Starting phenix.real_space_refine on Sat Jul 4 21:12:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yhd_39287/07_2026/8yhd_39287_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yhd_39287/07_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_39287/07_2026/8yhd_39287.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yhd_39287/07_2026/8yhd_39287.map" model { file = "/net/cci-nas-00/data/ceres_data/8yhd_39287/07_2026/8yhd_39287_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yhd_39287/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 4.16, per 1000 atoms: 0.17 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: 1.34 Conformation dependent library (CDL) restraints added in 921.4 milliseconds 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: 2.39 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: 3.93 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5806 1.33 - 1.45: 5451 1.45 - 1.58: 12818 1.58 - 1.70: 177 1.70 - 1.82: 148 Bond restraints: 24400 Sorted by residual: bond pdb=" C ARG C 40 " pdb=" N LYS C 41 " ideal model delta sigma weight residual 1.331 1.222 0.110 1.38e-02 5.25e+03 6.30e+01 bond pdb=" C ALA G 40 " pdb=" N PHE G 41 " ideal model delta sigma weight residual 1.334 1.435 -0.100 1.33e-02 5.65e+03 5.68e+01 bond pdb=" C ALA H 407 " pdb=" N LYS H 408 " ideal model delta sigma weight residual 1.334 1.238 0.096 1.33e-02 5.65e+03 5.21e+01 bond pdb=" C SER C 117 " pdb=" N THR C 118 " ideal model delta sigma weight residual 1.331 1.426 -0.095 1.33e-02 5.65e+03 5.08e+01 bond pdb=" C ARG B 40 " pdb=" N LYS B 41 " ideal model delta sigma weight residual 1.330 1.230 0.100 1.45e-02 4.76e+03 4.80e+01 ... (remaining 24395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 31561 2.61 - 5.22: 1468 5.22 - 7.83: 227 7.83 - 10.43: 60 10.43 - 13.04: 4 Bond angle restraints: 33320 Sorted by residual: angle pdb=" N HIS H 67 " pdb=" CA HIS H 67 " pdb=" C HIS H 67 " ideal model delta sigma weight residual 114.12 103.74 10.38 1.39e+00 5.18e-01 5.58e+01 angle pdb=" N ALA C 54 " pdb=" CA ALA C 54 " pdb=" C ALA C 54 " ideal model delta sigma weight residual 113.50 104.97 8.53 1.23e+00 6.61e-01 4.81e+01 angle pdb=" N GLY C 53 " pdb=" CA GLY C 53 " pdb=" C GLY C 53 " ideal model delta sigma weight residual 113.58 106.39 7.19 1.07e+00 8.73e-01 4.51e+01 angle pdb=" N PRO G 86 " pdb=" CA PRO G 86 " pdb=" C PRO G 86 " ideal model delta sigma weight residual 113.81 104.40 9.41 1.45e+00 4.76e-01 4.22e+01 angle pdb=" N LYS E 33 " pdb=" CA LYS E 33 " pdb=" C LYS E 33 " ideal model delta sigma weight residual 112.90 104.51 8.39 1.31e+00 5.83e-01 4.10e+01 ... (remaining 33315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 14291 35.97 - 71.95: 595 71.95 - 107.92: 41 107.92 - 143.89: 0 143.89 - 179.86: 4 Dihedral angle restraints: 14931 sinusoidal: 6717 harmonic: 8214 Sorted by residual: dihedral pdb=" O4' U M 5 " pdb=" C1' U M 5 " pdb=" N1 U M 5 " pdb=" C2 U M 5 " ideal model delta sinusoidal sigma weight residual -128.00 51.86 -179.86 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U M 11 " pdb=" C1' U M 11 " pdb=" N1 U M 11 " pdb=" C2 U M 11 " ideal model delta sinusoidal sigma weight residual -128.00 50.86 -178.86 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U M 23 " pdb=" C1' U M 23 " pdb=" N1 U M 23 " pdb=" C2 U M 23 " ideal model delta sinusoidal sigma weight residual -128.00 41.61 -169.61 1 1.70e+01 3.46e-03 6.59e+01 ... (remaining 14928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3295 0.098 - 0.196: 512 0.196 - 0.293: 40 0.293 - 0.391: 10 0.391 - 0.489: 13 Chirality restraints: 3870 Sorted by residual: chirality pdb=" CB VAL O 23 " pdb=" CA VAL O 23 " pdb=" CG1 VAL O 23 " pdb=" CG2 VAL O 23 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 5.97e+00 chirality pdb=" P U M 23 " pdb=" OP1 U M 23 " pdb=" OP2 U M 23 " pdb=" O5' U M 23 " both_signs ideal model delta sigma weight residual True 2.41 -2.90 -0.49 2.00e-01 2.50e+01 5.95e+00 chirality pdb=" CB ILE H 57 " pdb=" CA ILE H 57 " pdb=" CG1 ILE H 57 " pdb=" CG2 ILE H 57 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.71e+00 ... (remaining 3867 not shown) Planarity restraints: 3956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 78 " -0.520 9.50e-02 1.11e+02 2.33e-01 3.32e+01 pdb=" NE ARG H 78 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG H 78 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG H 78 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG H 78 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR H 133 " -0.023 2.00e-02 2.50e+03 4.72e-02 2.23e+01 pdb=" C THR H 133 " 0.082 2.00e-02 2.50e+03 pdb=" O THR H 133 " -0.032 2.00e-02 2.50e+03 pdb=" N ILE H 134 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 554 " -0.420 9.50e-02 1.11e+02 1.88e-01 2.18e+01 pdb=" NE ARG L 554 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG L 554 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG L 554 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG L 554 " -0.014 2.00e-02 2.50e+03 ... (remaining 3953 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5009 2.78 - 3.31: 21634 3.31 - 3.84: 42262 3.84 - 4.37: 50810 4.37 - 4.90: 83635 Nonbonded interactions: 203350 Sorted by model distance: nonbonded pdb=" OG SER D 117 " pdb=" OE2 GLU D 137 " model vdw 2.251 3.040 nonbonded pdb=" OE1 GLU C 123 " pdb=" OG SER C 128 " model vdw 2.273 3.040 nonbonded pdb=" OG SER K 527 " pdb=" OP1 U N 23 " model vdw 2.283 3.040 nonbonded pdb=" OG SER G 178 " pdb=" O PHE G 233 " model vdw 2.286 3.040 nonbonded pdb=" OG SER I 527 " pdb=" OP1 U N 17 " model vdw 2.287 3.040 ... (remaining 203345 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 73 or (resid 79 and (name N or name CA or name C \ or name O or name CB )) or resid 80 through 82 or (resid 83 and (name N or name \ CA or name C or name O or name CB )) or resid 84 through 94 or (resid 95 through \ 96 and (name N or name CA or name C or name O or name CB )) or resid 97 through \ 154 or (resid 155 through 156 and (name N or name CA or name C or name O or nam \ e CB )) or resid 157 through 165 or (resid 166 and (name N or name CA or name C \ or name O or name CB )) or resid 167 through 196 or resid 301)) selection = (chain 'O' and (resid 2 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 or (resid 15 and (name N or name CA or name \ C or name O or name CB )) or resid 16 through 19 or (resid 20 and (name N or na \ me CA or name C or name O or name CB )) or resid 21 through 23 or (resid 24 thro \ ugh 25 and (name N or name CA or name C or name O or name CB )) or (resid 41 thr \ ough 43 and (name N or name CA or name C or name O or name CB )) or resid 44 thr \ ough 63 or (resid 64 through 66 and (name N or name CA or name C or name O or na \ me CB )) or resid 67 through 68 or (resid 69 through 70 and (name N or name CA o \ r name C or name O or name CB )) or resid 71 through 109 or (resid 110 and (name \ N or name CA or name C or name O or name CB )) or resid 111 through 114 or (res \ id 115 through 116 and (name N or name CA or name C or name O or name CB )) or r \ esid 137 through 169 or (resid 170 and (name N or name CA or name C or name O or \ name CB )) or resid 171 through 176 or (resid 177 and (name N or name CA or nam \ e C or name O or name CB )) or resid 178 or (resid 179 and (name N or name CA or \ name C or name O or name CB )) or resid 180 or (resid 181 and (name N or name C \ A or name C or name O or name CB )) or resid 182 or (resid 183 and (name N or na \ me CA or name C or name O or name CB )) or resid 184 through 186 or (resid 187 a \ nd (name N or name CA or name C or name O or name CB )) or resid 188 or (resid 1 \ 89 and (name N or name CA or name C or name O or name CB )) or resid 190 through \ 301)) } ncs_group { reference = (chain 'B' and (resid 2 through 33 or (resid 34 and (name N or name CA or name C \ or name O or name CB )) or resid 35 through 94 or (resid 95 through 96 and (nam \ e N or name CA or name C or name O or name CB )) or resid 97 through 124 or (res \ id 125 and (name N or name CA or name C or name O or name CB )) or resid 126 thr \ ough 199 or (resid 200 and (name N or name CA or name C or name O or name CB )) \ or resid 301)) selection = (chain 'C' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 31 or (resid 32 through 34 and (name N or name CA \ or name C or name O or name CB )) or resid 35 through 94 or (resid 95 through 9 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 97 through 1 \ 09 or (resid 110 and (name N or name CA or name C or name O or name CB )) or res \ id 111 through 124 or (resid 125 and (name N or name CA or name C or name O or n \ ame CB )) or resid 126 through 199 or (resid 200 and (name N or name CA or name \ C or name O or name CB )) or resid 301)) selection = (chain 'D' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 31 or (resid 32 through 34 and (name N or name CA \ or name C or name O or name CB )) or resid 35 through 94 or (resid 95 through 9 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 97 through 1 \ 09 or (resid 110 and (name N or name CA or name C or name O or name CB )) or res \ id 111 through 199 or (resid 200 and (name N or name CA or name C or name O or n \ ame CB )) or resid 301)) selection = (chain 'E' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 31 or (resid 32 through 34 and (name N or name CA \ or name C or name O or name CB )) or