Starting phenix.real_space_refine on Tue May 20 20:28:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z4j_39766/05_2025/8z4j_39766.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z4j_39766/05_2025/8z4j_39766.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z4j_39766/05_2025/8z4j_39766.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z4j_39766/05_2025/8z4j_39766.map" model { file = "/net/cci-nas-00/data/ceres_data/8z4j_39766/05_2025/8z4j_39766.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z4j_39766/05_2025/8z4j_39766.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.039 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 7 6.06 5 P 72 5.49 5 S 84 5.16 5 C 12807 2.51 5 N 3554 2.21 5 O 4131 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20655 Number of models: 1 Model: "" Number of chains: 20 Chain: "B" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1075 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 4 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 6, 'ARG:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 69 Chain: "C" Number of atoms: 1402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1402 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 179} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 1529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1529 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1524 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 192} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1455 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "G" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1639 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain breaks: 6 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 59 Chain: "H" Number of atoms: 4431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4431 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 18, 'TRANS': 557} Chain breaks: 8 Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 162 Chain: "I" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1276 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 37 Chain: "J" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1534 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 192} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 2181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2181 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 11, 'TRANS': 269} Chain breaks: 11 Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'HIS:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 75 Chain: "L" Number of atoms: 1084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1084 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 3 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 259 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 113 Chain: "M" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 794 Classifications: {'RNA': 38} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 13, 'rna3p_pur': 12, 'rna3p_pyr': 7} Link IDs: {'rna2p': 18, 'rna3p': 19} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {' G%rna3p_pur:plan2': 1, ' G%rna3p_pur:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "N" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 724 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 1, 'rna3p_pur': 14, 'rna3p_pyr': 14} Link IDs: {'rna2p': 6, 'rna3p': 27} Chain breaks: 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: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 372 SG CYS B 71 34.913 60.406 160.149 1.00 97.51 S ATOM 436 SG CYS B 81 32.051 59.017 158.080 1.00 92.59 S ATOM 451 SG CYS B 84 31.417 61.676 161.021 1.00 88.14 S ATOM 471 SG CYS B 87 33.490 62.501 158.021 1.00 88.56 S ATOM 1567 SG CYS C 71 25.768 83.500 136.706 1.00 51.74 S ATOM 1641 SG CYS C 81 23.430 85.679 134.643 1.00 51.54 S ATOM 1662 SG CYS C 84 25.324 87.284 137.461 1.00 50.68 S ATOM 1682 SG CYS C 87 27.337 86.087 134.614 1.00 43.74 S ATOM 3019 SG CYS D 71 61.650 102.308 86.962 1.00 54.08 S ATOM 3114 SG CYS D 84 64.918 103.166 86.780 1.00 59.25 S ATOM 3134 SG CYS D 87 64.027 99.714 84.707 1.00 40.22 S ATOM 4548 SG CYS E 71 74.980 81.510 63.562 1.00 60.36 S ATOM 4622 SG CYS E 81 77.805 80.671 60.623 1.00 71.73 S ATOM 4643 SG CYS E 84 78.016 79.454 63.190 1.00 73.09 S ATOM 4663 SG CYS E 87 74.412 78.687 61.323 1.00 47.74 S ATOM 6069 SG CYS F 71 65.959 58.318 41.094 1.00 78.96 S ATOM 6146 SG CYS F 84 64.269 55.153 41.419 1.00 72.70 S ATOM 6166 SG CYS F 87 62.867 56.767 39.582 1.00 63.42 S ATOM 14874 SG CYS J 71 38.797 103.237 111.904 1.00 42.67 S ATOM 14948 SG CYS J 81 38.609 105.749 109.384 1.00 45.13 S ATOM 14969 SG CYS J 84 41.589 105.740 111.905 1.00 29.04 S ATOM 14989 SG CYS J 87 41.587 103.114 109.366 1.00 44.24 S Time building chain proxies: 12.28, per 1000 atoms: 0.59 Number of scatterers: 20655 At special positions: 0 Unit cell: (92.15, 129.2, 192.85, 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 7 29.99 S 84 16.00 P 72 15.00 O 4131 8.00 N 3554 7.00 C 12807 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: 5.27 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 71 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 87 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 84 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 81 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 71 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 87 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 84 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 81 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 87 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 84 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 71 " pdb=" ZN E 301 " 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 87 " 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 87 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 84 " 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=" NE2 HIS H 148 " pdb=" ZN J 301 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 71 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 84 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 87 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 81 " Number of angles added : 24 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4738 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 32 sheets defined 36.2% alpha, 19.8% beta 19 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 6.90 Creating SS restraints... Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 84 through 90 Processing helix chain 'B' and resid 156 through 172 Processing helix chain 'B' and resid 196 through 198 No H-bonds generated for 'chain 'B' and resid 196 through 198' Processing helix chain 'C' and resid 53 through 66 Processing helix chain 'C' and resid 84 through 90 Processing helix chain 'C' and resid 109 through 113 removed outlier: 3.583A pdb=" N ILE C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 109 through 113' Processing helix chain 'C' and resid 157 through 172 Processing helix chain 'C' and resid 176 through 180 Processing helix chain 'D' and resid 24 through 32 Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 155 through 172 removed outlier: 4.657A pdb=" N SER D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE D 161 " --> pdb=" O ASP D 157 " (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 31 Processing helix chain 'E' and resid 51 through 66 Processing helix chain 'E' and resid 84 through 91 Processing helix chain 'E' and resid 109 through 113 Processing helix chain 'E' and resid 156 through 172 Processing helix chain 'E' and resid 176 through 180 removed outlier: 3.664A pdb=" N GLY E 180 " --> pdb=" O LEU E 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 32 Processing helix chain 'F' and resid 52 through 67 Processing helix chain 'F' and resid 84 through 90 Processing helix chain 'F' and resid 109 through 113 removed outlier: 3.861A pdb=" N ILE F 113 " --> pdb=" O THR F 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 109 through 113' Processing helix chain 'F' and resid 157 through 172 Processing helix chain 'G' and resid 18 through 22 removed outlier: 3.809A pdb=" N GLY G 21 " --> pdb=" O LEU G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 44 Processing helix chain 'G' and resid 45 through 51 Processing helix chain 'G' and resid 93 through 95 No H-bonds generated for 'chain 'G' and resid 93 through 95' Processing helix chain 'G' and resid 124 through 139 removed outlier: 3.660A pdb=" N ILE G 134 " --> pdb=" O GLU G 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 53 removed outlier: 3.892A pdb=" N GLY H 53 " --> pdb=" O ILE H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 77 Processing helix chain 'H' and resid 86 through 108 Processing helix chain 'H' and resid 114 through 124 removed outlier: 3.967A pdb=" N ILE H 124 " --> pdb=" O SER H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 222 removed outlier: 3.801A pdb=" N LEU H 212 " --> pdb=" O ARG H 208 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 245 removed outlier: 3.715A pdb=" N TYR H 245 " --> pdb=" O THR H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 268 Processing helix chain 'H' and resid 269 through 272 Processing helix chain 'H' and resid 273 through 278 removed outlier: 4.037A pdb=" N ARG H 278 " --> pdb=" O LYS H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 305 Processing helix chain 'H' and resid 321 through 332 removed outlier: 4.017A pdb=" N ASN H 325 " --> pdb=" O GLY H 321 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLN H 329 " --> pdb=" O ASN H 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 348 through 355 Processing helix chain 'H' and resid 375 through 385 Processing helix chain 'H' and resid 399 through 413 Processing helix chain 'H' and resid 470 through 481 removed outlier: 3.605A 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 588 Processing helix chain 'H' and resid 594 through 606 removed outlier: 4.403A pdb=" N ASN H 604 " --> pdb=" O ASN H 600 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE H 605 " --> pdb=" O ILE H 601 " (cutoff:3.500A) Processing helix chain 'I' and resid 470 through 489 removed outlier: 3.846A pdb=" N PHE I 474 " --> pdb=" O