Starting phenix.real_space_refine on Thu Sep 18 21:45:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z4j_39766/09_2025/8z4j_39766.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z4j_39766/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8z4j_39766/09_2025/8z4j_39766.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z4j_39766/09_2025/8z4j_39766.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z4j_39766/09_2025/8z4j_39766.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z4j_39766/09_2025/8z4j_39766.map" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.039 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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, 'ARG:plan': 5, 'GLU:plan': 6, '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: {'ASP:plan': 1, 'PHE:plan': 1, 'GLU: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: {'ARG:plan': 3, 'GLU:plan': 2} 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: {'ASN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 2, 'TYR:plan': 1, 'ASP:plan': 3, 'HIS:plan': 1} 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: {'GLU:plan': 14, 'ASP:plan': 8, 'ASN:plan1': 5, 'ARG:plan': 6, 'TYR:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 2, 'TRP:plan': 1} 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: {'ASN:plan1': 1, 'ASP:plan': 4, 'ARG:plan': 2, 'GLU:plan': 3} 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: {'GLU:plan': 6, 'ARG:plan': 4, 'ASN:plan1': 3, 'HIS:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1} 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: {'ASN:plan1': 3, 'ASP:plan': 4, 'ARG:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 9, 'PHE:plan': 2, 'TRP:plan': 1, 'TYR:plan': 1} 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:plan': 1, ' G%rna3p_pur:plan2': 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: 4.77, per 1000 atoms: 0.23 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: 1.51 Conformation dependent library (CDL) restraints added in 773.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 3.19 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: 4.98 Time building geometry restraints manager: 2.10 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 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: 2.860 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: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 25.300 Find NCS groups from input model: 0.410 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: 0.010 Load rotamer database and sin/cos tables:7.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.320 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.99 (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 ARG 0.028 0.002 ARG G 117 TYR 0.048 0.004 TYR L 450 PHE 0.084 0.006 PHE G 56 TRP 0.083 0.005 TRP I 478 HIS 0.046 0.006 HIS H 326 Details of bonding type rmsd covalent geometry : bond 0.00843 (21113) covalent geometry : angle 1.36148 (28854) hydrogen bonds : bond 0.14200 ( 896) hydrogen bonds : angle 7.95968 ( 2589) metal coordination : bond 0.01484 ( 25) metal coordination : angle 10.36608 ( 24) *********************** 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 : 0.820 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: 0.6087 time to fit residues: 263.8761 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 : 0.756 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 247 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.159235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.126474 restraints weight = 26801.278| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.83 r_work: 0.3243 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 21138 Z= 0.164 Angle : 0.691 19.441 28878 Z= 0.351 Chirality : 0.045 0.313 3387 Planarity : 0.005 0.069 3437 Dihedral : 15.389 175.526 3766 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.75 % Favored : 96.08 % Rotamer: Outliers : 4.86 % Allowed : 26.64 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.16), residues: 2425 helix: -0.04 (0.17), residues: 850 sheet: -1.16 (0.23), residues: 448 loop : -1.93 (0.16), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 117 TYR 0.024 0.001 TYR K 599 PHE 0.020 0.002 PHE G 191 TRP 0.019 0.002 TRP I 478 HIS 0.009 0.002 HIS K 510 Details of bonding type rmsd covalent geometry : bond 0.00368 (21113) covalent geometry : angle 0.66569 (28854) hydrogen bonds : bond 0.04341 ( 896) hydrogen bonds : angle 5.36302 ( 2589) metal coordination : bond 0.00767 ( 25) metal coordination : angle 6.40402 ( 24) *********************** 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 460 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 