resid 35 through 94 or (resid 95 through 9 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 97 through 1 \ 09 or (resid 110 and (name N or name CA or name C or name O or name CB )) or res \ id 111 through 124 or (resid 125 and (name N or name CA or name C or name O or n \ ame CB )) or resid 126 through 199 or (resid 200 and (name N or name CA or name \ C or name O or name CB )) or resid 301)) selection = (chain 'F' and (resid 2 through 31 or (resid 32 through 34 and (name N or name C \ A or name C or name O or name CB )) or resid 35 through 109 or (resid 110 and (n \ ame N or name CA or name C or name O or name CB )) or resid 111 through 124 or ( \ resid 125 and (name N or name CA or name C or name O or name CB )) or resid 126 \ through 301)) selection = (chain 'J' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 31 or (resid 32 through 34 and (name N or name CA \ or name C or name O or name CB )) or resid 35 through 94 or (resid 95 through 9 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 97 through 1 \ 09 or (resid 110 and (name N or name CA or name C or name O or name CB )) or res \ id 111 through 124 or (resid 125 and (name N or name CA or name C or name O or n \ ame CB )) or resid 126 through 199 or (resid 200 and (name N or name CA or name \ C or name O or name CB )) or resid 301)) } ncs_group { reference = (chain 'I' and (resid 435 through 479 or (resid 480 through 481 and (name N or n \ ame CA or name C or name O or name CB )) or resid 482 through 483 or (resid 484 \ through 486 and (name N or name CA or name C or name O or name CB )) or resid 48 \ 7 through 490 or resid 505 through 510 or (resid 511 and (name N or name CA or n \ ame C or name O or name CB )) or resid 512 through 577 or (resid 578 and (name N \ or name CA or name C or name O or name CB )) or resid 579 through 595 or (resid \ 596 and (name N or name CA or name C or name O or name CB )) or resid 597 throu \ gh 607 or (resid 608 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'L' and (resid 435 through 461 or (resid 462 and (name N or name CA or na \ me C or name O or name CB )) or resid 465 through 485 or (resid 486 and (name N \ or name CA or name C or name O or name CB )) or resid 487 through 489 or (resid \ 490 through 505 and (name N or name CA or name C or name O or name CB )) or resi \ d 506 through 608)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 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: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 22.380 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.030 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:6.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.040 ------------------------------------------------------------------------------- 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= 0.542 Angle : 1.299 21.532 33368 Z= 0.801 Chirality : 0.074 0.489 3870 Planarity : 0.012 0.233 3956 Dihedral : 18.371 179.863 9601 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.02 % Allowed : 26.80 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they 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 0.00834 / 0.51 (24400) covalent geometry : angle 1.26453 / 0.80 (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 : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 THR cc_start: 0.8491 (m) cc_final: 0.8220 (p) REVERT: A 109 THR cc_start: 0.7078 (p) cc_final: 0.6430 (m) REVERT: A 169 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7514 (mm-30) REVERT: A 196 ASP cc_start: 0.7913 (p0) cc_final: 0.7667 (p0) REVERT: B 158 LEU cc_start: 0.7648 (tp) cc_final: 0.7397 (tp) REVERT: C 83 ARG cc_start: 0.8321 (mtm-85) cc_final: 0.8096 (ptp90) REVERT: D 131 ASP cc_start: 0.7766 (t70) cc_final: 0.7549 (t0) REVERT: E 13 LYS cc_start: 0.8615 (ttpp) cc_final: 0.8196 (ttpp) REVERT: E 92 SER cc_start: 0.8919 (p) cc_final: 0.8700 (t) REVERT: F 123 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7737 (mt-10) REVERT: F 127 LYS cc_start: 0.8365 (mttp) cc_final: 0.7533 (mtmm) REVERT: G 59 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7741 (OUTLIER) REVERT: H 117 ASP cc_start: 0.7245 (m-30) cc_final: 0.7016 (m-30) REVERT: H 253 ILE cc_start: 0.8045 (mt) cc_final: 0.7841 (mm) REVERT: H 443 ASN cc_start: 0.6956 (p0) cc_final: 0.6571 (m110) REVERT: H 596 ASN cc_start: 0.7693 (m-40) cc_final: 0.7362 (p0) REVERT: I 450 TYR cc_start: 0.6456 (m-80) cc_final: 0.6109 (m-10) REVERT: I 512 LYS cc_start: 0.8054 (tppt) cc_final: 0.7846 (tptp) REVERT: I 518 GLU cc_start: 0.7849 (tp30) cc_final: 0.7559 (tm-30) REVERT: I 550 THR cc_start: 0.8536 (m) cc_final: 0.8305 (p) REVERT: J 5 MET cc_start: 0.8137 (mtm) cc_final: 0.7742 (mtm) REVERT: J 13 LYS cc_start: 0.8290 (ttmm) cc_final: 0.7838 (ttpt) REVERT: J 108 ASP cc_start: 0.8207 (m-30) cc_final: 0.7964 (m-30) REVERT: K 386 LEU cc_start: 0.8119 (mt) cc_final: 0.7557 (tt) REVERT: K 461 GLU cc_start: 0.7418 (tt0) cc_final: 0.6971 (tt0) REVERT: K 529 ASN cc_start: 0.8381 (t0) cc_final: 0.7458 (m-40) REVERT: K 584 TYR cc_start: 0.7610 (t80) cc_final: 0.7368 (t80) REVERT: L 479 ASN cc_start: 0.8776 (m-40) cc_final: 0.8503 (m-40) REVERT: L 593 TYR cc_start: 0.7230 (m-10) cc_final: 0.7025 (m-10) outliers start: 47 outliers final: 5 residues processed: 765 average time/residue: 0.5984 time to fit residues: 523.3402 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 : 0.850 ------------------------------------------------------------------------------- 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: 4.9990 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 H 551 GLN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 472 ASN I 556 ASN ** I 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 154 GLN K 469 ASN ** L 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 553 HIS O 112 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.167076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.128981 restraints weight = 28284.884| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.28 r_work: 0.3249 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.664 24439 Z= 0.219 Angle : 0.695 19.321 33368 Z= 0.357 Chirality : 0.046 0.299 3870 Planarity : 0.005 0.067 3956 Dihedral : 15.228 179.657 4382 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.73 % Allowed : 28.52 % Favored : 67.75 % 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: -1.36 (0.14), residues: 2762 helix: 0.04 (0.16), residues: 939 sheet: -0.42 (0.22), residues: 507 loop : -1.81 (0.15), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 95 TYR 0.023 0.002 TYR G 137 PHE 0.037 0.002 PHE G 74 TRP 0.013 0.001 TRP I 478 HIS 0.005 0.001 HIS H 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (24400) covalent geometry : angle 0.64489 / 0.35 (33320) hydrogen bonds : bond 0.04568 / 3.03 ( 1037) hydrogen bonds : angle 5.50095 / 3.81 ( 3063) metal coordination : bond 0.10707 / 4.29 ( 39) metal coordination : angle 6.82916 / 4.29 ( 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 542 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 455 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7039 (OUTLIER) cc_final: 0.6602 (tpp) REVERT: A 51 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7710 (t80) REVERT: A 55 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7754 (mm) REVERT: A 93 MET cc_start: 0.8174 (tpp) cc_final: 0.7923 (tpp) REVERT: A 165 LEU cc_start: 0.8191 (mt) cc_final: 0.7532 (mt) REVERT: A 169 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7253 (mp0) REVERT: A 191 GLU cc_start: 0.8221 (tt0) cc_final: 0.7916 (tp30) REVERT: A 196 ASP cc_start: 0.8032 (p0) cc_final: 0.7554 (p0) REVERT: B 76 SER cc_start: 0.8287 (t) cc_final: 0.7981 (m) REVERT: C 36 ASN cc_start: 0.8367 (m-40) cc_final: 0.7991 (m-40) REVERT: C 83 ARG cc_start: 0.8249 (mtm-85) cc_final: 0.7845 (ptp90) REVERT: C 123 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7312 (mm-30) REVERT: D 13 LYS cc_start: 0.8243 (tptt) cc_final: 0.8021 (tptm) REVERT: D 25 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7946 (ttp80) REVERT: D 29 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8327 (mt-10) REVERT: D 123 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.8015 (mt-10) REVERT: D 131 ASP cc_start: 0.7967 (t70) cc_final: 0.7679 (t0) REVERT: E 13 LYS cc_start: 0.8653 (ttpp) cc_final: 0.8323 (ttpp) REVERT: E 92 SER cc_start: 0.8885 (p) cc_final: 0.8626 (t) REVERT: E 110 LYS cc_start: 0.8178 (ptmm) cc_final: 0.7918 (ptpt) REVERT: F 123 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7824 (mt-10) REVERT: F 127 LYS cc_start: 0.8253 (mttp) cc_final: 0.7451 (mtmt) REVERT: F 145 THR cc_start: 0.8494 (m) cc_final: 0.8243 (p) REVERT: G 25 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7612 (mm) REVERT: G 130 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7707 (mt-10) REVERT: H 253 ILE cc_start: 0.7440 (mt) cc_final: 0.7098 (mm) REVERT: H 290 TYR cc_start: 0.7472 (p90) cc_final: 0.7246 (p90) REVERT: H 384 GLU cc_start: 0.8202 (tt0) cc_final: 0.7975 (tp30) REVERT: H 443 ASN cc_start: 0.6790 (p0) cc_final: 0.6398 (m110) REVERT: H 596 ASN cc_start: 0.7899 (m-40) cc_final: 0.7381 (p0) REVERT: I 450 TYR cc_start: 0.5794 (m-80) cc_final: 0.5253 (m-10) REVERT: I 485 MET cc_start: 0.6435 (ttm) cc_final: 0.5547 (ttp) REVERT: I 512 LYS cc_start: 0.7988 (tppt) cc_final: 0.7565 (tptp) REVERT: I 518 GLU cc_start: 0.7998 (tp30) cc_final: 0.7389 (tm-30) REVERT: J 5 MET cc_start: 0.8280 (mtm) cc_final: 0.8016 (mtm) REVERT: J 13 LYS cc_start: 0.8418 (ttmm) cc_final: 0.7766 (ttpt) REVERT: J 52 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8761 (tttt) REVERT: J 137 GLU cc_start: 0.8424 (pt0) cc_final: 0.8178 (pt0) REVERT: K 166 PHE cc_start: 0.6299 (m-80) cc_final: 0.5126 (p90) REVERT: K 386 LEU cc_start: 0.7826 (mt) cc_final: 0.7573 (tt) REVERT: K 394 PHE cc_start: 0.7707 (m-80) cc_final: 0.7359 (m-80) REVERT: K 461 GLU cc_start: 0.7639 (tt0) cc_final: 0.7217 (tt0) REVERT: K 529 ASN cc_start: 0.8443 (t0) cc_final: 0.7314 (m110) REVERT: K 561 ARG cc_start: 0.8638 (tpp80) cc_final: 0.8328 (ttm110) REVERT: L 462 LYS cc_start: 0.6002 (mmmm) cc_final: 0.5651 (mmmm) REVERT: L 467 GLU cc_start: 0.6661 (pt0) cc_final: 0.6287 (pt0) REVERT: L 479 ASN cc_start: 0.8824 (m-40) cc_final: 0.8342 (m-40) REVERT: L 577 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: L 593 TYR cc_start: 0.6994 (m-10) cc_final: 0.6726 (m-10) REVERT: L 603 ILE cc_start: 0.7312 (pp) cc_final: 0.7023 (pt) REVERT: O 16 SER cc_start: 0.9096 (m) cc_final: 0.8863 (p) REVERT: O 123 GLU cc_start: 0.8430 (mt-10) cc_final: 0.7990 (mm-30) REVERT: O 152 ASN cc_start: 0.8146 (t0) cc_final: 0.7942 (t0) outliers start: 87 outliers final: 24 residues processed: 514 average time/residue: 0.5853 time to fit residues: 346.3161 Evaluate side-chains 403 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 370 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 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 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 147 THR Chi-restraints excluded: chain O residue 190 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 7 optimal weight: 7.9990 chunk 214 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 229 optimal weight: 0.8980 chunk 275 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 267 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 251 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 107 ASN D 178 ASN E 32 GLN E 178 ASN F 171 ASN G 20 ASN G 42 ASN G 81 ASN ** H 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 479 ASN H 551 GLN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 119 HIS ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.163135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.124118 restraints weight = 28272.332| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.47 r_work: 0.3166 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24439 Z= 0.186 Angle : 0.650 18.440 33368 Z= 0.333 Chirality : 0.046 0.293 3870 Planarity : 0.005 0.053 3956 Dihedral : 15.004 179.604 4375 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.63 % Allowed : 27.10 % 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: -0.76 (0.15), residues: 2762 helix: 0.77 (0.16), residues: 940 sheet: -0.44 (0.22), residues: 528 loop : -1.49 (0.15), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 95 TYR 0.020 0.001 TYR L 599 PHE 0.025 0.002 PHE C 133 TRP 0.012 0.001 TRP H 125 HIS 0.012 0.002 HIS H 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (24400) covalent geometry : angle 0.60324 / 0.33 (33320) hydrogen bonds : bond 0.04133 / 2.70 ( 1037) hydrogen bonds : angle 4.94907 / 3.44 ( 3063) metal coordination : bond 0.00808 / 0.55 ( 39) metal coordination : angle 6.37691 / 4.04 ( 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 524 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 416 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.6988 (OUTLIER) cc_final: 0.6572 (tpp) REVERT: A 7 LYS cc_start: 0.7824 (mmtp) cc_final: 0.7449 (mmtp) REVERT: A 18 LEU cc_start: 0.6237 (tp) cc_final: 0.5426 (mp) REVERT: A 51 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7761 (t80) REVERT: A 55 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7686 (mm) REVERT: A 93 MET cc_start: 0.8141 (tpp) cc_final: 0.7925 (mmm) REVERT: A 169 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7253 (mp0) REVERT: A 191 GLU cc_start: 0.8270 (tt0) cc_final: 0.7934 (tp30) REVERT: B 76 SER cc_start: 0.8414 (t) cc_final: 0.8112 (m) REVERT: B 79 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7672 (ttp80) REVERT: B 154 GLN cc_start: 0.7971 (mm110) cc_final: 0.7713 (mm110) REVERT: C 25 ARG cc_start: 0.8198 (ttp80) cc_final: 0.7922 (ttp-170) REVERT: C 36 ASN cc_start: 0.8327 (m-40) cc_final: 0.7941 (m110) REVERT: C 83 ARG cc_start: 0.8232 (mtm-85) cc_final: 0.7891 (ptp90) REVERT: C 85 VAL cc_start: 0.7985 (m) cc_final: 0.7722 (p) REVERT: C 111 GLU cc_start: 0.8512 (pm20) cc_final: 0.8277 (pm20) REVERT: D 3 LYS cc_start: 0.7953 (mtpp) cc_final: 0.7587 (mttm) REVERT: D 29 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8454 (mt-10) REVERT: D 131 ASP cc_start: 0.8259 (t70) cc_final: 0.7851 (t0) REVERT: E 13 LYS cc_start: 0.8734 (ttpp) cc_final: 0.8505 (ttpt) REVERT: E 92 SER cc_start: 0.8891 (p) cc_final: 0.8579 (t) REVERT: F 123 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7937 (mt-10) REVERT: F 127 LYS cc_start: 0.8284 (mttp) cc_final: 0.7426 (mtmt) REVERT: F 145 THR cc_start: 0.8613 (m) cc_final: 0.8310 (p) REVERT: G 56 PHE cc_start: 0.7728 (t80) cc_final: 0.7323 (t80) REVERT: G 130 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7770 (mt-10) REVERT: G 195 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7545 (tp30) REVERT: H 99 ASP cc_start: 0.8532 (t70) cc_final: 0.8255 (t70) REVERT: H 152 SER cc_start: 0.8526 (OUTLIER) cc_final: 0.7965 (p) REVERT: H 253 ILE cc_start: 0.7306 (mt) cc_final: 0.6972 (mm) REVERT: H 395 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8035 (tt) REVERT: H 596 ASN cc_start: 0.7950 (m-40) cc_final: 0.7383 (p0) REVERT: I 450 TYR cc_start: 0.5658 (m-80) cc_final: 0.5029 (m-10) REVERT: I 485 MET cc_start: 0.6387 (OUTLIER) cc_final: 0.5517 (ttp) REVERT: I 518 GLU cc_start: 0.7973 (tp30) cc_final: 0.7330 (tm-30) REVERT: J 13 LYS cc_start: 0.8529 (ttmm) cc_final: 0.7790 (ttpt) REVERT: J 29 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7888 (mt-10) REVERT: J 52 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8746 (tttt) REVERT: J 68 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7612 (mt-10) REVERT: J 137 GLU cc_start: 0.8590 (pt0) cc_final: 0.8340 (pt0) REVERT: K 386 LEU cc_start: 0.7755 (mt) cc_final: 0.7550 (tt) REVERT: K 394 PHE cc_start: 0.7668 (m-80) cc_final: 0.7267 (m-80) REVERT: K 461 GLU cc_start: 0.7728 (tt0) cc_final: 0.7291 (tt0) REVERT: K 529 ASN cc_start: 0.8397 (t0) cc_final: 0.7063 (m-40) REVERT: K 561 ARG cc_start: 0.8625 (tpp80) cc_final: 0.8373 (mtm110) REVERT: L 462 LYS cc_start: 0.6119 (mmmm) cc_final: 0.5695 (mmmm) REVERT: L 467 GLU cc_start: 0.6652 (pt0) cc_final: 0.6137 (pt0) REVERT: L 469 ASN cc_start: 0.7401 (m110) cc_final: 0.6597 (m-40) REVERT: L 512 LYS cc_start: 0.8569 (tppp) cc_final: 0.7932 (tppt) REVERT: L 561 ARG cc_start: 0.7856 (ttp80) cc_final: 0.7565 (ttp-170) REVERT: L 577 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: O 152 ASN cc_start: 0.8165 (t0) cc_final: 0.7886 (t0) REVERT: O 191 GLU cc_start: 0.7326 (tm-30) cc_final: 0.7096 (tm-30) outliers start: 108 outliers final: 28 residues processed: 490 average time/residue: 0.6023 time to fit residues: 338.7848 Evaluate side-chains 395 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 358 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 28 LYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 158 LEU 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 F residue 11 THR Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain 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 395 LEU Chi-restraints excluded: chain H residue 399 GLU Chi-restraints excluded: chain I residue 485 MET Chi-restraints excluded: chain I residue 606 ASN Chi-restraints excluded: chain I residue 608 LYS Chi-restraints excluded: chain J residue 52 LYS 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 594 ASP 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: 1.9990 chunk 77 optimal weight: 0.5980 chunk 199 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 174 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 166 optimal weight: 0.6980 chunk 223 optimal weight: 0.0980 chunk 156 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 162 GLN G 42 ASN G 81 ASN H 443 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.165308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.126244 restraints weight = 28233.583| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.35 r_work: 0.3215 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24439 Z= 0.124 Angle : 0.583 16.485 33368 Z= 0.301 Chirality : 0.043 0.320 3870 Planarity : 0.004 0.052 3956 Dihedral : 15.021 179.988 4375 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.60 % Allowed : 28.09 % Favored : 68.31 % 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: -0.31 (0.15), residues: 2762 helix: 1.17 (0.17), residues: 939 sheet: -0.07 (0.22), residues: 490 loop : -1.28 (0.15), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 102 TYR 0.021 0.001 TYR G 92 PHE 0.025 0.001 PHE C 133 TRP 0.017 0.001 TRP L 535 HIS 0.005 0.001 HIS H 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (24400) covalent geometry : angle 0.54236 / 0.30 (33320) hydrogen bonds : bond 0.03832 / 2.51 ( 1037) hydrogen bonds : angle 4.69450 / 3.26 ( 3063) metal coordination : bond 0.00840 / 0.53 ( 39) metal