ASP I 470 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE I 489 " --> pdb=" O MET I 485 " (cutoff:3.500A) Processing helix chain 'I' and resid 509 through 523 Processing helix chain 'I' and resid 527 through 541 Processing helix chain 'I' and resid 542 through 554 Processing helix chain 'I' and resid 572 through 590 Processing helix chain 'I' and resid 591 through 593 No H-bonds generated for 'chain 'I' and resid 591 through 593' Processing helix chain 'I' and resid 594 through 603 Processing helix chain 'J' and resid 24 through 29 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 removed outlier: 3.588A pdb=" N ILE J 113 " --> pdb=" O THR J 109 " (cutoff:3.500A) No H-bonds generated for '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 Processing helix chain 'K' and resid 377 through 384 Processing helix chain 'K' and resid 399 through 413 removed outlier: 3.832A pdb=" N ARG K 409 " --> pdb=" O ILE K 405 " (cutoff:3.500A) Processing helix chain 'K' and resid 470 through 487 removed outlier: 3.506A pdb=" N PHE K 474 " --> pdb=" O ASP K 470 " (cutoff:3.500A) Processing helix chain 'K' and resid 509 through 523 removed outlier: 3.648A pdb=" N ILE K 523 " --> pdb=" O TYR K 519 " (cutoff:3.500A) Processing helix chain 'K' and resid 527 through 540 Processing helix chain 'K' and resid 541 through 554 Processing helix chain 'K' and resid 573 through 592 removed outlier: 3.528A pdb=" N GLU K 577 " --> pdb=" O ASP K 573 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS K 592 " --> pdb=" O LEU K 588 " (cutoff:3.500A) Processing helix chain 'K' and resid 594 through 603 Processing helix chain 'L' and resid 470 through 486 removed outlier: 3.744A pdb=" N PHE L 474 " --> pdb=" O ASP L 470 " (cutoff:3.500A) Processing helix chain 'L' and resid 511 through 523 removed outlier: 3.881A pdb=" N ASN L 522 " --> pdb=" O GLU L 518 " (cutoff:3.500A) Processing helix chain 'L' and resid 527 through 541 Processing helix chain 'L' and resid 542 through 554 Processing helix chain 'L' and resid 573 through 591 Processing helix chain 'L' and resid 594 through 606 removed outlier: 3.844A pdb=" N ASN L 604 " --> pdb=" O ASN L 600 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE L 605 " --> pdb=" O ILE L 601 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 48 through 49 Processing sheet with id=AA2, first strand: chain 'B' and resid 99 through 101 Processing sheet with id=AA3, first strand: chain 'C' and resid 99 through 101 Processing sheet with id=AA4, first strand: chain 'C' and resid 99 through 101 Processing sheet with id=AA5, first strand: chain 'C' and resid 114 through 120 Processing sheet with id=AA6, first strand: chain 'D' and resid 99 through 101 removed outlier: 3.508A pdb=" N THR D 149 " --> pdb=" O SER D 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 99 through 101 removed outlier: 3.508A pdb=" N THR D 149 " --> pdb=" O SER D 100 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 114 through 122 removed outlier: 6.497A pdb=" N ARG D 115 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLU D 136 " --> pdb=" O ARG D 115 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N SER D 117 " --> pdb=" O LYS D 134 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS D 134 " --> pdb=" O SER D 117 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N HIS D 119 " --> pdb=" O THR D 132 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N THR D 132 " --> pdb=" O HIS D 119 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG D 121 " --> pdb=" O SER D 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 99 through 101 Processing sheet with id=AB1, first strand: chain 'E' and resid 99 through 101 Processing sheet with id=AB2, first strand: chain 'E' and resid 114 through 115 Processing sheet with id=AB3, first strand: chain 'E' and resid 119 through 122 Processing sheet with id=AB4, first strand: chain 'F' and resid 99 through 101 Processing sheet with id=AB5, first strand: chain 'F' and resid 99 through 101 Processing sheet with id=AB6, first strand: chain 'F' and resid 114 through 116 Processing sheet with id=AB7, first strand: chain 'F' and resid 119 through 122 Processing sheet with id=AB8, first strand: chain 'G' and resid 115 through 118 removed outlier: 3.689A pdb=" N ILE G 143 " --> pdb=" O PHE G 156 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 83 through 84 Processing sheet with id=AC1, first strand: chain 'G' and resid 97 through 101 Processing sheet with id=AC2, first strand: chain 'G' and resid 187 through 192 Processing sheet with id=AC3, first strand: chain 'H' and resid 2 through 5 removed outlier: 6.932A pdb=" N SER H 14 " --> pdb=" O CYS H 29 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N CYS H 29 " --> pdb=" O SER H 14 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N CYS H 58 " --> pdb=" O ILE H 84 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 134 through 136 removed outlier: 8.823A pdb=" N VAL H 153 " --> pdb=" O GLY H 168 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N GLY H 168 " --> pdb=" O VAL H 153 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 290 through 292 removed outlier: 3.523A pdb=" N ILE H 291 " --> pdb=" O VAL H 251 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N TYR H 252 " --> pdb=" O ILE H 312 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL H 225 " --> pdb=" O ILE H 311 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N SER H 313 " --> pdb=" O VAL H 225 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ILE H 227 " --> pdb=" O SER H 313 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 434 through 437 removed outlier: 6.206A pdb=" N LYS H 434 " --> pdb=" O ILE H 466 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE H 468 " --> pdb=" O LYS H 434 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL H 436 " --> pdb=" O ILE H 468 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE H 459 " --> pdb=" O MET K 453 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL K 435 " --> pdb=" O ILE K 466 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE K 468 " --> pdb=" O VAL K 435 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU K 437 " --> pdb=" O ILE K 468 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 445 through 446 Processing sheet with id=AC8, first strand: chain 'I' and resid 445 through 447 Processing sheet with id=AC9, first strand: chain 'I' and resid 445 through 447 removed outlier: 4.180A pdb=" N ARG I 451 " --> pdb=" O GLU L 461 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG L 451 " --> pdb=" O GLU I 461 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN L 469 " --> pdb=" O PHE L 458 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL L 436 " --> pdb=" O ILE L 468 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 48 through 49 removed outlier: 3.519A pdb=" N ILE J 105 " --> pdb=" O THR J 145 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 48 through 49 removed outlier: 3.519A pdb=" N ILE J 105 " --> pdb=" O THR J 145 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 114 through 122 removed outlier: 6.457A pdb=" N ARG J 115 " --> pdb=" O GLU J 136 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLU J 136 " --> pdb=" O ARG J 115 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N SER J 117 " --> pdb=" O LYS J 134 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LYS J 134 " --> pdb=" O SER J 117 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N HIS J 119 " --> pdb=" O THR J 132 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N THR J 132 " --> pdb=" O HIS J 119 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ARG J 121 " --> pdb=" O SER J 130 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 2 through 3 Processing sheet with id=AD5, first strand: chain 'K' and resid 140 through 144 removed outlier: 6.310A pdb=" N LEU K 165 " --> pdb=" O ILE K 193 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N GLU K 195 " --> pdb=" O LEU K 165 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU K 192 " --> pdb=" O PHE K 394 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL K 396 " --> pdb=" O LEU K 192 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU K 194 " --> pdb=" O VAL K 396 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU K 395 " --> pdb=" O GLU K 418 " (cutoff:3.500A) 870 hydrogen bonds defined for protein. 2493 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 6.85 Time building geometry restraints manager: 5.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5242 1.33 - 1.46: 6052 1.46 - 1.59: 9593 1.59 - 1.72: 98 1.72 - 1.85: 128 Bond restraints: 21113 Sorted by residual: bond pdb=" C THR B 11 " pdb=" N MET B 12 " ideal model delta sigma weight residual 1.331 1.243 0.088 1.26e-02 6.30e+03 4.93e+01 bond pdb=" C GLU H 384 " pdb=" N ARG H 385 " ideal model delta sigma weight residual 1.335 1.426 -0.091 1.35e-02 5.49e+03 4.58e+01 bond pdb=" C LYS H 54 " pdb=" N ALA H 55 " ideal model delta sigma weight residual 1.331 1.239 0.091 1.42e-02 4.96e+03 4.13e+01 bond pdb=" C ARG G 62 " pdb=" N ASP G 63 " ideal model delta sigma weight residual 1.331 1.255 0.076 1.29e-02 6.01e+03 3.48e+01 bond pdb=" C MET B 12 " pdb=" N LYS B 13 " ideal model delta sigma weight residual 1.329 1.251 0.078 1.36e-02 5.41e+03 3.30e+01 ... (remaining 21108 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 27607 3.05 - 6.11: 1032 6.11 - 9.16: 190 9.16 - 12.22: 24 12.22 - 15.27: 1 Bond angle restraints: 28854 Sorted by residual: angle pdb=" N ILE G 166 " pdb=" CA ILE G 166 " pdb=" C ILE G 166 " ideal model delta sigma weight residual 108.23 119.37 -11.14 1.53e+00 4.27e-01 5.30e+01 angle pdb=" N LEU K 452 " pdb=" CA LEU K 452 " pdb=" C LEU K 452 " ideal model delta sigma weight residual 108.96 119.02 -10.06 1.49e+00 4.50e-01 4.56e+01 angle pdb=" N LEU L 526 " pdb=" CA LEU L 526 " pdb=" C LEU L 526 " ideal model delta sigma weight residual 109.76 99.03 10.73 1.64e+00 3.72e-01 4.28e+01 angle pdb=" O3' G M 28 " pdb=" C3' G M 28 " pdb=" C2' G M 28 " ideal model delta sigma weight residual 109.50 118.68 -9.18 1.50e+00 4.44e-01 3.75e+01 angle pdb=" O THR B 11 " pdb=" C THR B 11 " pdb=" N MET B 12 " ideal model delta sigma weight residual 123.10 116.52 6.58 1.15e+00 7.56e-01 