365 time to evaluate : 0.769 Fit side-chains REVERT: B 7 LYS cc_start: 0.6599 (mttm) cc_final: 0.6234 (mttt) REVERT: B 59 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7524 (mt) REVERT: C 102 ASP cc_start: 0.8110 (m-30) cc_final: 0.7896 (m-30) REVERT: C 173 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8467 (tp) REVERT: D 69 ASN cc_start: 0.7986 (p0) cc_final: 0.7759 (p0) REVERT: D 157 ASP cc_start: 0.7862 (m-30) cc_final: 0.7610 (m-30) REVERT: D 187 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8507 (mm-30) REVERT: E 79 ARG cc_start: 0.8285 (tpp80) cc_final: 0.7891 (ttm-80) REVERT: E 122 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8871 (mp) REVERT: G 22 GLU cc_start: 0.7348 (tp30) cc_final: 0.6997 (tm-30) REVERT: G 41 PHE cc_start: 0.7743 (t80) cc_final: 0.6890 (t80) REVERT: G 123 LYS cc_start: 0.7718 (mmmm) cc_final: 0.7455 (mmmt) REVERT: H 113 TYR cc_start: 0.8321 (p90) cc_final: 0.7584 (p90) REVERT: H 273 LYS cc_start: 0.8160 (tttt) cc_final: 0.7672 (ttpp) REVERT: H 381 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.7807 (t70) REVERT: H 458 PHE cc_start: 0.7166 (m-80) cc_final: 0.6912 (m-80) REVERT: H 461 GLU cc_start: 0.7075 (pm20) cc_final: 0.6596 (pt0) REVERT: H 542 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7572 (tt0) REVERT: H 568 GLU cc_start: 0.8176 (tt0) cc_final: 0.7843 (mm-30) REVERT: I 529 ASN cc_start: 0.8279 (t0) cc_final: 0.7749 (m-40) REVERT: I 561 ARG cc_start: 0.7511 (mtm110) cc_final: 0.7298 (ttp-170) REVERT: J 87 CYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7435 (m) REVERT: K 391 TYR cc_start: 0.8339 (t80) cc_final: 0.8089 (t80) REVERT: K 416 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.6941 (mtt90) REVERT: K 456 SER cc_start: 0.7662 (p) cc_final: 0.7288 (p) REVERT: K 465 ARG cc_start: 0.7704 (mtp85) cc_final: 0.7401 (mtp180) REVERT: K 470 ASP cc_start: 0.7339 (t0) cc_final: 0.7137 (t0) REVERT: K 573 ASP cc_start: 0.6851 (t0) cc_final: 0.6640 (p0) REVERT: L 481 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7305 (mp0) outliers start: 95 outliers final: 24 residues processed: 426 average time/residue: 0.5492 time to fit residues: 266.5074 Evaluate side-chains 343 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 311 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 481 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 107 optimal weight: 6.9990 chunk 193 optimal weight: 0.9990 chunk 231 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 chunk 192 optimal weight: 0.7980 chunk 207 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 237 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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** J 45 ASN J 107 ASN K 510 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.157522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.124632 restraints weight = 26766.538| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.68 r_work: 0.3225 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21138 Z= 0.156 Angle : 0.636 18.825 28878 Z= 0.321 Chirality : 0.043 0.231 3387 Planarity : 0.005 0.061 3437 Dihedral : 15.088 172.923 3751 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.55 % Favored : 96.29 % Rotamer: Outliers : 5.06 % Allowed : 26.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.16), residues: 2425 helix: 0.89 (0.18), residues: 851 sheet: -1.06 (0.23), residues: 447 loop : -1.65 (0.17), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 554 TYR 0.023 0.001 TYR L 450 PHE 0.016 0.002 PHE H 458 TRP 0.014 0.002 TRP L 564 HIS 0.004 0.001 HIS H 62 Details of bonding type rmsd covalent geometry : bond 0.00344 (21113) covalent geometry : angle 0.61251 (28854) hydrogen bonds : bond 0.03779 ( 896) hydrogen bonds : angle 4.85766 ( 2589) metal coordination : bond 0.00640 ( 25) metal coordination : angle 6.03246 ( 24) *********************** 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 442 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 343 time to evaluate : 0.775 Fit side-chains REVERT: B 5 MET cc_start: 0.7361 (ttm) cc_final: 0.7100 (mtp) REVERT: B 12 MET cc_start: 0.7595 (ptm) cc_final: 0.7321 (ptm) REVERT: B 59 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7444 (mt) REVERT: B 93 MET cc_start: 0.7836 (tpp) cc_final: 0.7616 (tpt) REVERT: C 134 LYS cc_start: 0.8077 (ttpt) cc_final: 0.7847 (ttpt) REVERT: C 173 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8405 (tp) REVERT: D 69 ASN cc_start: 0.7947 (p0) cc_final: 0.7736 (p0) REVERT: D 157 ASP cc_start: 0.7809 (m-30) cc_final: 0.7503 (m-30) REVERT: E 13 LYS cc_start: 0.8653 (ttpp) cc_final: 0.8366 (ttpp) REVERT: E 79 ARG cc_start: 0.8377 (tpp80) cc_final: 