coordination : angle 5.66599 / 3.54 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 403 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.6895 (ttm) cc_final: 0.6567 (tpp) REVERT: A 18 LEU cc_start: 0.6216 (tp) cc_final: 0.5395 (mp) REVERT: A 51 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7745 (t80) REVERT: A 55 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7773 (mm) REVERT: A 169 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7141 (mp0) REVERT: A 191 GLU cc_start: 0.8274 (tt0) cc_final: 0.7935 (tp30) REVERT: B 22 GLU cc_start: 0.8059 (tp30) cc_final: 0.7733 (tp30) REVERT: B 76 SER cc_start: 0.8402 (t) cc_final: 0.8122 (m) REVERT: B 154 GLN cc_start: 0.7998 (mm110) cc_final: 0.7735 (mm110) REVERT: B 181 TYR cc_start: 0.7868 (m-80) cc_final: 0.7635 (m-80) REVERT: C 36 ASN cc_start: 0.8298 (m-40) cc_final: 0.8029 (m110) REVERT: C 83 ARG cc_start: 0.8182 (mtm-85) cc_final: 0.7834 (ptp90) REVERT: C 85 VAL cc_start: 0.7760 (m) cc_final: 0.7497 (p) REVERT: C 111 GLU cc_start: 0.8511 (pm20) cc_final: 0.8303 (pm20) REVERT: D 3 LYS cc_start: 0.7934 (mtpp) cc_final: 0.7581 (mttm) REVERT: D 131 ASP cc_start: 0.8183 (t70) cc_final: 0.7660 (t0) REVERT: D 179 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8373 (ptpt) REVERT: E 13 LYS cc_start: 0.8610 (ttpp) cc_final: 0.8406 (ttpt) REVERT: E 35 VAL cc_start: 0.8696 (t) cc_final: 0.8449 (p) REVERT: E 92 SER cc_start: 0.8770 (p) cc_final: 0.8489 (t) REVERT: E 127 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8340 (mmtm) REVERT: F 75 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7636 (mm-30) REVERT: F 93 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.7210 (mpt) REVERT: F 123 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7810 (mt-10) REVERT: F 127 LYS cc_start: 0.8230 (mttp) cc_final: 0.7294 (mtmm) REVERT: F 145 THR cc_start: 0.8571 (m) cc_final: 0.8334 (p) REVERT: G 56 PHE cc_start: 0.7705 (t80) cc_final: 0.7337 (t80) REVERT: G 92 TYR cc_start: 0.8020 (t80) cc_final: 0.7777 (t80) REVERT: G 130 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7700 (mt-10) REVERT: G 132 GLU cc_start: 0.7156 (pp20) cc_final: 0.6898 (pp20) REVERT: G 191 PHE cc_start: 0.7621 (p90) cc_final: 0.7217 (p90) REVERT: G 195 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7638 (tp30) REVERT: H 99 ASP cc_start: 0.8517 (t70) cc_final: 0.8208 (t70) REVERT: H 127 GLU cc_start: 0.7765 (pt0) cc_final: 0.7363 (pt0) REVERT: H 152 SER cc_start: 0.8544 (OUTLIER) cc_final: 0.8086 (p) REVERT: H 253 ILE cc_start: 0.7152 (mt) cc_final: 0.6771 (mm) REVERT: H 395 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8017 (tt) REVERT: H 444 MET cc_start: 0.7155 (OUTLIER) cc_final: 0.6825 (mtt) REVERT: H 596 ASN cc_start: 0.7940 (m-40) cc_final: 0.7369 (p0) REVERT: I 450 TYR cc_start: 0.5553 (m-80) cc_final: 0.5016 (m-10) REVERT: I 518 GLU cc_start: 0.7873 (tp30) cc_final: 0.7131 (pt0) REVERT: J 13 LYS cc_start: 0.8500 (ttmm) cc_final: 0.7714 (ttpt) REVERT: J 52 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8312 (tptm) REVERT: J 68 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7579 (mt-10) REVERT: J 125 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8037 (mp10) REVERT: J 137 GLU cc_start: 0.8528 (pt0) cc_final: 0.8233 (pt0) REVERT: K 166 PHE cc_start: 0.6280 (m-80) cc_final: 0.5261 (p90) REVERT: K 386 LEU cc_start: 0.7932 (mt) cc_final: 0.7705 (tt) REVERT: K 461 GLU cc_start: 0.7674 (tt0) cc_final: 0.7205 (tt0) REVERT: K 483 ASN cc_start: 0.7732 (OUTLIER) cc_final: 0.7435 (m110) REVERT: L 462 LYS cc_start: 0.6172 (mmmm) cc_final: 0.5739 (mmmm) REVERT: L 467 GLU cc_start: 0.6640 (pt0) cc_final: 0.6123 (pt0) REVERT: L 469 ASN cc_start: 0.7397 (m110) cc_final: 0.6638 (m-40) REVERT: L 512 LYS cc_start: 0.8654 (tppp) cc_final: 0.8349 (tppp) REVERT: L 524 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.8051 (mmtm) REVERT: L 577 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: O 16 SER cc_start: 0.9165 (m) cc_final: 0.8911 (p) REVERT: O 110 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7884 (ptpt) REVERT: O 111 GLU cc_start: 0.8302 (mp0) cc_final: 0.8012 (mp0) REVERT: O 123 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8030 (mm-30) REVERT: O 152 ASN cc_start: 0.8143 (t0) cc_final: 0.7874 (t0) outliers start: 84 outliers final: 23 residues processed: 459 average time/residue: 0.5979 time to fit residues: 314.2644 Evaluate side-chains 390 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 353 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 39 VAL Chi-restraints excluded: chain B residue 195 THR 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 88 SER Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain H residue 29 CYS Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 399 GLU Chi-restraints excluded: chain H residue 444 MET 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 483 ASN 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 O residue 10 VAL Chi-restraints excluded: chain O residue 39 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 90 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 141 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 187 optimal weight: 0.9980 chunk 250 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 10 optimal weight: 30.0000 chunk 14 optimal weight: 30.0000 chunk 9 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 162 GLN C 36 ASN C 178 ASN D 112 GLN E 32 GLN F 178 ASN G 42 ASN G 81 ASN ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 469 ASN H 479 ASN H 551 GLN I 438 ASN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 119 HIS J 178 ASN ** K 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 556 ASN L 574 ASN O 112 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.155157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.115604 restraints weight = 28238.770| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.53 r_work: 0.3025 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.076 24439 Z= 0.388 Angle : 0.774 23.154 33368 Z= 0.391 Chirality : 0.052 0.269 3870 Planarity : 0.006 0.054 3956 Dihedral : 14.901 178.971 4375 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 5.23 % Allowed : 26.97 % Favored : 67.80 % 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: -0.48 (0.15), residues: 2762 helix: 1.03 (0.16), residues: 937 sheet: -0.26 (0.22), residues: 494 loop : -1.34 (0.16), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 102 TYR 0.027 0.002 TYR L 450 PHE 0.025 0.003 PHE B 198 TRP 0.020 0.002 TRP H 125 HIS 0.006 0.002 HIS O 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00887 / 0.39 (24400) covalent geometry : angle 0.72348 / 0.39 (33320) hydrogen bonds : bond 0.04513 / 2.97 ( 1037) hydrogen bonds : angle 5.01216 / 3.47 ( 3063) metal coordination : bond 0.01792 / 1.17 ( 39) metal coordination : angle 7.29972 / 4.47 ( 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 517 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 395 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.6921 (ttm) cc_final: 0.6436 (tpp) REVERT: A 18 LEU cc_start: 0.6277 (tp) cc_final: 0.5471 (mp) REVERT: A 51 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7869 (t80) REVERT: A 55 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7740 (mm) REVERT: A 150 ILE cc_start: 0.7167 (mt) cc_final: 0.6699 (mt) REVERT: A 166 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7483 (tmmt) REVERT: A 169 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7168 (mp0) REVERT: A 191 GLU cc_start: 0.8411 (tt0) cc_final: 0.8050 (tp30) REVERT: B 154 GLN cc_start: 0.7938 (mm110) cc_final: 0.7693 (mm110) REVERT: B 181 TYR cc_start: 0.7940 (m-80) cc_final: 0.7735 (m-80) REVERT: C 5 MET cc_start: 0.8532 (mtm) cc_final: 0.8035 (mtt) REVERT: C 33 LYS cc_start: 0.8621 (mptt) cc_final: 0.8225 (ptmt) REVERT: C 83 ARG cc_start: 0.8085 (mtm-85) cc_final: 0.7651 (mtm-85) REVERT: C 85 VAL cc_start: 0.8185 (m) cc_final: 0.7962 (p) REVERT: C 156 LYS cc_start: 0.8314 (mttt) cc_final: 0.7623 (pttp) REVERT: D 3 LYS cc_start: 0.7947 (mtpp) cc_final: 0.7493 (mttm) REVERT: D 13 LYS cc_start: 0.8702 (tptt) cc_final: 0.8183 (ttpp) REVERT: D 75 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7859 (mm-30) REVERT: D 111 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7964 (mt-10) REVERT: D 178 ASN cc_start: 0.8595 (m110) cc_final: 0.8364 (m-40) REVERT: E 87 CYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8539 (m) REVERT: E 110 LYS cc_start: 0.8558 (ptmm) cc_final: 0.8160 (ptpt) REVERT: E 127 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8374 (mmtm) REVERT: F 112 GLN cc_start: 0.8477 (mt0) cc_final: 0.8245 (mp10) REVERT: F 123 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8174 (mt-10) REVERT: F 127 LYS cc_start: 0.8359 (mttp) cc_final: 0.7565 (mtmt) REVERT: G 56 PHE cc_start: 0.7672 (t80) cc_final: 0.7183 (t80) REVERT: G 129 ASN cc_start: 0.6717 (OUTLIER) cc_final: 0.6247 (m110) REVERT: G 132 GLU cc_start: 0.7298 (pp20) cc_final: 0.6925 (pp20) REVERT: G 195 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7949 (tp30) REVERT: H 99 ASP cc_start: 0.8689 (t70) cc_final: 0.8345 (t0) REVERT: H 253 ILE cc_start: 0.7363 (mt) cc_final: 0.6964 (mm) REVERT: H 395 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8032 (tt) REVERT: H 596 ASN cc_start: 0.8046 (m-40) cc_final: 0.7405 (p0) REVERT: I 450 TYR cc_start: 0.5996 (m-80) cc_final: 0.4989 (m-10) REVERT: I 518 GLU cc_start: 0.7934 (tp30) cc_final: 0.7364 (tm-30) REVERT: J 13 LYS cc_start: 0.8651 (ttmm) cc_final: 0.7979 (ttpt) REVERT: J 29 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7826 (mt-10) REVERT: J 52 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8823 (tttt) REVERT: J 125 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8098 (mp10) REVERT: J 171 ASN cc_start: 0.8728 (m-40) cc_final: 0.8437 (m-40) REVERT: K 191 TYR cc_start: 0.7277 (m-80) cc_final: 0.7025 (m-80) REVERT: K 386 LEU cc_start: 0.7886 (mt) cc_final: 0.7661 (tt) REVERT: K 461 GLU cc_start: 0.7701 (tt0) cc_final: 0.7185 (tt0) REVERT: L 469 ASN cc_start: 0.7595 (m110) cc_final: 0.7002 (m-40) REVERT: L 512 LYS cc_start: 0.8644 (tppp) cc_final: 0.8387 (tppp) REVERT: L 548 TYR cc_start: 0.8040 (t80) cc_final: 0.7837 (t80) REVERT: L 577 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7151 (mp0) REVERT: L 603 ILE cc_start: 0.7634 (pp) cc_final: 0.7364 (mm) REVERT: O 5 MET cc_start: 0.8481 (ttp) cc_final: 0.8251 (ttp) REVERT: O 9 TYR cc_start: 0.8383 (m-80) cc_final: 0.8122 (m-80) REVERT: O 93 MET cc_start: 0.8280 (tpt) cc_final: 0.7899 (mmm) REVERT: O 110 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8149 (ttpt) REVERT: O 111 GLU cc_start: 0.8461 (mp0) cc_final: 0.8134 (mp0) REVERT: O 115 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8686 (mmt90) REVERT: O 152 ASN cc_start: 0.8161 (t0) cc_final: 0.7864 (t0) outliers start: 122 outliers final: 38 residues processed: 490 average time/residue: 0.5693 time to fit residues: 320.8511 Evaluate side-chains 398 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 347 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 60 GLU 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 114 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 126 THR Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain E residue 87 CYS 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 E residue 132 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 G residue 129 ASN Chi-restraints excluded: chain H residue 29 CYS Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 399 GLU Chi-restraints excluded: chain H residue 408 LYS Chi-restraints excluded: chain J residue 4 THR 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 O residue 10 VAL Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 110 LYS Chi-restraints excluded: chain O residue 115 ARG Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 190 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 176 optimal weight: 0.9990 chunk 129 optimal weight: 20.0000 chunk 175 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 277 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 153 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 162 GLN C 112 GLN D 112 GLN E 32 GLN E 171 ASN G 42 ASN G 81 ASN ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 479 ASN H 542 GLN I 438 ASN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 178 ASN ** K 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 469 ASN L 574 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.159642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.120357 restraints weight = 28170.092| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.31 r_work: 0.3117 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24439 Z= 0.155 Angle : 0.611 19.748 33368 Z= 0.311 Chirality : 0.044 0.317 3870 Planarity : 0.004 0.057 3956 Dihedral : 14.976 179.739 4375 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.69 % Allowed : 28.73 % Favored : 67.58 % 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: -0.26 (0.15), residues: 2762 helix: 1.32 (0.17), residues: 937 sheet: -0.19 (0.22), residues: 490 loop : -1.27 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 95 TYR 0.024 0.001 TYR I 599 PHE 0.023 0.002 PHE C 133 TRP 0.019 0.001 TRP L 535 HIS 0.005 0.001 HIS K 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (24400) covalent geometry : angle 0.56213 / 0.31 (33320) hydrogen bonds : bond 0.03830 / 2.51 ( 1037) hydrogen bonds : angle 4.79257 / 3.32 ( 3063) metal coordination : bond 0.00849 / 0.52 ( 39) metal coordination : angle 6.30651 / 3.81 ( 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 460 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 374 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.6912 (ttm) cc_final: 0.6385 (tpp) REVERT: A 18 LEU cc_start: 0.6286 (tp) cc_final: 0.5454 (mp) REVERT: A 51 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7832 (t80) REVERT: A 55 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7726 (mm) REVERT: A 166 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7472 (tmmt) REVERT: A 169 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7073 (mp0) REVERT: B 22 GLU cc_start: 0.8237 (tp30) cc_final: 0.8033 (tp30) REVERT: B 28 LYS cc_start: 0.7377 (OUTLIER) cc_final: 0.7081 (ttpt) REVERT: B 154 GLN cc_start: 0.7882 (mm110) cc_final: 0.7588 (mm110) REVERT: C 5 MET cc_start: 0.8526 (mtm) cc_final: 0.8006 (mtt) REVERT: C 33 LYS cc_start: 0.8616 (mptt) cc_final: 0.8233 (ptmt) REVERT: C 36 ASN cc_start: 0.8586 (m110) cc_final: 0.8380 (m110) REVERT: C 83 ARG cc_start: 0.8124 (mtm-85) cc_final: 0.7692 (mtm-85) REVERT: C 85 VAL cc_start: 0.8046 (m) cc_final: 0.7823 (p) REVERT: C 156 LYS cc_start: 0.8299 (mttt) cc_final: 0.7555 (pttp) REVERT: D 3 LYS cc_start: 0.8004 (mtpp) cc_final: 0.7611 (mttm) REVERT: D 13 LYS cc_start: 0.8515 (tptt) cc_final: 0.8056 (ttpp) REVERT: D 137 GLU cc_start: 0.8574 (pt0) cc_final: 0.8354 (pt0) REVERT: E 29 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7842 (mm-30) REVERT: E 69 ASN cc_start: 0.7476 (m-40) cc_final: 0.6970 (p0) REVERT: E 87 CYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8490 (m) REVERT: E 127 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8352 (mmtm) REVERT: E 154 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7504 (mm-40) REVERT: F 93 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7273 (mpt) REVERT: F 112 GLN cc_start: 0.8398 (mt0) cc_final: 0.8055 (mp10) REVERT: F 123 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8040 (mt-10) REVERT: F 127 LYS cc_start: 0.8360 (mttp) cc_final: 0.7527 (mtmm) REVERT: G 56 PHE cc_start: 0.7798 (t80) cc_final: 0.7268 (t80) REVERT: G 129 ASN cc_start: 0.6786 (OUTLIER) cc_final: 0.6331 (m110) REVERT: G 132 GLU cc_start: 0.7302 (pp20) cc_final: 0.6997 (pp20) REVERT: G 195 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7863 (tp30) REVERT: H 99 ASP cc_start: 0.8718 (t70) cc_final: 0.8384 (t0) REVERT: H 152 SER cc_start: 0.8546 (OUTLIER) cc_final: 0.8222 (p) REVERT: H 178 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.7229 (mmm) REVERT: H 596 ASN cc_start: 0.8008 (m-40) cc_final: 0.7411 (p0) REVERT: I 450 TYR cc_start: 0.5844 (m-80) cc_final: 0.4966 (m-10) REVERT: I 451 ARG cc_start: 0.7577 (mtp180) cc_final: 0.6863 (mmm-85) REVERT: I 518 GLU cc_start: 0.7942 (tp30) cc_final: 0.7509 (tp30) REVERT: J 13 LYS cc_start: 0.8613 (ttmm) cc_final: 0.7880 (ttpt) REVERT: J 52 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8757 (tttt) REVERT: J 125 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8119 (mp10) REVERT: K 191 TYR cc_start: 0.7223 (m-80) cc_final: 0.6930 (m-80) REVERT: K 394 PHE cc_start: 0.7887 (m-80) cc_final: 0.7462 (m-80) REVERT: K 461 GLU cc_start: 0.7654 (tt0) cc_final: 0.7178 (tt0) REVERT: K 466 ILE cc_start: 0.7309 (OUTLIER) cc_final: 0.7063 (tt) REVERT: L 469 ASN cc_start: 0.7848 (m-40) cc_final: 0.7382 (m-40) REVERT: L 542 GLN cc_start: 0.7876 (mt0) cc_final: 0.7417 (mt0) REVERT: L 548 TYR cc_start: 0.8030 (t80) cc_final: 0.7826 (t80) REVERT: L 577 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: L 603 ILE cc_start: 0.7625 (pp) cc_final: 0.7322 (mm) REVERT: O 87 CYS cc_start: 0.7300 (OUTLIER) cc_final: 0.6753 (m) REVERT: O 93 MET cc_start: 0.8328 (tpt) cc_final: 0.8007 (mmm) REVERT: O 111 GLU cc_start: 0.8414 (mp0) cc_final: 0.8105 (mp0) REVERT: O 115 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8731 (mmt90) REVERT: O 152 ASN cc_start: 0.8168 (t0) cc_final: 0.7932 (t0) outliers start: 86 outliers final: 32 residues processed: 439 average time/residue: 0.5789 time to fit residues: 291.7595 Evaluate side-chains 389 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 340 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 28 LYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 120 LEU 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 158 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain H residue 29 CYS Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 178 MET 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 455 PHE Chi-restraints excluded: chain K residue 466 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 87 CYS Chi-restraints excluded: chain O residue 115 ARG Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 187 GLU Chi-restraints excluded: chain O residue 190 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 5 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 240 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 192 optimal weight: 0.6980 chunk 218 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 162 GLN E 107 ASN G 42 ASN G 81 ASN G 99 ASN ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 479 ASN H 551 GLN I 438 ASN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 