3.27e+01 ... (remaining 28849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.02: 12223 35.02 - 70.03: 533 70.03 - 105.05: 43 105.05 - 140.06: 1 140.06 - 175.08: 3 Dihedral angle restraints: 12803 sinusoidal: 5511 harmonic: 7292 Sorted by residual: dihedral pdb=" O4' C N -16 " pdb=" C1' C N -16 " pdb=" N1 C N -16 " pdb=" C2 C N -16 " ideal model delta sinusoidal sigma weight residual 232.00 60.06 171.94 1 1.70e+01 3.46e-03 6.61e+01 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 35.79 -163.79 1 1.70e+01 3.46e-03 6.51e+01 dihedral pdb=" CA PHE F 51 " pdb=" C PHE F 51 " pdb=" N LYS F 52 " pdb=" CA LYS F 52 " ideal model delta harmonic sigma weight residual 180.00 150.89 29.11 0 5.00e+00 4.00e-02 3.39e+01 ... (remaining 12800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 3047 0.113 - 0.227: 299 0.227 - 0.340: 30 0.340 - 0.453: 9 0.453 - 0.566: 2 Chirality restraints: 3387 Sorted by residual: chirality pdb=" CB ILE F 113 " pdb=" CA ILE F 113 " pdb=" CG1 ILE F 113 " pdb=" CG2 ILE F 113 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.57 2.00e-01 2.50e+01 8.02e+00 chirality pdb=" CB ILE G 59 " pdb=" CA ILE G 59 " pdb=" CG1 ILE G 59 " pdb=" CG2 ILE G 59 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.52 2.00e-01 2.50e+01 6.86e+00 chirality pdb=" CB ILE B 173 " pdb=" CA ILE B 173 " pdb=" CG1 ILE B 173 " pdb=" CG2 ILE B 173 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.90e+00 ... (remaining 3384 not shown) Planarity restraints: 3437 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 56 " 0.033 2.00e-02 2.50e+03 3.93e-02 2.70e+01 pdb=" CG PHE G 56 " -0.084 2.00e-02 2.50e+03 pdb=" CD1 PHE G 56 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE G 56 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 PHE G 56 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE G 56 " -0.023 2.00e-02 2.50e+03 pdb=" CZ PHE G 56 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 478 " 0.028 2.00e-02 2.50e+03 3.20e-02 2.55e+01 pdb=" CG TRP I 478 " -0.083 2.00e-02 2.50e+03 pdb=" CD1 TRP I 478 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP I 478 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP I 478 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP I 478 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP I 478 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 478 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 478 " 0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP I 478 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY H 53 " 0.023 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C GLY H 53 " -0.079 2.00e-02 2.50e+03 pdb=" O GLY H 53 " 0.030 2.00e-02 2.50e+03 pdb=" N LYS H 54 " 0.026 2.00e-02 2.50e+03 ... (remaining 3434 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 390 2.63 - 3.20: 17850 3.20 - 3.77: 34487 3.77 - 4.33: 47353 4.33 - 4.90: 75900 Nonbonded interactions: 175980 Sorted by model distance: nonbonded pdb=" OD2 ASP H 169 " pdb="ZN ZN H 701 " model vdw 2.067 2.230 nonbonded pdb=" O2' G M 28 " pdb=" O5' C M 29 " model vdw 2.258 3.040 nonbonded pdb=" O SER J 92 " pdb=" O2' A M 14 " model vdw 2.265 3.040 nonbonded pdb=" O SER E 92 " pdb=" O2' U M 2 " model vdw 2.269 3.040 nonbonded pdb=" OE1 GLU K 533 " pdb=" OH TYR K 548 " model vdw 2.271 3.040 ... (remaining 175975 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 'C' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 75 or (resid 77 through 79 and (name N or name CA or name C \ or name O or name CB )) or resid 80 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 186 or (res \ id 187 and (name N or name CA or name C or name O or name CB )) or resid 188 or \ (resid 189 and (name N or name CA or name C or name O or name CB )) or resid 190 \ through 196 or resid 301)) selection = (chain 'D' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 26 or (resid 27 and (name N or name CA or name C or name O \ or name CB )) or resid 35 through 75 or (resid 77 through 79 and (name N or name \ CA or name C or name O or name CB )) or resid 80 through 94 or (resid 95 throug \ h 96 and (name N or name CA or name C or name O or name CB )) or resid 97 throug \ h 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) or \ resid 111 through 121 or resid 129 through 132 or (resid 133 and (name N or name \ CA or name C or name O or name CB )) or resid 134 through 154 or (resid 155 thr \ ough 156 and (name N or name CA or name C or name O or name CB )) or resid 157 t \ hrough 165 or (resid 166 and (name N or name CA or name C or name O or name CB ) \ ) or resid 167 through 186 or (resid 187 and (name N or name CA or name C or nam \ e O or name CB )) or resid 188 through 196 or resid 301)) selection = (chain 'E' and (resid 3 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB )) or resid 35 through 75 or (resid 77 through 79 and (nam \ e N or name CA or name C or name O or name CB )) or resid 80 through 94 or (resi \ d 95 through 96 and (name N or name CA or name C or name O or name CB )) or resi \ d 97 through 109 or (resid 110 and (name N or name CA or name C or name O or nam \ e CB )) or resid 111 through 121 or resid 129 through 132 or (resid 133 and (nam \ e N or name CA or name C or name O or name CB )) or resid 134 through 154 or (re \ sid 155 through 156 and (name N or name CA or name C or name O or name CB )) or \ resid 157 through 165 or (resid 166 and (name N or name CA or name C or name O o \ r name CB )) or resid 167 through 186 or (resid 187 and (name N or name CA or na \ me C or name O or name CB )) or resid 188 or (resid 189 and (name N or name CA o \ r name C or name O or name CB )) or resid 190 through 196 or resid 301)) selection = (chain 'F' and (resid 3 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB )) or resid 35 through 109 or (resid 110 and (name N or na \ me CA or name C or name O or name CB )) or resid 111 through 121 or resid 129 th \ rough 132 or (resid 133 and (name N or name CA or name C or name O or name CB )) \ or resid 134 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 'J' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 26 or (resid 27 and (name N or name CA or name C or name O \ or name CB )) or resid 35 through 75 or (resid 77 through 79 and (name N or name \ CA or name C or name O or name CB )) or resid 80 through 94 or (resid 95 throug \ h 96 and (name N or name CA or name C or name O or name CB )) or resid 97 throug \ h 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) or \ resid 111 through 121 or resid 129 through 132 or (resid 133 and (name N or name \ CA or name C or name O or name CB )) or resid 134 through 155 or (resid 156 and \ (name N or name CA or name C or name O or name CB )) or resid 157 through 165 o \ r (resid 166 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 67 through 186 or (resid 187 and (name N or name CA or name C or name O or name \ CB )) or resid 188 or (resid 189 and (name N or name CA or name C or name O or n \ ame CB )) or resid 190 through 196 or resid 301)) } ncs_group { reference = (chain 'I' and (resid 434 through 452 or (resid 453 and (name N or name CA or na \ me C or name O or name CB )) or resid 454 through 470 or (resid 471 and (name N \ or name CA or name C or name O or name CB )) or resid 472 through 484 or (resid \ 485 through 486 and (name N or name CA or name C or name O or name CB )) or resi \ d 487 or (resid 488 and (name N or name CA or name C or name O or name CB )) or \ (resid 510 through 512 and (name N or name CA or name C or name O or name CB )) \ or resid 513 or (resid 514 through 515 and (name N or name CA or name C or name \ O or name CB )) or resid 516 through 517 or (resid 518 and (name N or name CA or \ name C or name O or name CB )) or resid 519 through 523 or (resid 524 and (name \ N or name CA or name C or name O or name CB )) or resid 525 through 527 or (res \ id 528 and (name N or name CA or name C or name O or name CB )) or resid 529 thr \ ough 531 or (resid 532 through 540 and (name N or name CA or name C or name O or \ name CB )) or resid 541 or (resid 542 through 547 and (name N or name CA or nam \ e C or name O or name CB )) or resid 548 through 549 or (resid 550 and (name N o \ r name CA or name C or name O or name CB )) or resid 551 through 553 or (resid 5 \ 54 and (name N or name CA or name C or name O or name CB )) or resid 555 through \ 560 or (resid 561 and (name N or name CA or name C or name O or name CB )) or r \ esid 562 through 567 or (resid 568 and (name N or name CA or name C or name O or \ name CB )) or resid 572 or (resid 573 through 578 and (name N or name CA or nam \ e C or name O or name CB )) or resid 579 through 587 or (resid 588 and (name N o \ r name CA or name C or name O or name CB )) or resid 589 through 590 or (resid 5 \ 91 through 592 and (name N or name CA or name C or name O or name CB )) or resid \ 593 or (resid 594 through 597 and (name N or name CA or name C or name O or nam \ e CB )) or resid 598 or (resid 599 and (name N or name CA or name C or name O or \ name CB )) or resid 600 through 601 or (resid 602 through 603 and (name N or na \ me CA or name C or name O or name CB )) or resid 604 through 607 or (resid 608 t \ hrough 609 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'L' and (resid 434 through 440 or (resid 441 through 442 and (name N or n \ ame CA or name C or name O or name CB )) or resid 443 through 461 or (resid 462 \ through 467 and (name N or name CA or name C or name O or name CB )) or resid 46 \ 8 through 475 or (resid 476 and (name N or name CA or name C or name O or name C \ B )) or resid 477 through 485 or (resid 486 and (name N or name CA or name C or \ name O or name CB )) or resid 487 through 609)) } 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: 1.670 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: 0.870 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 53.030 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.090 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:12.