0.3144 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24439 Z= 0.150 Angle : 0.613 16.624 33368 Z= 0.310 Chirality : 0.043 0.200 3870 Planarity : 0.004 0.063 3956 Dihedral : 14.821 179.731 4373 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.36 % Allowed : 31.86 % Favored : 65.78 % 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 are not related in a simple way. whole: 0.16 (0.15), residues: 2762 helix: 1.70 (0.17), residues: 939 sheet: -0.04 (0.21), residues: 497 loop : -1.02 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 102 TYR 0.019 0.001 TYR G 92 PHE 0.026 0.001 PHE C 133 TRP 0.042 0.001 TRP L 535 HIS 0.005 0.001 HIS K 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (24400) covalent geometry : angle 0.56999 / 0.31 (33320) hydrogen bonds : bond 0.03672 / 2.39 ( 1037) hydrogen bonds : angle 4.59058 / 3.19 ( 3063) metal coordination : bond 0.00868 / 0.52 ( 39) metal coordination : angle 5.97270 / 3.68 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9213.03 seconds wall clock time: 157 minutes 30.84 seconds (9450.84 seconds total)