178 ASN ** K 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 574 ASN L 606 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.157468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.118378 restraints weight = 28267.203| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.34 r_work: 0.3084 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 24439 Z= 0.236 Angle : 0.645 19.830 33368 Z= 0.326 Chirality : 0.046 0.286 3870 Planarity : 0.004 0.057 3956 Dihedral : 14.898 179.565 4375 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.33 % Allowed : 28.69 % Favored : 66.98 % 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: 1.35 (0.17), residues: 938 sheet: -0.24 (0.22), residues: 496 loop : -1.24 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 102 TYR 0.020 0.001 TYR G 92 PHE 0.026 0.002 PHE C 133 TRP 0.020 0.001 TRP L 535 HIS 0.005 0.001 HIS K 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.24 (24400) covalent geometry : angle 0.59840 / 0.32 (33320) hydrogen bonds : bond 0.03856 / 2.51 ( 1037) hydrogen bonds : angle 4.78903 / 3.32 ( 3063) metal coordination : bond 0.01113 / 0.71 ( 39) metal coordination : angle 6.35540 / 3.91 ( 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 470 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 369 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.6860 (ttm) cc_final: 0.6350 (tpp) REVERT: A 18 LEU cc_start: 0.6241 (tp) cc_final: 0.5464 (mp) REVERT: A 51 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7881 (t80) REVERT: A 55 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7767 (mm) REVERT: A 166 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7493 (tmmt) REVERT: A 167 PHE cc_start: 0.6928 (t80) cc_final: 0.6726 (t80) REVERT: A 169 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7063 (mp0) REVERT: B 28 LYS cc_start: 0.7073 (OUTLIER) cc_final: 0.6748 (ttpt) REVERT: B 154 GLN cc_start: 0.7922 (mm110) cc_final: 0.7676 (mm110) REVERT: C 5 MET cc_start: 0.8518 (mtm) cc_final: 0.8046 (mtt) REVERT: C 33 LYS cc_start: 0.8660 (mptt) cc_final: 0.8215 (ptmt) REVERT: C 36 ASN cc_start: 0.8551 (m110) cc_final: 0.8339 (m110) REVERT: C 83 ARG cc_start: 0.8099 (mtm-85) cc_final: 0.7626 (mtm-85) REVERT: C 85 VAL cc_start: 0.8051 (m) cc_final: 0.7836 (p) REVERT: C 108 ASP cc_start: 0.8337 (m-30) cc_final: 0.7889 (t0) REVERT: C 156 LYS cc_start: 0.8289 (mttt) cc_final: 0.7586 (pttp) REVERT: C 171 ASN cc_start: 0.8854 (m-40) cc_final: 0.8653 (m110) REVERT: D 3 LYS cc_start: 0.8027 (mtpp) cc_final: 0.7635 (mttm) REVERT: D 13 LYS cc_start: 0.8554 (tptt) cc_final: 0.8070 (ttpp) REVERT: D 75 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7767 (mm-30) REVERT: E 29 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7647 (mm-30) REVERT: E 69 ASN cc_start: 0.7583 (m-40) cc_final: 0.7040 (p0) REVERT: E 87 CYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8453 (m) REVERT: E 110 LYS cc_start: 0.8456 (ptmm) cc_final: 0.8088 (pttt) REVERT: E 127 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8337 (mmtm) REVERT: E 154 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.7565 (mm-40) REVERT: F 93 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.7267 (mpt) REVERT: F 112 GLN cc_start: 0.8409 (mt0) cc_final: 0.8158 (mp10) REVERT: F 123 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8125 (mt-10) REVERT: F 127 LYS cc_start: 0.8315 (mttp) cc_final: 0.7493 (mtmm) REVERT: G 56 PHE cc_start: 0.7772 (t80) cc_final: 0.7175 (t80) REVERT: G 129 ASN cc_start: 0.6759 (OUTLIER) cc_final: 0.6361 (m110) REVERT: G 195 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7888 (tp30) REVERT: H 99 ASP cc_start: 0.8891 (t70) cc_final: 0.8559 (t0) REVERT: H 127 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7486 (pt0) REVERT: H 152 SER cc_start: 0.8592 (OUTLIER) cc_final: 0.8276 (p) REVERT: H 395 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7968 (tt) REVERT: H 596 ASN cc_start: 0.8001 (m-40) cc_final: 0.7381 (p0) REVERT: I 450 TYR cc_start: 0.6012 (m-80) cc_final: 0.5071 (m-10) REVERT: I 451 ARG cc_start: 0.7595 (mtp180) cc_final: 0.6884 (mmm-85) REVERT: I 518 GLU cc_start: 0.7886 (tp30) cc_final: 0.7466 (tp30) REVERT: J 7 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8700 (mmmm) REVERT: J 13 LYS cc_start: 0.8619 (ttmm) cc_final: 0.7883 (ttpt) REVERT: J 52 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8655 (tttm) REVERT: J 125 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8072 (mp10) REVERT: K 191 TYR cc_start: 0.7257 (m-80) cc_final: 0.6993 (m-80) REVERT: K 394 PHE cc_start: 0.7880 (m-80) cc_final: 0.7478 (m-80) REVERT: K 461 GLU cc_start: 0.7662 (tt0) cc_final: 0.7179 (tt0) REVERT: K 466 ILE cc_start: 0.7313 (OUTLIER) cc_final: 0.7048 (tt) REVERT: L 467 GLU cc_start: 0.6652 (pt0) cc_final: 0.6442 (pt0) REVERT: L 469 ASN cc_start: 0.7801 (m-40) cc_final: 0.7151 (m-40) REVERT: L 542 GLN cc_start: 0.7803 (mt0) cc_final: 0.7389 (mt0) REVERT: L 548 TYR cc_start: 0.8036 (t80) cc_final: 0.7823 (t80) REVERT: L 577 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: O 5 MET cc_start: 0.8409 (ttp) cc_final: 0.8170 (ttp) REVERT: O 87 CYS cc_start: 0.7305 (OUTLIER) cc_final: 0.6730 (m) REVERT: O 93 MET cc_start: 0.8324 (tpt) cc_final: 0.8001 (mmm) REVERT: O 111 GLU cc_start: 0.8453 (mp0) cc_final: 0.8170 (mp0) REVERT: O 115 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8510 (mmt90) REVERT: O 152 ASN cc_start: 0.8173 (t0) cc_final: 0.7931 (t0) outliers start: 101 outliers final: 32 residues processed: 444 average time/residue: 0.6016 time to fit residues: 306.4750 Evaluate side-chains 400 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 348 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 28 LYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain H residue 29 CYS Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 128 ILE 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 I residue 444 MET Chi-restraints excluded: chain J residue 7 LYS 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 466 ILE Chi-restraints excluded: chain K residue 603 ILE Chi-restraints excluded: chain L residue 577 GLU Chi-restraints excluded: chain L residue 594 ASP Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 87 CYS Chi-restraints excluded: chain O residue 115 ARG Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 190 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 51 optimal weight: 0.8980 chunk 227 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 195 optimal weight: 0.5980 chunk 212 optimal weight: 0.7980 chunk 233 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 240 optimal weight: 7.9990 chunk 147 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 32 GLN E 171 ASN F 178 ASN G 42 ASN G 81 ASN H 479 ASN I 438 ASN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 574 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.160765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.121640 restraints weight = 28015.302| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.23 r_work: 0.3147 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24439 Z= 0.131 Angle : 0.587 17.190 33368 Z= 0.302 Chirality : 0.043 0.321 3870 Planarity : 0.004 0.059 3956 Dihedral : 14.940 179.931 4375 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.17 % Allowed : 29.85 % Favored : 66.98 % 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: -0.04 (0.15), residues: 2762 helix: 1.53 (0.17), residues: 938 sheet: -0.19 (0.22), residues: 489 loop : -1.11 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 102 TYR 0.021 0.001 TYR I 599 PHE 0.025 0.001 PHE C 133 TRP 0.025 0.001 TRP L 535 HIS 0.008 0.001 HIS H 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (24400) covalent geometry : angle 0.54624 / 0.30 (33320) hydrogen bonds : bond 0.03699 / 2.40 ( 1037) hydrogen bonds : angle 4.63995 / 3.22 ( 3063) metal coordination : bond 0.00677 / 0.41 ( 39) metal coordination : angle 5.71296 / 3.49 ( 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 437 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 363 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.6955 (ttm) cc_final: 0.6448 (tpp) REVERT: A 18 LEU cc_start: 0.6315 (tp) cc_final: 0.5513 (mp) REVERT: A 51 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7811 (t80) REVERT: A 55 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7789 (mm) REVERT: A 85 VAL cc_start: 0.7759 (OUTLIER) cc_final: 0.7435 (p) REVERT: A 154 GLN cc_start: 0.7539 (mm-40) cc_final: 0.7320 (mm110) REVERT: A 166 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7515 (tmmt) REVERT: A 169 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7083 (mp0) REVERT: B 79 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7783 (ttp80) REVERT: B 154 GLN cc_start: 0.7862 (mm110) cc_final: 0.7611 (mm110) REVERT: B 171 ASN cc_start: 0.7640 (m-40) cc_final: 0.7068 (t0) REVERT: C 5 MET cc_start: 0.8502 (mtm) cc_final: 0.8016 (mtt) REVERT: C 33 LYS cc_start: 0.8659 (mptt) cc_final: 0.8245 (ptmt) REVERT: C 83 ARG cc_start: 0.8143 (mtm-85) cc_final: 0.7733 (ptp90) REVERT: C 85 VAL cc_start: 0.7937 (m) cc_final: 0.7730 (p) REVERT: C 108 ASP cc_start: 0.8273 (m-30) cc_final: 0.7879 (t0) REVERT: C 111 GLU cc_start: 0.8471 (pm20) cc_final: 0.7929 (pm20) REVERT: D 3 LYS cc_start: 0.8020 (mtpp) cc_final: 0.7647 (mttm) REVERT: D 13 LYS cc_start: 0.8432 (tptt) cc_final: 