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.126 21138 Z= 0.409 Angle : 1.393 33.611 28878 Z= 0.748 Chirality : 0.073 0.566 3387 Planarity : 0.011 0.104 3437 Dihedral : 18.566 175.075 8065 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.57 % Favored : 94.10 % Rotamer: Outliers : 1.94 % Allowed : 33.54 % Favored : 64.52 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.15), residues: 2425 helix: -1.77 (0.15), residues: 831 sheet: -1.34 (0.24), residues: 465 loop : -2.37 (0.15), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.005 TRP I 478 HIS 0.046 0.006 HIS H 326 PHE 0.084 0.006 PHE G 56 TYR 0.048 0.004 TYR L 450 ARG 0.028 0.002 ARG G 117 Details of bonding type rmsd hydrogen bonds : bond 0.14200 ( 896) hydrogen bonds : angle 7.95968 ( 2589) metal coordination : bond 0.01484 ( 25) metal coordination : angle 10.36608 ( 24) covalent geometry : bond 0.00843 (21113) covalent geometry : angle 1.36148 (28854) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 359 time to evaluate : 2.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 48 LEU cc_start: 0.7943 (tm) cc_final: 0.7508 (mm) REVERT: C 41 LYS cc_start: 0.8211 (mttt) cc_final: 0.7905 (mttm) REVERT: C 134 LYS cc_start: 0.8022 (ttpt) cc_final: 0.7800 (ttpt) REVERT: G 41 PHE cc_start: 0.7696 (t80) cc_final: 0.7148 (t80) REVERT: G 125 GLU cc_start: 0.7294 (pm20) cc_final: 0.6905 (pm20) REVERT: H 113 TYR cc_start: 0.8041 (p90) cc_final: 0.7498 (p90) REVERT: I 536 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7557 (mt-10) REVERT: K 456 SER cc_start: 0.7097 (p) cc_final: 0.6791 (p) REVERT: K 573 ASP cc_start: 0.7016 (t0) cc_final: 0.6685 (m-30) REVERT: L 476 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7962 (tmt) REVERT: L 481 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7636 (mp0) outliers start: 38 outliers final: 10 residues processed: 381 average time/residue: 1.2004 time to fit residues: 522.4225 Evaluate side-chains 319 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 307 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain F residue 84 CYS Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 436 VAL Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain L residue 476 MET Chi-restraints excluded: chain L residue 481 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 10.0000 chunk 191 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 197 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 228 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 36 ASN E 107 ASN G 42 ASN ** H 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 558 ASN K 161 ASN K 510 HIS K 551 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.158442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.125591 restraints weight = 26782.670| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.84 r_work: 0.3228 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21138 Z= 0.174 Angle : 0.699 20.051 28878 Z= 0.355 Chirality : 0.045 0.315 3387 Planarity : 0.005 0.070 3437 Dihedral : 15.387 174.867 3766 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.84 % Favored : 95.96 % Rotamer: Outliers : 4.96 % Allowed : 26.79 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.16), residues: 2425 helix: -0.06 (0.17), residues: 850 sheet: -1.16 (0.23), residues: 454 loop : -1.93 (0.16), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 478 HIS 0.008 0.002 HIS K 510 PHE 0.021 0.002 PHE G 191 TYR 0.025 0.001 TYR K 599 ARG 0.008 0.001 ARG G 117 Details of bonding type rmsd hydrogen bonds : bond 0.04393 ( 896) hydrogen bonds : angle 5.37600 ( 2589) metal coordination : bond 0.00817 ( 25) metal coordination : angle 6.56805 ( 24) covalent geometry : bond 0.00390 (21113) covalent geometry : angle 0.67360 (28854) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 367 time to evaluate : 2.338 Fit side-chains REVERT: B 7 LYS cc_start: 0.6613 (mttm) cc_final: 0.6251 (mttt) REVERT: B 59 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7471 (mt) REVERT: C 102 ASP cc_start: 0.8159 (m-30) cc_final: 0.7953 (m-30) REVERT: C 173 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8473 (tp) REVERT: D 69 ASN cc_start: 0.8019 (p0) cc_final: 0.7792 (p0) REVERT: D 187 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8516 (mm-30) REVERT: E 79 ARG cc_start: 0.8257 (tpp80) cc_final: 0.7894 (ttm-80) REVERT: E 122 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8900 (mp) REVERT: G 3 GLU cc_start: 0.5347 (mp0) cc_final: 0.5050 (mp0) REVERT: G 22 GLU cc_start: 0.7327 (tp30) cc_final: 0.6979 (tm-30) REVERT: G 41 PHE cc_start: 0.7757 (t80) cc_final: 0.6915 (t80) REVERT: G 123 LYS cc_start: 0.7714 (mmmm) cc_final: 0.7456 (mmmt) REVERT: H 273 LYS cc_start: 0.8159 (tttt) cc_final: 0.7670 (ttpp) REVERT: H 381 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.7831 (t70) REVERT: H 458 PHE cc_start: 0.7162 (m-80) cc_final: 0.6914 (m-80) REVERT: H 461 GLU cc_start: 0.7089 (pm20) cc_final: 0.6611 (pt0) REVERT: H 542 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7588 (tt0) REVERT: H 568 GLU cc_start: 0.8195 (tt0) cc_final: 0.7843 (mm-30) REVERT: I 529 ASN cc_start: 0.8292 (t0) cc_final: 0.7743 (m-40) REVERT: I 561 ARG cc_start: 0.7519 (mtm110) cc_final: 0.7294 (ttp-170) REVERT: J 87 CYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7461 (m) REVERT: K 391 TYR cc_start: 0.8367 (t80) cc_final: 0.8162 (t80) REVERT: K 416 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7063 (mtt90) REVERT: K 456 SER cc_start: 0.7677 (p) cc_final: 0.7310 (p) REVERT: K 465 ARG cc_start: 0.7745 (mtp85) cc_final: 0.7427 (mtp180) REVERT: K 470 ASP cc_start: 0.7357 (t0) cc_final: 0.7155 (t0) REVERT: K 480 GLU cc_start: 0.7657 (tp30) cc_final: 0.7451 (tp30) REVERT: K 573 ASP cc_start: 0.6860 (t0) cc_final: 0.6547 (m-30) REVERT: L 472 ASN cc_start: 0.6830 (OUTLIER) cc_final: 0.6275 (m-40) REVERT: L 481 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7311 (mp0) outliers start: 97 outliers final: 24 residues processed: 429 average time/residue: 1.1729 time to fit residues: 575.7175 Evaluate side-chains 343 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 310 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 154 GLN Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 198 SER Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 312 ILE Chi-restraints excluded: chain H residue 381 ASP Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain H residue 542 GLN Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain K residue 157 ILE Chi-restraints excluded: chain K residue 416 ARG Chi-restraints excluded: chain K residue 417 VAL Chi-restraints excluded: chain K residue 559 THR Chi-restraints excluded: chain K residue 572 THR Chi-restraints excluded: chain L residue 472 ASN Chi-restraints excluded: chain L residue 481 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 78 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 236 optimal weight: 8.9990 chunk 194 optimal weight: 1.9990 chunk 59 optimal weight: 0.0870 chunk 173 optimal weight: 1.9990 chunk 244 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 178 ASN G 129 ASN ** H 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 ASN I 596 ASN J 107 ASN K 510 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.155859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.123933 restraints weight = 26547.244| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.59 r_work: 0.3195 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21138 Z= 0.180 Angle : 0.654 18.807 28878 Z= 0.330 Chirality : 0.044 0.237 3387 Planarity : 0.005 0.067 3437 Dihedral : 15.121 174.101 3751 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.46 % Favored : 96.37 % Rotamer: Outliers : 5.16 % Allowed : 26.18 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.16), residues: 2425 helix: 0.81 (0.18), residues: 850 sheet: -1.09 (0.23), residues: 449 loop : -1.67 (0.17), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 473 HIS 0.004 0.001 HIS H 62 PHE 0.015 0.002 PHE G 191 TYR 0.021 0.001 TYR L 450 ARG 0.008 0.001 ARG I 554 Details of bonding type rmsd hydrogen bonds : bond 0.03891 ( 896) hydrogen bonds : angle 4.94672 ( 2589) metal coordination : bond 0.00724 ( 25) metal coordination : angle 6.19068 ( 24) covalent geometry : bond 0.00406 (21113) covalent geometry : angle 0.62938 (28854) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 333 time to evaluate : 2.079 Fit side-chains REVERT: B 59 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7599 (mt) REVERT: B 93 MET cc_start: 0.7812 (tpp) cc_final: 0.7517 (tpt) REVERT: C 134 LYS cc_start: 0.8120 (ttpt) cc_final: 0.7918 (ttpt) REVERT: C 173 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8426 (tp) REVERT: E 13 LYS cc_start: 0.8691 (ttpp) cc_final: 0.8448 (tttp) REVERT: E 79 ARG cc_start: 0.8372 (tpp80) cc_final: 0.8018 (ttm-80) REVERT: E 122 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8936 (mp) REVERT: E 149 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8322 (p) REVERT: G 3 GLU cc_start: 0.5538 (mp0) cc_final: 0.5238 (mp0) REVERT: G 22 GLU cc_start: 0.7504 (tp30) cc_final: 0.7267 (tm-30) REVERT: G 41 PHE cc_start: 0.7852 (t80) cc_final: 0.6850 (t80) REVERT: G 123 LYS cc_start: 0.7748 (mmmm) cc_final: 0.7474 (mmmt) REVERT: H 52 ILE cc_start: 0.8382 (mt) cc_final: 0.8133 (mp) REVERT: H 273 LYS cc_start: 0.8284 (tttt) cc_final: 0.7816 (ttpp) REVERT: H 297 ASN cc_start: 0.8277 (m-40) cc_final: 0.7815 (m110) REVERT: H 461 GLU cc_start: 0.6961 (pm20) cc_final: 0.6436 (pt0) REVERT: H 542 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7650 (tt0) REVERT: H 568 GLU cc_start: 0.8195 (tt0) cc_final: 0.7880 (mm-30) REVERT: I 453 MET cc_start: 0.8564 (ttp) cc_final: 0.8155 (ttm) REVERT: I 488 GLN cc_start: 0.6968 (tp-100) cc_final: 0.6759 (tp-100) REVERT: I 529 ASN cc_start: 0.8305 (t0) cc_final: 0.7802 (m-40) REVERT: J 87 CYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7518 (m) REVERT: K 157 ILE cc_start: 0.7187 (OUTLIER) cc_final: 0.6696 (pt) REVERT: K 456 SER cc_start: 0.7599 (p) cc_final: 0.7205 (p) REVERT: K 465 ARG cc_start: 0.7767 (mtp85) cc_final: 0.7460 (mtp180) REVERT: L 467 GLU cc_start: 0.7858 (pt0) cc_final: 0.7584 (pt0) REVERT: L 472 ASN cc_start: 0.6813 (OUTLIER) cc_final: 0.6470 (m-40) REVERT: L 476 MET cc_start: 0.8631 (tmt) cc_final: 0.8427 (tmt) REVERT: L 481 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7296 (mp0) outliers start: 101 outliers final: 29 residues processed: 397 average time/residue: 1.1516 time to fit residues: 525.0849 Evaluate side-chains 341 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 303 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 312 ILE Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 362 CYS Chi-restraints excluded: chain H residue 436 VAL Chi-restraints excluded: chain H residue 456 SER Chi-restraints excluded: chain H residue 542 GLN Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain K residue 157 ILE Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 417 VAL Chi-restraints excluded: chain K residue 476 MET Chi-restraints excluded: chain K residue 559 THR Chi-restraints excluded: chain K residue 572 THR Chi-restraints excluded: chain L residue 472 ASN Chi-restraints excluded: chain L residue 481 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 137 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 159 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 41 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 127 optimal weight: 0.3980 chunk 93 optimal weight: 8.