0.7910 (ttpp) REVERT: D 75 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7803 (mm-30) REVERT: E 29 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7742 (mm-30) REVERT: E 87 CYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8477 (m) REVERT: E 127 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8367 (mmtm) REVERT: E 154 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7496 (mm-40) REVERT: F 93 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7251 (mpt) REVERT: F 112 GLN cc_start: 0.8326 (mt0) cc_final: 0.8073 (mp10) REVERT: F 123 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8026 (mt-10) REVERT: F 127 LYS cc_start: 0.8293 (mttp) cc_final: 0.7433 (mtmm) REVERT: F 187 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7340 (pp20) REVERT: G 56 PHE cc_start: 0.7779 (t80) cc_final: 0.7245 (t80) REVERT: G 191 PHE cc_start: 0.7703 (p90) cc_final: 0.7313 (p90) REVERT: H 99 ASP cc_start: 0.8834 (t70) cc_final: 0.8546 (t0) REVERT: H 152 SER cc_start: 0.8512 (OUTLIER) cc_final: 0.8192 (p) REVERT: H 253 ILE cc_start: 0.7360 (mt) cc_final: 0.6911 (mm) REVERT: H 395 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7912 (tt) REVERT: H 596 ASN cc_start: 0.7994 (m-40) cc_final: 0.7395 (p0) REVERT: I 450 TYR cc_start: 0.5896 (m-80) cc_final: 0.5008 (m-10) REVERT: I 451 ARG cc_start: 0.7560 (mtp180) cc_final: 0.6870 (mmm-85) REVERT: I 518 GLU cc_start: 0.7772 (tp30) cc_final: 0.7350 (tp30) REVERT: J 13 LYS cc_start: 0.8539 (ttmm) cc_final: 0.7762 (ttpt) REVERT: J 52 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8751 (tttt) REVERT: J 125 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8058 (mp10) REVERT: K 191 TYR cc_start: 0.7272 (m-80) cc_final: 0.6927 (m-80) REVERT: K 394 PHE cc_start: 0.7846 (m-80) cc_final: 0.7508 (m-80) REVERT: K 461 GLU cc_start: 0.7554 (tt0) cc_final: 0.7076 (tt0) REVERT: L 447 PHE cc_start: 0.7611 (t80) cc_final: 0.7205 (t80) REVERT: L 469 ASN cc_start: 0.7900 (m-40) cc_final: 0.7254 (m-40) REVERT: L 512 LYS cc_start: 0.8504 (tppp) cc_final: 0.7818 (tppt) REVERT: L 542 GLN cc_start: 0.7869 (mt0) cc_final: 0.7456 (mt0) REVERT: L 577 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: O 5 MET cc_start: 0.8355 (ttp) cc_final: 0.8138 (ttp) REVERT: O 87 CYS cc_start: 0.7298 (OUTLIER) cc_final: 0.6746 (m) REVERT: O 93 MET cc_start: 0.8333 (tpt) cc_final: 0.8023 (mmm) REVERT: O 111 GLU cc_start: 0.8408 (mp0) cc_final: 0.8128 (mp0) REVERT: O 115 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8553 (mmt90) outliers start: 74 outliers final: 28 residues processed: 414 average time/residue: 0.6771 time to fit residues: 320.9948 Evaluate side-chains 391 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 345 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain 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 408 LYS Chi-restraints excluded: chain I residue 444 MET 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 509 SER Chi-restraints excluded: chain K residue 603 ILE Chi-restraints excluded: chain L residue 556 ASN Chi-restraints excluded: chain L residue 577 GLU Chi-restraints excluded: chain L residue 594 ASP Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 87 CYS Chi-restraints excluded: chain O residue 115 ARG 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: 6.9990 chunk 246 optimal weight: 30.0000 chunk 272 optimal weight: 4.9990 chunk 208 optimal weight: 0.6980 chunk 144 optimal weight: 10.0000 chunk 163 optimal weight: 8.9990 chunk 169 optimal weight: 5.9990 chunk 227 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 chunk 127 optimal weight: 8.9990 chunk 164 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 32 GLN G 42 ASN G 81 ASN H 479 ASN H 551 GLN I 438 ASN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 178 ASN ** K 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 438 ASN L 469 ASN L 574 ASN O 32 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.156949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.117748 restraints weight = 28285.123| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.38 r_work: 0.3071 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 24439 Z= 0.263 Angle : 0.664 19.705 33368 Z= 0.336 Chirality : 0.046 0.279 3870 Planarity : 0.005 0.058 3956 Dihedral : 14.884 179.722 4375 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.26 % Allowed : 30.15 % Favored : 66.60 % 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: -0.14 (0.15), residues: 2762 helix: 1.43 (0.17), residues: 938 sheet: -0.20 (0.22), residues: 491 loop : -1.18 (0.16), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 102 TYR 0.024 0.001 TYR G 161 PHE 0.032 0.002 PHE A 167 TRP 0.027 0.001 TRP L 535 HIS 0.005 0.001 HIS K 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00614 / 0.26 (24400) covalent geometry : angle 0.61934 / 0.33 (33320) hydrogen bonds : bond 0.03825 / 2.48 ( 1037) hydrogen bonds : angle 4.76819 / 3.31 ( 3063) metal coordination : bond 0.01174 / 0.75 ( 39) metal coordination : angle 6.33728 / 3.92 ( 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 434 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 358 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7005 (ttm) cc_final: 0.6510 (tpp) REVERT: A 18 LEU cc_start: 0.6293 (tp) cc_final: 0.5511 (mp) REVERT: A 51 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7887 (t80) REVERT: A 55 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7827 (mm) REVERT: A 62 MET cc_start: 0.6500 (mpp) cc_final: 0.6085 (mpt) REVERT: A 85 VAL cc_start: 0.7873 (OUTLIER) cc_final: 0.7549 (p) REVERT: A 154 GLN cc_start: 0.7581 (mm-40) cc_final: 0.7363 (mm110) REVERT: A 166 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7528 (tmmt) REVERT: A 169 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7060 (mp0) REVERT: B 28 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6932 (ttpt) REVERT: B 29 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6741 (mt-10) REVERT: B 70 VAL cc_start: 0.7820 (OUTLIER) cc_final: 0.7582 (p) REVERT: B 79 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7804 (ttp80) REVERT: B 154 GLN cc_start: 0.7922 (mm110) cc_final: 0.7681 (mm110) REVERT: C 5 MET cc_start: 0.8553 (mtm) cc_final: 0.8019 (mtt) REVERT: C 33 LYS cc_start: 0.8622 (mptt) cc_final: 0.8213 (ptmt) REVERT: C 83 ARG cc_start: 0.8147 (mtm-85) cc_final: 0.7695 (mtm-85) REVERT: C 85 VAL cc_start: 0.8078 (m) cc_final: 0.7873 (p) REVERT: C 108 ASP cc_start: 0.8351 (m-30) cc_final: 0.7957 (t0) REVERT: C 156 LYS cc_start: 0.8281 (mttt) cc_final: 0.7643 (pttp) REVERT: C 171 ASN cc_start: 0.8884 (m-40) cc_final: 0.8673 (m110) REVERT: D 3 LYS cc_start: 0.8046 (mtpp) cc_final: 0.7668 (mttm) REVERT: D 13 LYS cc_start: 0.8624 (tptt) cc_final: 0.8174 (ttpt) REVERT: D 75 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7801 (mm-30) REVERT: D 111 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8073 (pm20) REVERT: D 123 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8101 (mt-10) REVERT: E 29 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7710 (mm-30) REVERT: E 69 ASN cc_start: 0.7719 (m-40) cc_final: 0.7119 (p0) REVERT: E 87 CYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8512 (m) REVERT: E 110 LYS cc_start: 0.8519 (ptmm) cc_final: 0.8159 (pttt) REVERT: E 127 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8432 (mmtm) REVERT: E 154 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.7532 (mt0) REVERT: F 112 GLN cc_start: 0.8461 (mt0) cc_final: 0.8212 (mp10) REVERT: F 123 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8184 (mt-10) REVERT: F 127 LYS cc_start: 0.8348 (mttp) cc_final: 0.7747 (mtmt) REVERT: F 187 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7386 (pp20) REVERT: G 56 PHE cc_start: 0.7797 (t80) cc_final: 0.7256 (t80) REVERT: G 191 PHE cc_start: 0.7763 (p90) cc_final: 0.7346 (p90) REVERT: H 127 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7495 (pt0) REVERT: H 152 SER cc_start: 0.8590 (OUTLIER) cc_final: 0.8260 (p) REVERT: H 253 ILE cc_start: 0.7619 (mt) cc_final: 0.7234 (mm) REVERT: H 395 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.7993 (tt) REVERT: H 596 ASN cc_start: 0.8009 (m-40) cc_final: 0.7395 (p0) REVERT: I 451 ARG cc_start: 0.7688 (mtp180) cc_final: 0.7002 (mmm-85) REVERT: I 518 GLU cc_start: 0.7830 (tp30) cc_final: 0.7426 (tp30) REVERT: J 13 LYS cc_start: 0.8663 (ttmm) cc_final: 0.7961 (ttpt) REVERT: J 52 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8686 (tttm) REVERT: J 125 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8073 (mp10) REVERT: K 191 TYR cc_start: 0.7312 (m-80) cc_final: 0.7081 (m-80) REVERT: K 394 PHE cc_start: 0.7915 (m-80) cc_final: 0.7435 (m-80) REVERT: K 461 GLU cc_start: 0.7679 (tt0) cc_final: 0.7232 (tt0) REVERT: K 466 ILE cc_start: 0.7326 (OUTLIER) cc_final: 0.7064 (tt) REVERT: L 542 GLN cc_start: 0.7896 (mt0) cc_final: 0.7497 (mt0) REVERT: L 577 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: L 603 ILE cc_start: 0.7718 (pp) cc_final: 0.7470 (mm) REVERT: O 5 MET cc_start: 0.8423 (ttp) cc_final: 0.8195 (ttp) REVERT: O 87 CYS cc_start: 0.7392 (OUTLIER) cc_final: 0.6814 (m) REVERT: O 93 MET cc_start: 0.8402 (tpt) cc_final: 0.8076 (mmm) REVERT: O 111 GLU cc_start: 0.8434 (mp0) cc_final: 0.8200 (mp0) REVERT: O 115 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8722 (mmt90) outliers start: 76 outliers final: 30 residues