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 178 ASN G 42 ASN ** H 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 ASN K 529 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.151621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.116946 restraints weight = 26956.898| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.88 r_work: 0.3105 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 21138 Z= 0.264 Angle : 0.703 22.074 28878 Z= 0.351 Chirality : 0.046 0.214 3387 Planarity : 0.005 0.065 3437 Dihedral : 15.060 170.060 3747 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.04 % Favored : 95.75 % Rotamer: Outliers : 5.27 % Allowed : 26.28 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.16), residues: 2425 helix: 1.08 (0.18), residues: 844 sheet: -1.14 (0.22), residues: 470 loop : -1.59 (0.17), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 125 HIS 0.003 0.001 HIS H 326 PHE 0.022 0.002 PHE H 458 TYR 0.019 0.002 TYR K 391 ARG 0.006 0.001 ARG E 95 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 896) hydrogen bonds : angle 4.86575 ( 2589) metal coordination : bond 0.01067 ( 25) metal coordination : angle 7.09290 ( 24) covalent geometry : bond 0.00599 (21113) covalent geometry : angle 0.67250 (28854) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 323 time to evaluate : 2.053 Fit side-chains REVERT: B 59 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7452 (mt) REVERT: B 93 MET cc_start: 0.8165 (tpp) cc_final: 0.7852 (ttt) REVERT: B 196 ASP cc_start: 0.7543 (p0) cc_final: 0.7233 (p0) REVERT: C 134 LYS cc_start: 0.8061 (ttpt) cc_final: 0.7857 (ttpp) REVERT: C 173 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8441 (tp) REVERT: E 13 LYS cc_start: 0.8773 (ttpp) cc_final: 0.8491 (ttpp) REVERT: E 26 GLU cc_start: 0.8114 (mp0) cc_final: 0.7605 (mp0) REVERT: E 79 ARG cc_start: 0.8428 (tpp80) cc_final: 0.8053 (mtm-85) REVERT: E 110 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8185 (ptmm) REVERT: E 149 THR cc_start: 0.8771 (OUTLIER) cc_final: 0.8440 (p) REVERT: G 9 GLU cc_start: 0.8323 (tp30) cc_final: 0.7657 (tp30) REVERT: G 22 GLU cc_start: 0.7631 (tp30) cc_final: 0.7341 (tm-30) REVERT: G 33 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7681 (ttt180) REVERT: G 41 PHE cc_start: 0.7880 (t80) cc_final: 0.6783 (t80) REVERT: G 114 LYS cc_start: 0.7923 (mtpt) cc_final: 0.7452 (mmmt) REVERT: G 123 LYS cc_start: 0.7726 (mmmm) cc_final: 0.7399 (mmmt) REVERT: H 273 LYS cc_start: 0.8275 (tttt) cc_final: 0.7772 (ttpp) REVERT: H 297 ASN cc_start: 0.8129 (m-40) cc_final: 0.7709 (m110) REVERT: H 461 GLU cc_start: 0.6946 (pm20) cc_final: 0.6462 (pt0) REVERT: H 542 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7764 (tt0) REVERT: I 453 MET cc_start: 0.8632 (ttp) cc_final: 0.8163 (ttm) REVERT: I 472 ASN cc_start: 0.8365 (t0) cc_final: 0.8145 (m110) REVERT: I 488 GLN cc_start: 0.7030 (tp-100) cc_final: 0.6813 (tp-100) REVERT: J 83 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7489 (mtm110) REVERT: J 87 CYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7521 (m) REVERT: K 387 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8277 (tttt) REVERT: K 456 SER cc_start: 0.7763 (p) cc_final: 0.7384 (p) REVERT: K 465 ARG cc_start: 0.7776 (mtp85) cc_final: 0.7397 (mtp180) REVERT: L 472 ASN cc_start: 0.6760 (OUTLIER) cc_final: 0.6510 (m110) REVERT: L 476 MET cc_start: 0.8575 (tmt) cc_final: 0.8343 (tmt) outliers start: 103 outliers final: 41 residues processed: 391 average time/residue: 1.2315 time to fit residues: 550.0969 Evaluate side-chains 359 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 308 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 192 ASP Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 33 ARG Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 312 ILE Chi-restraints excluded: chain H residue 324 LEU Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 362 CYS Chi-restraints excluded: chain H residue 369 SER Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 436 VAL Chi-restraints excluded: chain H residue 456 SER Chi-restraints excluded: chain H residue 542 GLN Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 83 ARG Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain K residue 157 ILE Chi-restraints excluded: chain K residue 170 ILE Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 387 LYS Chi-restraints excluded: chain K residue 417 VAL Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain K residue 476 MET Chi-restraints excluded: chain K residue 559 THR Chi-restraints excluded: chain K residue 579 LEU Chi-restraints excluded: chain L residue 455 PHE Chi-restraints excluded: chain L residue 472 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 124 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 13 optimal weight: 20.0000 chunk 134 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 178 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 ASN K 529 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.152929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.120156 restraints weight = 26735.056| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.64 r_work: 0.3153 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21138 Z= 0.187 Angle : 0.637 18.315 28878 Z= 0.320 Chirality : 0.044 0.206 3387 Planarity : 0.004 0.049 3437 Dihedral : 14.979 170.985 3743 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.59 % Favored : 96.25 % Rotamer: Outliers : 4.70 % Allowed : 27.66 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.17), residues: 2425 helix: 1.30 (0.18), residues: 845 sheet: -1.10 (0.22), residues: 472 loop : -1.47 (0.17), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 478 HIS 0.002 0.001 HIS E 119 PHE 0.025 0.002 PHE B 167 TYR 0.019 0.001 TYR L 450 ARG 0.010 0.001 ARG D 95 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 896) hydrogen bonds : angle 4.67661 ( 2589) metal coordination : bond 0.00733 ( 25) metal coordination : angle 6.01714 ( 24) covalent geometry : bond 0.00426 (21113) covalent geometry : angle 0.61318 (28854) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 332 time to evaluate : 2.233 Fit side-chains REVERT: B 59 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7468 (mt) REVERT: B 93 MET cc_start: 0.8063 (tpp) cc_final: 0.7757 (ttt) REVERT: B 170 GLU cc_start: 0.6190 (OUTLIER) cc_final: 0.5905 (pp20) REVERT: B 196 ASP cc_start: 0.7544 (p0) cc_final: 0.7236 (p0) REVERT: B 198 PHE cc_start: 0.6577 (m-80) cc_final: 0.6259 (m-80) REVERT: C 13 LYS cc_start: 0.7904 (tptt) cc_final: 0.7700 (tptt) REVERT: C 41 LYS cc_start: 0.8198 (mttt) cc_final: 0.7826 (mttt) REVERT: C 173 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8436 (tp) REVERT: D 157 ASP cc_start: 0.7977 (m-30) cc_final: 0.7671 (m-30) REVERT: E 79 ARG cc_start: 0.8364 (tpp80) cc_final: 0.8064 (mtm-85) REVERT: E 110 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8123 (ptmm) REVERT: E 149 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8365 (p) REVERT: G 9 GLU cc_start: 0.8316 (tp30) cc_final: 0.7680 (tp30) REVERT: G 33 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7670 (ttt-90) REVERT: G 41 PHE cc_start: 0.7863 (t80) cc_final: 0.6802 (t80) REVERT: G 57 ASP cc_start: 0.7891 (t0) cc_final: 0.7603 (t70) REVERT: G 114 LYS cc_start: 0.7930 (mtpt) cc_final: 0.7376 (mmtt) REVERT: G 123 LYS cc_start: 0.7700 (mmmm) cc_final: 0.7329 (mmmt) REVERT: H 52 ILE cc_start: 0.8360 (mt) cc_final: 0.8104 (mp) REVERT: H 99 ASP cc_start: 0.8438 (t0) cc_final: 0.8190 (t0) REVERT: H 201 LYS cc_start: 0.5598 (tptt) cc_final: 0.5340 (tptp) REVERT: H 273 LYS cc_start: 0.8262 (tttt) cc_final: 0.7768 (ttpp) REVERT: H 297 ASN cc_start: 0.8128 (m-40) cc_final: 0.7734 (m-40) REVERT: H 328 GLU cc_start: 0.7271 (tp30) cc_final: 0.6997 (mm-30) REVERT: H 389 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8710 (m) REVERT: H 461 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6422 (pt0) REVERT: H 542 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7615 (tt0) REVERT: I 453 MET cc_start: 0.8626 (ttp) cc_final: 0.8095 (ttm) REVERT: I 472 ASN cc_start: 0.8320 (t0) cc_final: 0.8112 (m110) REVERT: I 488 GLN cc_start: 0.7025 (tp-100) cc_final: 0.6822 (tp-100) REVERT: I 551 GLN cc_start: 0.8062 (tt0) cc_final: 0.7300 (tp-100) REVERT: J 87 CYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7474 (m) REVERT: J 150 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8071 (mt) REVERT: K 157 ILE cc_start: 0.7050 (OUTLIER) cc_final: 0.6574 (pt) REVERT: K 189 VAL cc_start: 0.8529 (t) cc_final: 0.8267 (p) REVERT: K 439 ILE cc_start: 0.7766 (mt) cc_final: 0.7543 (mm) REVERT: K 456 SER cc_start: 0.7779 (p) cc_final: 0.7345 (p) REVERT: K 465 ARG cc_start: 0.7772 (mtp85) cc_final: 0.7373 (mtp180) REVERT: L 467 GLU cc_start: 0.7829 (pt0) cc_final: 0.7586 (pt0) REVERT: L 476 MET cc_start: 0.8545 (tmt) cc_final: 0.8290 (tmt) REVERT: L 481 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7352 (mp0) outliers start: 92 outliers final: 33 residues processed: 391 average time/residue: 1.1937 time to fit residues: 533.2428 Evaluate side-chains 350 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 304 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 192 ASP Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 33 ARG Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 312 ILE Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 362 CYS Chi-restraints excluded: chain H residue 369 SER Chi-restraints excluded: chain H residue 389 THR Chi-restraints excluded: chain H residue 436 VAL Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 461 GLU Chi-restraints excluded: chain H residue 542 GLN Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain J residue 150 ILE Chi-restraints excluded: chain K residue 157 ILE Chi-restraints excluded: chain K residue 170 ILE Chi-restraints excluded: chain K residue 417 VAL Chi-restraints excluded: chain K residue 476 MET Chi-restraints excluded: chain K residue 559 THR Chi-restraints excluded: chain K residue 579 LEU Chi-restraints excluded: chain L residue 455 PHE Chi-restraints excluded: chain L residue 481 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 101 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 237 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 197 optimal weight: 0.3980 chunk 98 optimal weight: 20.0000 chunk 83 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN D 178 ASN F 125 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.150455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.116011 restraints weight = 26821.236| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.71 r_work: 0.3119 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 21138 Z= 0.259 Angle : 0.686 21.131 28878 Z= 0.343 Chirality : 0.046 0.203 3387 Planarity : 0.004 0.051 3437 Dihedral : 14.980 170.367 3743 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.21 % Favored : 95.63 % Rotamer: Outliers : 5.16 % Allowed : 27.51 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.17), residues: 2425 helix: 1.30 (0.18), residues: 841 sheet: -1.04 (0.23), residues: 464 loop : -1.43 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 478 HIS 0.004 0.001 HIS H 326 PHE 0.038 0.002 PHE K 455 TYR 0.019 0.001 TYR K 391 ARG 0.007 0.001 ARG E 95 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 896) hydrogen bonds : angle 4.73521 ( 2589) metal coordination : bond 0.01004 ( 25) metal coordination : angle 6.77279 ( 24) covalent geometry : bond 0.00595 (21113) covalent geometry : angle 0.65842 (28854) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 312 time to evaluate : 2.163 Fit side-chains REVERT: B 5 MET cc_start: 0.6993 (mtp) cc_final: 0.6759 (mtp) REVERT: B 59 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7469 (mt) REVERT: B 93 MET cc_start: 0.8172 (tpp) cc_final: 0.7865 (ttt) REVERT: B 170 GLU cc_start: 0.6244 (OUTLIER) cc_final: 0.5978 (pp20) REVERT: B 196 ASP cc_start: 0.7631 (p0) cc_final: 0.7252 (p0) REVERT: B 198 PHE cc_start: 0.6684 (m-80) cc_final: 0.6275 (m-80) REVERT: C 134 LYS cc_start: 0.8008 (ttpt) cc_final: 0.7756 (ttpt) REVERT: C 173 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8436 (tp) REVERT: D 157 ASP cc_start: 0.8061 (m-30) cc_final: 0.7749 (m-30) REVERT: E 79 ARG cc_start: 0.8335 (tpp80) cc_final: 0.8064 (mtm-85) REVERT: E 149 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8405 (p) REVERT: F 152 ASN cc_start: 0.8567 (m-40) cc_final: 0.7832 (t0) REVERT: G 3 GLU cc_start: 0.5339 (mp0) cc_final: 0.5131 (mp0) REVERT: G 9 GLU cc_start: 0.8342 (tp30) cc_final: 0.7677 (tp30) REVERT: G 22 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7509 (tm-30) REVERT: G 33 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7673 (ttt180) REVERT: G 41 PHE cc_start: 0.7914 (t80) cc_final: 0.6771 (t80) REVERT: G 114 LYS cc_start: 0.7876 (mtpt) cc_final: 0.7294 (mmtt) REVERT: G 123 LYS cc_start: 0.7547 (mmmm) cc_final: 0.7216 (mmmt) REVERT: G 188 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7998 (m-30) REVERT: H 178 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.7191 (mmm) REVERT: H 201 LYS cc_start: 0.5556 (tptt) cc_final: 0.5332 (tptp) REVERT: H 273 LYS cc_start: 0.8254 (tttt) cc_final: 0.7759 (ttpp) REVERT: H 297 ASN cc_start: 0.8180 (m-40) cc_final: 0.7796 (m-40) REVERT: H 328 GLU cc_start: 0.7261 (tp30) cc_final: 0.6880 (mm-30) REVERT: H 378 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7492 (mt-10) REVERT: H 389 THR cc_start: 0.9104 (OUTLIER) cc_final: 0.8841 (m) REVERT: H 461 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.6305 (pt0) REVERT: H 542 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7724 (tt0) REVERT: I 472 ASN cc_start: 0.8346 (t0) cc_final: 0.8126 (m110) REVERT: I 551 GLN cc_start: 0.8152 (tt0) cc_final: 0.7357 (tp-100) REVERT: J 87 CYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7479 (m) REVERT: J 150 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8146 (mt) REVERT: K 387 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8269 (tttt) REVERT: K 456 SER cc_start: 0.7790 (p) cc_final: 0.7384 (p) REVERT: K 465 ARG cc_start: 0.7816 (mtp85) cc_final: 0.7425 (mtp180) REVERT: L 476 MET cc_start: 0.8623 (tmt) cc_final: 0.8372 (tmt) REVERT: L 481 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7340 (mp0) outliers start: 101 outliers final: 49 residues processed: 378 average time/residue: 1.1941 time to fit residues: 515.5584 Evaluate side-chains 364 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 301 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 MET Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 192 ASP Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 33 ARG Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain H residue 312 ILE Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 362 CYS Chi-restraints excluded: chain H residue 369 SER Chi-restraints excluded: chain H residue 389 THR Chi-restraints excluded: chain H residue 436 VAL Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 456 SER Chi-restraints excluded: chain H residue 461 GLU Chi-restraints excluded: chain H residue 542 GLN Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain J residue 150 ILE Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 157 ILE Chi-restraints excluded: chain K residue 170 ILE Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 387 LYS Chi-restraints excluded: chain K residue 417 VAL Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain K residue 476 MET Chi-restraints excluded: chain K residue 559 THR Chi-restraints excluded: chain K residue 579 LEU Chi-restraints excluded: chain L residue 455 PHE Chi-restraints excluded: chain L residue 481 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 144 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 119 optimal weight: 0.3980 chunk 249 optimal weight: 10.9990 chunk 123 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 178 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 250 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN D 125 GLN D 178 ASN H 81 ASN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.154100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.120078 restraints weight = 26615.326| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.65 r_work: 0.3184 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21138 Z= 0.148 Angle : 0.616 15.972 28878 Z= 0.311 Chirality : 0.043 0.217 3387 Planarity : 0.004 0.044 3437 Dihedral : 14.938 171.411 3743 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.26 % Favored : 96.58 % Rotamer: Outliers : 4.24 % Allowed : 28.78 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.17), residues: 2425 helix: 1.48 (0.18), residues: 844 sheet: -1.07 (0.22), residues: 488 loop : -1.30 (0.18), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 478 HIS 0.003 0.001 HIS H 62 PHE 0.026 0.002 PHE B 167 TYR 0.020 0.001 TYR L 450 ARG 0.008 0.001 ARG D 95 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 896) hydrogen bonds : angle 4.55470 ( 2589) metal coordination : bond 0.00565 ( 25) metal coordination : angle 5.41976 ( 24) covalent geometry : bond 0.00336 (21113) covalent geometry : angle 0.59642 (28854) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 323 time to evaluate : 2.212 Fit side-chains REVERT: B 59 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7452 (mt) REVERT: B 93 MET cc_start: 0.8082 (tpp) cc_final: 0.7840 (ttt) REVERT: B 100 SER cc_start: 0.7683 (OUTLIER) cc_final: 0.7222 (t) REVERT: B 170 GLU cc_start: 0.6031 (OUTLIER) cc_final: 0.5775 (pp20) REVERT: B 196 ASP cc_start: 0.7623 (p0) cc_final: 0.7306 (p0) REVERT: B 198 PHE cc_start: 0.6469 (m-80) cc_final: 0.6211 (m-80) REVERT: C 3 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8775 (mtmt) REVERT: C 173 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8385 (tp) REVERT: D 87 CYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7776 (m) REVERT: D 157 ASP cc_start: 0.7907 (m-30) cc_final: 0.7612 (m-30) REVERT: E 79 ARG cc_start: 0.8269 (tpp80) cc_final: 0.8043 (ttm-80) REVERT: E 149 THR cc_start: 0.8770 (OUTLIER) cc_final: 0.8403 (p) REVERT: G 22 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7486 (tm-30) REVERT: G 41 PHE cc_start: 0.7860 (t80) cc_final: 0.6717 (t80) REVERT: G 57 ASP cc_start: 0.7775 (t0) cc_final: 0.7355 (t70) REVERT: G 58 ASP cc_start: 0.7184 (m-30) cc_final: 0.6501 (m-30) REVERT: G 123 LYS cc_start: 0.7540 (mmmm) cc_final: 0.7204 (mmpt) REVERT: G 147 ASN cc_start: 0.8863 (p0) cc_final: 0.8645 (p0) REVERT: G 188 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.8002 (m-30) REVERT: H 52 ILE cc_start: 0.8302 (mt) cc_final: 0.8069 (mp) REVERT: H 99 ASP cc_start: 0.8425 (t0) cc_final: 0.8209 (t0) REVERT: H 201 LYS cc_start: 0.5575 (tptt) cc_final: 0.5357 (tptp) REVERT: H 273 LYS cc_start: 0.8262 (tttt) cc_final: 0.7767 (ttpp) REVERT: H 297 ASN cc_start: 0.8150 (m-40) cc_final: 0.7753 (m-40) REVERT: H 326 HIS cc_start: 0.8220 (m-70) cc_final: 0.7999 (m170) REVERT: H 328 GLU cc_start: 0.7189 (tp30) cc_final: 0.6878 (mm-30) REVERT: H 389 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8687 (m) REVERT: H 461 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6388 (pt0) REVERT: H 568 GLU cc_start: 0.8388 (tt0) cc_final: 0.7943 (mm-30) REVERT: I 453 MET cc_start: 0.8677 (ttm) cc_final: 0.8215 (ttm) REVERT: I 472 ASN cc_start: 0.8323 (t0) cc_final: 0.8120 (m110) REVERT: I 508 MET cc_start: 0.5960 (mtp) cc_final: 0.5731 (mtm) REVERT: I 529 ASN cc_start: 