processed: 413 average time/residue: 0.6860 time to fit residues: 324.1218 Evaluate side-chains 401 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 349 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain C residue 39 VAL 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 145 THR Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain 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 395 LEU Chi-restraints excluded: chain H residue 408 LYS Chi-restraints excluded: chain I residue 444 MET 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 411 ILE Chi-restraints excluded: chain K residue 466 ILE Chi-restraints excluded: chain K residue 603 ILE Chi-restraints excluded: chain L residue 577 GLU Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 87 CYS Chi-restraints excluded: chain O residue 115 ARG Chi-restraints excluded: chain O residue 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: 0.7980 chunk 153 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 252 optimal weight: 0.3980 chunk 129 optimal weight: 20.0000 chunk 80 optimal weight: 0.8980 chunk 184 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 102 optimal weight: 0.6980 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** J 178 ASN ** K 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 574 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.158350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.119297 restraints weight = 28232.053| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.27 r_work: 0.3101 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24439 Z= 0.186 Angle : 0.639 18.954 33368 Z= 0.324 Chirality : 0.045 0.289 3870 Planarity : 0.005 0.067 3956 Dihedral : 14.933 179.789 4373 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.87 % Allowed : 31.00 % Favored : 66.12 % 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: -0.10 (0.15), residues: 2762 helix: 1.49 (0.17), residues: 937 sheet: -0.23 (0.22), residues: 490 loop : -1.15 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 102 TYR 0.030 0.001 TYR I 599 PHE 0.023 0.002 PHE C 133 TRP 0.035 0.001 TRP L 535 HIS 0.004 0.001 HIS K 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (24400) covalent geometry : angle 0.59468 / 0.32 (33320) hydrogen bonds : bond 0.03716 / 2.42 ( 1037) hydrogen bonds : angle 4.74537 / 3.29 ( 3063) metal coordination : bond 0.00916 / 0.58 ( 39) metal coordination : angle 6.16059 / 3.78 ( 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 421 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 354 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.6974 (OUTLIER) cc_final: 0.6491 (tpp) REVERT: A 18 LEU cc_start: 0.6171 (tp) cc_final: 0.5395 (mp) REVERT: A 51 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7839 (t80) REVERT: A 55 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7757 (mm) REVERT: A 60 GLU cc_start: 0.7188 (tp30) cc_final: 0.6754 (tp30) REVERT: A 62 MET cc_start: 0.6532 (mpp) cc_final: 0.5995 (mpt) REVERT: A 85 VAL cc_start: 0.7797 (OUTLIER) cc_final: 0.7480 (p) REVERT: A 157 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8390 (p0) REVERT: A 169 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7112 (mp0) REVERT: B 28 LYS cc_start: 0.7133 (OUTLIER) cc_final: 0.6898 (ttpt) REVERT: B 29 GLU cc_start: 0.7004 (mt-10) cc_final: 0.6723 (mt-10) REVERT: B 70 VAL cc_start: 0.7764 (OUTLIER) cc_final: 0.7515 (p) REVERT: B 79 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7786 (ttp80) REVERT: B 154 GLN cc_start: 0.7895 (mm110) cc_final: 0.7648 (mm110) REVERT: B 171 ASN cc_start: 0.7635 (m-40) cc_final: 0.7067 (t0) REVERT: C 5 MET cc_start: 0.8518 (mtm) cc_final: 0.7994 (mtt) REVERT: C 33 LYS cc_start: 0.8603 (mptt) cc_final: 0.8186 (ptmt) REVERT: C 83 ARG cc_start: 0.8138 (mtm-85) cc_final: 0.7678 (mtm-85) REVERT: C 85 VAL cc_start: 0.8016 (m) cc_final: 0.7811 (p) REVERT: C 108 ASP cc_start: 0.8268 (m-30) cc_final: 0.7891 (t0) REVERT: C 111 GLU cc_start: 0.8500 (pm20) cc_final: 0.7966 (pm20) REVERT: C 156 LYS cc_start: 0.8243 (mttt) cc_final: 0.7594 (pttp) REVERT: D 3 LYS cc_start: 0.8034 (mtpp) cc_final: 0.7650 (mttm) REVERT: D 13 LYS cc_start: 0.8491 (tptt) cc_final: 0.8030 (ttpp) REVERT: D 75 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7786 (mm-30) REVERT: D 111 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7907 (pm20) REVERT: D 137 GLU cc_start: 0.8606 (pt0) cc_final: 0.8157 (pm20) REVERT: E 29 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7634 (mm-30) REVERT: E 69 ASN cc_start: 0.7704 (m-40) cc_final: 0.7087 (p0) REVERT: E 87 CYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8493 (m) REVERT: E 110 LYS cc_start: 0.8431 (ptmm) cc_final: 0.8065 (pttt) REVERT: E 127 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8418 (mmtm) REVERT: E 154 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7561 (mm-40) REVERT: F 112 GLN cc_start: 0.8412 (mt0) cc_final: 0.8158 (mp10) REVERT: F 123 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8056 (mt-10) REVERT: F 127 LYS cc_start: 0.8299 (mttp) cc_final: 0.7480 (mtmm) REVERT: F 187 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7366 (pp20) REVERT: G 56 PHE cc_start: 0.7795 (t80) cc_final: 0.7254 (t80) REVERT: G 191 PHE cc_start: 0.7734 (p90) cc_final: 0.7327 (p90) REVERT: H 127 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7474 (pt0) REVERT: H 152 SER cc_start: 0.8541 (OUTLIER) cc_final: 0.8206 (p) REVERT: H 253 ILE cc_start: 0.7654 (mt) cc_final: 0.7223 (mm) REVERT: H 395 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7929 (tt) REVERT: H 596 ASN cc_start: 0.7979 (m-40) cc_final: 0.7366 (p0) REVERT: I 450 TYR cc_start: 0.5667 (m-80) cc_final: 0.5096 (m-10) REVERT: I 451 ARG cc_start: 0.7684 (mtp180) cc_final: 0.7008 (mmm-85) REVERT: I 518 GLU cc_start: 0.7789 (tp30) cc_final: 0.7386 (tp30) REVERT: J 13 LYS cc_start: 0.8615 (ttmm) cc_final: 0.7881 (ttpt) REVERT: J 52 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8722 (tttt) REVERT: J 125 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8069 (mp10) REVERT: K 191 TYR cc_start: 0.7330 (m-80) cc_final: 0.7094 (m-80) REVERT: K 394 PHE cc_start: 0.7858 (m-80) cc_final: 0.7436 (m-80) REVERT: K 461 GLU cc_start: 0.7649 (tt0) cc_final: 0.7173 (tt0) REVERT: L 542 GLN cc_start: 0.7887 (mt0) cc_final: 0.7458 (mt0) REVERT: L 577 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7216 (mp0) REVERT: L 601 ILE cc_start: 0.7429 (OUTLIER) cc_final: 0.6968 (pt) REVERT: L 603 ILE cc_start: 0.7652 (pp) cc_final: 0.7401 (mm) REVERT: O 5 MET cc_start: 0.8376 (ttp) cc_final: 0.8152 (ttp) REVERT: O 25 ARG cc_start: 0.8360 (ttm-80) cc_final: 0.8125 (mtm110) REVERT: O 87 CYS cc_start: 0.7321 (OUTLIER) cc_final: 0.6777 (m) REVERT: O 93 MET cc_start: 0.8392 (tpt) cc_final: 0.8075 (mmm) REVERT: O 111 GLU cc_start: 0.8388 (mp0) cc_final: 0.8110 (mp0) REVERT: O 115 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8695 (mmt90) outliers start: 67 outliers final: 26 residues processed: 401 average time/residue: 0.6700 time to fit residues: 307.2280 Evaluate side-chains 394 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 346 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain C residue 39 VAL 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 145 THR Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain H residue 29 CYS Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain I residue 444 MET 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 L residue 601 ILE Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 87 CYS Chi-restraints excluded: chain O residue 115 ARG Chi-restraints excluded: chain O residue 190 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 85 optimal weight: 0.7980 chunk 272 optimal weight: 1.9990 chunk 2 optimal weight: 20.0000 chunk 110 optimal weight: 0.9990 chunk 226 optimal weight: 8.9990 chunk 266 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 219 optimal weight: 2.9990 chunk 247 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN G 42 ASN G 81 ASN H 104 GLN H 479 ASN I 438 ASN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 178 ASN ** K 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.160095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.120620 restraints weight = 28031.480| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.27 r_work: 0.3129 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24439 Z= 0.155 Angle : 0.604 17.577 33368 Z= 0.309 Chirality : 0.044 0.308 3870 Planarity : 0.004 0.066 3956 Dihedral : 14.936 179.923 4373 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.62 % Allowed : 31.26 % Favored : 66.12 % 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: -0.00 (0.15), residues: 2762 helix: 1.57 (0.17), residues: 937 sheet: -0.18 (0.22), residues: 491 loop : -1.09 (0.16), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 409 TYR 0.027 0.001 TYR I 450 PHE 0.026 0.001 PHE C 133 TRP 0.035 0.001 TRP L 535 HIS 0.004 0.001 HIS K 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (24400) covalent geometry : angle 0.56168 / 0.31 (33320) hydrogen bonds : bond 0.03622 / 2.35 ( 1037) hydrogen bonds : angle 4.62893 / 3.21 ( 3063) metal coordination : bond 0.00769 / 0.47 ( 39) metal coordination : angle 5.86399 / 3.60 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9255.92 seconds wall clock time: 158 minutes 15.06 seconds (9495.06 seconds total)