0.8382 (t0) cc_final: 0.7682 (m-40) REVERT: I 551 GLN cc_start: 0.8108 (tt0) cc_final: 0.7311 (tp-100) REVERT: J 87 CYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7439 (m) REVERT: K 157 ILE cc_start: 0.7090 (OUTLIER) cc_final: 0.6654 (pt) REVERT: K 439 ILE cc_start: 0.7301 (OUTLIER) cc_final: 0.7056 (mt) REVERT: K 456 SER cc_start: 0.7763 (p) cc_final: 0.7363 (p) REVERT: K 465 ARG cc_start: 0.7840 (mtp85) cc_final: 0.7445 (mtp180) REVERT: K 509 SER cc_start: 0.6275 (p) cc_final: 0.6065 (p) REVERT: L 467 GLU cc_start: 0.7797 (pt0) cc_final: 0.7582 (pt0) REVERT: L 476 MET cc_start: 0.8605 (tmt) cc_final: 0.8365 (tmt) REVERT: L 481 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7248 (mp0) outliers start: 83 outliers final: 34 residues processed: 377 average time/residue: 1.1755 time to fit residues: 507.9783 Evaluate side-chains 350 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 302 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain C residue 3 LYS Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 192 ASP Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 312 ILE Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 362 CYS Chi-restraints excluded: chain H residue 389 THR Chi-restraints excluded: chain H residue 436 VAL Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 461 GLU Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain K residue 157 ILE Chi-restraints excluded: chain K residue 170 ILE Chi-restraints excluded: chain K residue 412 SER Chi-restraints excluded: chain K residue 417 VAL Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain K residue 476 MET Chi-restraints excluded: chain K residue 551 GLN Chi-restraints excluded: chain K residue 559 THR Chi-restraints excluded: chain L residue 481 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 159 optimal weight: 0.4980 chunk 147 optimal weight: 20.0000 chunk 94 optimal weight: 0.9980 chunk 242 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 40 optimal weight: 0.0670 chunk 118 optimal weight: 9.9990 chunk 197 optimal weight: 0.4980 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN D 178 ASN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 ASN ** L 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.155392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.121057 restraints weight = 26907.566| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.65 r_work: 0.3206 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 21138 Z= 0.138 Angle : 0.611 15.357 28878 Z= 0.310 Chirality : 0.043 0.199 3387 Planarity : 0.004 0.042 3437 Dihedral : 14.869 171.676 3743 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.51 % Favored : 96.33 % Rotamer: Outliers : 3.58 % Allowed : 30.01 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.17), residues: 2425 helix: 1.63 (0.18), residues: 844 sheet: -0.99 (0.23), residues: 489 loop : -1.27 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP L 478 HIS 0.004 0.001 HIS G 31 PHE 0.026 0.002 PHE B 167 TYR 0.020 0.001 TYR L 450 ARG 0.008 0.001 ARG J 34 Details of bonding type rmsd hydrogen bonds : bond 0.03441 ( 896) hydrogen bonds : angle 4.45372 ( 2589) metal coordination : bond 0.00494 ( 25) metal coordination : angle 5.18786 ( 24) covalent geometry : bond 0.00313 (21113) covalent geometry : angle 0.59313 (28854) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 316 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 93 MET cc_start: 0.8034 (tpp) cc_final: 0.7757 (ttt) REVERT: B 100 SER cc_start: 0.7641 (OUTLIER) cc_final: 0.7172 (t) REVERT: B 170 GLU cc_start: 0.6113 (OUTLIER) cc_final: 0.5770 (pp20) REVERT: C 3 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8767 (mtmt) REVERT: C 173 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8361 (tp) REVERT: D 157 ASP cc_start: 0.7923 (m-30) cc_final: 0.7675 (m-30) REVERT: E 149 THR cc_start: 0.8730 (OUTLIER) cc_final: 0.8377 (p) REVERT: G 41 PHE cc_start: 0.7838 (t80) cc_final: 0.6678 (t80) REVERT: G 57 ASP cc_start: 0.7742 (t0) cc_final: 0.7301 (t70) REVERT: G 123 LYS cc_start: 0.7558 (mmmm) cc_final: 0.7194 (mmpt) REVERT: G 188 ASP cc_start: 0.8190 (m-30) cc_final: 0.7768 (m-30) REVERT: H 52 ILE cc_start: 0.8140 (mt) cc_final: 0.7903 (mp) REVERT: H 99 ASP cc_start: 0.8465 (t0) cc_final: 0.8208 (t0) REVERT: H 176 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7155 (pt0) REVERT: H 201 LYS cc_start: 0.5538 (tptt) cc_final: 0.5330 (tptp) REVERT: H 273 LYS cc_start: 0.8268 (tttt) cc_final: 0.7821 (ttpp) REVERT: H 297 ASN cc_start: 0.8134 (m-40) cc_final: 0.7772 (m-40) REVERT: H 326 HIS cc_start: 0.8229 (m-70) cc_final: 0.7994 (m170) REVERT: H 328 GLU cc_start: 0.7156 (tp30) cc_final: 0.6807 (mm-30) REVERT: H 389 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8648 (m) REVERT: H 461 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6353 (pt0) REVERT: H 568 GLU cc_start: 0.8340 (tt0) cc_final: 0.7951 (mm-30) REVERT: I 453 MET cc_start: 0.8653 (ttm) cc_final: 0.8302 (ttm) REVERT: I 508 MET cc_start: 0.5804 (mtp) cc_final: 0.5558 (mtm) REVERT: I 529 ASN cc_start: 0.8367 (t0) cc_final: 0.7703 (m-40) REVERT: I 551 GLN cc_start: 0.8074 (tt0) cc_final: 0.7308 (tp-100) REVERT: J 87 CYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7384 (m) REVERT: K 157 ILE cc_start: 0.7012 (OUTLIER) cc_final: 0.6531 (pt) REVERT: K 194 LEU cc_start: 0.7621 (pp) cc_final: 0.7346 (tp) REVERT: K 387 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8248 (tttt) REVERT: K 439 ILE cc_start: 0.7429 (OUTLIER) cc_final: 0.7188 (mt) REVERT: K 456 SER cc_start: 0.7732 (p) cc_final: 0.7320 (p) REVERT: K 465 ARG cc_start: 0.7877 (mtp85) cc_final: 0.7474 (mtp180) REVERT: K 509 SER cc_start: 0.6439 (p) cc_final: 0.6219 (p) REVERT: L 467 GLU cc_start: 0.7749 (pt0) cc_final: 0.7533 (pt0) REVERT: L 470 ASP cc_start: 0.7799 (p0) cc_final: 0.7493 (p0) REVERT: L 476 MET cc_start: 0.8569 (tmt) cc_final: 0.8369 (tmt) REVERT: L 481 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7246 (mp0) outliers start: 70 outliers final: 39 residues processed: 360 average time/residue: 1.1170 time to fit residues: 463.1439 Evaluate side-chains 353 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 301 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain C residue 3 LYS Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 192 ASP Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 176 GLN Chi-restraints excluded: chain H residue 312 ILE Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 362 CYS Chi-restraints excluded: chain H residue 384 GLU Chi-restraints excluded: chain H residue 389 THR Chi-restraints excluded: chain H residue 436 VAL Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 456 SER Chi-restraints excluded: chain H residue 461 GLU Chi-restraints excluded: chain H residue 576 ILE Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain K residue 157 ILE Chi-restraints excluded: chain K residue 387 LYS Chi-restraints excluded: chain K residue 412 SER Chi-restraints excluded: chain K residue 417 VAL Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain K residue 514 ILE Chi-restraints excluded: chain K residue 551 GLN Chi-restraints excluded: chain K residue 559 THR Chi-restraints excluded: chain L residue 481 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 180 optimal weight: 0.6980 chunk 165 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 166 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 234 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 223 optimal weight: 0.6980 chunk 183 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 178 ASN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 ASN I 472 ASN ** L 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.155705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.121862 restraints weight = 26836.484| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.61 r_work: 0.3211 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 21138 Z= 0.139 Angle : 0.614 14.925 28878 Z= 0.310 Chirality : 0.043 0.200 3387 Planarity : 0.004 0.041 3437 Dihedral : 14.858 172.043 3743 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.51 % Favored : 96.33 % Rotamer: Outliers : 3.73 % Allowed : 29.40 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.17), residues: 2425 helix: 1.71 (0.18), residues: 843 sheet: -0.91 (0.23), residues: 489 loop : -1.22 (0.18), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP L 478 HIS 0.002 0.001 HIS H 326 PHE 0.027 0.002 PHE B 167 TYR 0.022 0.001 TYR G 137 ARG 0.008 0.001 ARG E 95 Details of bonding type rmsd hydrogen bonds : bond 0.03379 ( 896) hydrogen bonds : angle 4.40681 ( 2589) metal coordination : bond 0.00501 ( 25) metal coordination : angle 5.17739 ( 24) covalent geometry : bond 0.00317 (21113) covalent geometry : angle 0.59534 (28854) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 329 time to evaluate : 2.089 Fit side-chains revert: symmetry clash REVERT: B 93 MET cc_start: 0.8018 (tpp) cc_final: 0.7760 (ttt) REVERT: B 104 LEU cc_start: 0.7464 (mm) cc_final: 0.7041 (mm) REVERT: B 170 GLU cc_start: 0.6074 (OUTLIER) cc_final: 0.5747 (pp20) REVERT: C 3 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8770 (mtmt) REVERT: C 13 LYS cc_start: 0.7873 (tptt) cc_final: 0.7661 (tptt) REVERT: C 41 LYS cc_start: 0.7979 (mttt) cc_final: 0.7614 (mttt) REVERT: C 134 LYS cc_start: 0.7940 (ttpt) cc_final: 0.7697 (ttpt) REVERT: C 173 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8360 (tp) REVERT: C 189 LYS cc_start: 0.8027 (mmmm) cc_final: 0.7817 (mmpt) REVERT: D 157 ASP cc_start: 0.7870 (m-30) cc_final: 0.7634 (m-30) REVERT: E 137 GLU cc_start: 0.8189 (pt0) cc_final: 0.7975 (pt0) REVERT: E 149 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8387 (p) REVERT: G 41 PHE cc_start: 0.7838 (t80) cc_final: 0.6619 (t80) REVERT: G 57 ASP cc_start: 0.7685 (t0) cc_final: 0.7234 (t70) REVERT: G 63 ASP cc_start: 0.7743 (m-30) cc_final: 0.7470 (t0) REVERT: G 123 LYS cc_start: 0.7482 (mmmm) cc_final: 0.7054 (mmpt) REVERT: H 52 ILE cc_start: 0.8143 (mt) cc_final: 0.7930 (mp) REVERT: H 99 ASP cc_start: 0.8423 (t0) cc_final: 0.8144 (t0) REVERT: H 176 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7304 (pt0) REVERT: H 273 LYS cc_start: 0.8266 (tttt) cc_final: 0.7815 (ttpp) REVERT: H 297 ASN cc_start: 0.8144 (m-40) cc_final: 0.7786 (m-40) REVERT: H 326 HIS cc_start: 0.8220 (m-70) cc_final: 0.7953 (m170) REVERT: H 328 GLU cc_start: 0.7065 (tp30) cc_final: 0.6708 (mm-30) REVERT: H 347 ASN cc_start: 0.7467 (t0) cc_final: 0.6854 (t0) REVERT: H 389 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8631 (m) REVERT: H 461 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6328 (pt0) REVERT: H 568 GLU cc_start: 0.8290 (tt0) cc_final: 0.7941 (mm-30) REVERT: I 453 MET cc_start: 0.8317 (ttm) cc_final: 0.8074 (ttt) REVERT: I 508 MET cc_start: 0.5725 (mtp) cc_final: 0.5523 (mtm) REVERT: I 529 ASN cc_start: 0.8352 (t0) cc_final: 0.7626 (m-40) REVERT: I 551 GLN cc_start: 0.8068 (tt0) cc_final: 0.7312 (tp-100) REVERT: J 87 CYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7402 (m) REVERT: K 157 ILE cc_start: 0.7063 (OUTLIER) cc_final: 0.6596 (pt) REVERT: K 194 LEU cc_start: 0.7573 (pp) cc_final: 0.7364 (tp) REVERT: K 387 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8253 (tttt) REVERT: K 439 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7233 (mt) REVERT: K 456 SER cc_start: 0.7724 (p) cc_final: 0.7412 (p) REVERT: K 465 ARG cc_start: 0.7844 (mtp85) cc_final: 0.7446 (mtp180) REVERT: K 470 ASP cc_start: 0.7101 (t0) cc_final: 0.6559 (p0) REVERT: K 486 ARG cc_start: 0.6931 (mmm160) cc_final: 0.6729 (mmm-85) REVERT: K 509 SER cc_start: 0.6438 (p) cc_final: 0.6214 (p) REVERT: L 470 ASP cc_start: 0.7775 (p0) cc_final: 0.7471 (p0) REVERT: L 481 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: L 555 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7240 (ttmm) outliers start: 73 outliers final: 39 residues processed: 378 average time/residue: 1.1846 time to fit residues: 513.8574 Evaluate side-chains 363 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 311 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain C residue 3 LYS Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 192 ASP Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 176 GLN Chi-restraints excluded: chain H residue 312 ILE Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 362 CYS Chi-restraints excluded: chain H residue 389 THR Chi-restraints excluded: chain H residue 436 VAL Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 456 SER Chi-restraints excluded: chain H residue 461 GLU Chi-restraints excluded: chain H residue 576 ILE Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain K residue 157 ILE Chi-restraints excluded: chain K residue 387 LYS Chi-restraints excluded: chain K residue 412 SER Chi-restraints excluded: chain K residue 417 VAL Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain K residue 514 ILE Chi-restraints excluded: chain K residue 551 GLN Chi-restraints excluded: chain K residue 559 THR Chi-restraints excluded: chain L residue 481 GLU Chi-restraints excluded: chain L residue 555 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 159 optimal weight: 0.5980 chunk 201 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 206 optimal weight: 2.9990 chunk 5 optimal weight: 0.0060 chunk 205 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 178 ASN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 472 ASN ** L 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.155888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.121925 restraints weight = 26787.299| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.65 r_work: 0.3213 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 21138 Z= 0.141 Angle : 0.622 16.809 28878 Z= 0.312 Chirality : 0.043 0.198 3387 Planarity : 0.004 0.041 3437 Dihedral : 14.843 172.300 3743 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.71 % Favored : 96.12 % Rotamer: Outliers : 3.43 % Allowed : 30.32 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.17), residues: 2425 helix: 1.80 (0.18), residues: 843 sheet: -0.91 (0.23), residues: 490 loop : -1.22 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP L 478 HIS 0.002 0.001 HIS G 31 PHE 0.026 0.002 PHE H 474 TYR 0.022 0.001 TYR L 450 ARG 0.010 0.001 ARG H 451 Details of bonding type rmsd hydrogen bonds : bond 0.03395 ( 896) hydrogen bonds : angle 4.36820 ( 2589) metal coordination : bond 0.00555 ( 25) metal coordination : angle 5.45426 ( 24) covalent geometry : bond 0.00323 (21113) covalent geometry : angle 0.60198 (28854) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 319 time to evaluate : 2.244 Fit side-chains revert: symmetry clash REVERT: B 93 MET cc_start: 0.8008 (tpp) cc_final: 0.7747 (ttt) REVERT: B 104 LEU cc_start: 0.7432 (mm) cc_final: 0.6988 (mm) REVERT: B 170 GLU cc_start: 0.6212 (OUTLIER) cc_final: 0.5947 (pp20) REVERT: C 3 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8776 (mtmt) REVERT: C 173 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8362 (tp) REVERT: D 157 ASP cc_start: 0.7859 (m-30) cc_final: 0.7632 (m-30) REVERT: E 149 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8395 (p) REVERT: G 9 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7985 (tp30) REVERT: G 41 PHE cc_start: 0.7822 (t80) cc_final: 0.6611 (t80) REVERT: G 57 ASP cc_start: 0.7734 (t0) cc_final: 0.7384 (t70) REVERT: G 63 ASP cc_start: 0.7746 (m-30) cc_final: 0.7467 (t0) REVERT: G 123 LYS cc_start: 0.7441 (mmmm) cc_final: 0.6715 (mmpt) REVERT: G 124 ASP cc_start: 0.7051 (m-30) cc_final: 0.6777 (m-30) REVERT: H 52 ILE cc_start: 0.8096 (mt) cc_final: 0.7890 (mp) REVERT: H 99 ASP cc_start: 0.8426 (t0) cc_final: 0.8198 (t0) REVERT: H 176 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7195 (pt0) REVERT: H 273 LYS cc_start: 0.8257 (tttt) cc_final: 0.7803 (ttpp) REVERT: H 297 ASN cc_start: 0.8131 (m-40) cc_final: 0.7777 (m-40) REVERT: H 328 GLU cc_start: 0.7099 (tp30) cc_final: 0.6733 (mm-30) REVERT: H 347 ASN cc_start: 0.7526 (t0) cc_final: 0.6993 (t0) REVERT: H 389 THR cc_start: 0.8873 (OUTLIER) cc_final: 0.8620 (m) REVERT: H 461 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.6315 (pt0) REVERT: H 568 GLU cc_start: 0.8271 (tt0) cc_final: 0.7938 (mm-30) REVERT: I 444 MET cc_start: 0.8173 (mmm) cc_final: 0.7937 (mmm) REVERT: I 453 MET cc_start: 0.8404 (ttm) cc_final: 0.8150 (ttt) REVERT: I 508 MET cc_start: 0.5665 (mtp) cc_final: 0.5452 (mtm) REVERT: I 529 ASN cc_start: 0.8350 (t0) cc_final: 0.7622 (m-40) REVERT: I 551 GLN cc_start: 0.8079 (tt0) cc_final: 0.7318 (tp-100) REVERT: J 87 CYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7381 (m) REVERT: K 157 ILE cc_start: 0.7055 (OUTLIER) cc_final: 0.6584 (pt) REVERT: K 387 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8239 (tttt) REVERT: K 439 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.7311 (mt) REVERT: K 456 SER cc_start: 0.7716 (p) cc_final: 0.7367 (p) REVERT: K 465 ARG cc_start: 0.7803 (mtp85) cc_final: 0.7408 (mtp180) REVERT: K 470 ASP cc_start: 0.7075 (t0) cc_final: 0.6568 (p0) REVERT: K 486 ARG cc_start: 0.6822 (mmm160) cc_final: 0.6607 (mmm-85) REVERT: K 509 SER cc_start: 0.6457 (p) cc_final: 0.6220 (p) REVERT: L 467 GLU cc_start: 0.7658 (pt0) cc_final: 0.7325 (pt0) REVERT: L 470 ASP cc_start: 0.7805 (p0) cc_final: 0.7498 (p0) REVERT: L 481 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: L 555 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7226 (ttmm) outliers start: 67 outliers final: 44 residues processed: 366 average time/residue: 1.1481 time to fit residues: 484.1549 Evaluate side-chains 361 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 303 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain C residue 3 LYS Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 162 GLN Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 192 ASP Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 176 GLN Chi-restraints excluded: chain H residue 312 ILE Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 362 CYS Chi-restraints excluded: chain H residue 384 GLU Chi-restraints excluded: chain H residue 389 THR Chi-restraints excluded: chain H residue 436 VAL Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 456 SER Chi-restraints excluded: chain H residue 461 GLU Chi-restraints excluded: chain H residue 576 ILE Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain K residue 157 ILE Chi-restraints excluded: chain K residue 387 LYS Chi-restraints excluded: chain K residue 412 SER Chi-restraints excluded: chain K residue 417 VAL Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain K residue 514 ILE Chi-restraints excluded: chain K residue 551 GLN Chi-restraints excluded: chain K residue 559 THR Chi-restraints excluded: chain K residue 579 LEU Chi-restraints excluded: chain L residue 481 GLU Chi-restraints excluded: chain L residue 555 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 206 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 185 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 225 optimal weight: 0.8980 chunk 236 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 178 ASN H 22 ASN ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 472 ASN J 45 ASN ** L 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.153433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.119016 restraints weight = 26991.792| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.83 r_work: 0.3149 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 21138 Z= 0.187 Angle : 0.652 18.866 28878 Z= 0.326 Chirality : 0.044 0.197 3387 Planarity : 0.004 0.056 3437 Dihedral : 14.823 171.730 3743 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.79 % Favored : 96.04 % Rotamer: Outliers : 3.37 % Allowed : 30.27 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.17), residues: 2425 helix: 1.75 (0.18), residues: 845 sheet: -0.87 (0.23), residues: 481 loop : -1.20 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP L 478 HIS 0.003 0.001 HIS G 31 PHE 0.026 0.002 PHE H 474 TYR 0.022 0.001 TYR G 137 ARG 0.015 0.001 ARG D 95 Details of bonding type rmsd hydrogen bonds : bond 0.03456 ( 896) hydrogen bonds : angle 4.45203 ( 2589) metal coordination : bond 0.00734 ( 25) metal coordination : angle 6.03429 ( 24) covalent geometry : bond 0.00429 (21113) covalent geometry : angle 0.62893 (28854) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12817.37 seconds wall clock time: 222 minutes 9.23 seconds (13329.23 seconds total)