0.8044 (ttm-80) REVERT: E 122 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8966 (mp) REVERT: E 149 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8326 (p) REVERT: F 152 ASN cc_start: 0.8294 (m-40) cc_final: 0.7671 (t0) REVERT: G 3 GLU cc_start: 0.5439 (mp0) cc_final: 0.5015 (mp0) REVERT: G 22 GLU cc_start: 0.7500 (tp30) cc_final: 0.7126 (tm-30) REVERT: G 41 PHE cc_start: 0.7795 (t80) cc_final: 0.6817 (t80) REVERT: G 123 LYS cc_start: 0.7675 (mmmm) cc_final: 0.7363 (mmmt) REVERT: G 147 ASN cc_start: 0.8787 (p0) cc_final: 0.8500 (p0) REVERT: G 207 ARG cc_start: 0.7690 (mtp180) cc_final: 0.7390 (mtp180) REVERT: H 52 ILE cc_start: 0.8266 (mt) cc_final: 0.7936 (mp) REVERT: H 113 TYR cc_start: 0.8425 (p90) cc_final: 0.7860 (p90) REVERT: H 273 LYS cc_start: 0.8214 (tttt) cc_final: 0.7713 (ttpp) REVERT: H 297 ASN cc_start: 0.8223 (m-40) cc_final: 0.7754 (m110) REVERT: H 458 PHE cc_start: 0.7263 (m-80) cc_final: 0.7060 (m-80) REVERT: H 461 GLU cc_start: 0.7118 (pm20) cc_final: 0.6551 (pt0) REVERT: H 542 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7576 (tt0) REVERT: H 554 ARG cc_start: 0.8346 (ttm170) cc_final: 0.8073 (ttp80) REVERT: H 568 GLU cc_start: 0.8165 (tt0) cc_final: 0.7818 (mm-30) REVERT: I 453 MET cc_start: 0.8517 (ttp) cc_final: 0.8144 (ttm) REVERT: I 488 GLN cc_start: 0.6977 (tp-100) cc_final: 0.6718 (tp-100) REVERT: I 529 ASN cc_start: 0.8349 (t0) cc_final: 0.7743 (m-40) REVERT: J 87 CYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7449 (m) REVERT: K 157 ILE cc_start: 0.6968 (OUTLIER) cc_final: 0.6508 (pt) REVERT: K 456 SER cc_start: 0.7517 (p) cc_final: 0.6970 (p) REVERT: K 465 ARG cc_start: 0.7716 (mtp85) cc_final: 0.7416 (mtp180) REVERT: L 472 ASN cc_start: 0.6832 (OUTLIER) cc_final: 0.6478 (m-40) REVERT: L 476 MET cc_start: 0.8577 (tmt) cc_final: 0.8337 (tmt) outliers start: 99 outliers final: 25 residues processed: 403 average time/residue: 0.5529 time to fit residues: 254.4464 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 : 0.758 ------------------------------------------------------------------------------- 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 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 108 ASP Chi-restraints excluded: chain E residue 122 ILE 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 108 ASP 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 369 SER Chi-restraints excluded: chain H residue 436 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 197 THR 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 176 optimal weight: 1.9990 chunk 40 optimal weight: 0.0170 chunk 135 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 overall best weight: 2.1824 ------------------------------------------------------------------------------- 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 81 ASN ** H 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 ASN I 596 ASN J 45 ASN K 529 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.152249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.118019 restraints weight = 26920.025| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.88 r_work: 0.3130 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2791 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= 0.241 Angle : 0.690 23.110 28878 Z= 0.343 Chirality : 0.045 0.208 3387 Planarity : 0.005 0.061 3437 Dihedral : 15.003 170.125 3743 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.04 % Favored : 95.79 % Rotamer: Outliers : 5.16 % Allowed : 26.23 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.16), residues: 2425 helix: 1.14 (0.18), residues: 844 sheet: -1.12 (0.22), residues: 467 loop : -1.54 (0.17), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 95 TYR 0.019 0.002 TYR L 450 PHE 0.026 0.002 PHE K 455 TRP 0.016 0.002 TRP L 478 HIS 0.003 0.001 HIS H 326 Details of bonding type rmsd covalent geometry : bond 0.00552 (21113) covalent geometry : angle 0.65886 (28854) hydrogen bonds : bond 0.03917 ( 896) hydrogen bonds : angle 4.77271 ( 2589) metal coordination : bond 0.00978 ( 25) metal coordination : angle 7.18608 ( 24) *********************** 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 428 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 327 time to evaluate : 0.948 Fit side-chains REVERT: B 59 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7415 (mt) REVERT: B 93 MET cc_start: 0.8218 (tpp) cc_final: 0.7940 (tpt) REVERT: B 196 ASP cc_start: 0.7536 (p0) cc_final: 0.7220 (p0) REVERT: C 13 LYS cc_start: 0.7926 (tptt) cc_final: 0.7713 (tptt) REVERT: C 36 ASN cc_start: 0.7400 (t0) cc_final: 0.7138 (t0) REVERT: C 41 LYS cc_start: 0.8312 (mttt) cc_final: 0.7937 (mttt) REVERT: C 134 LYS cc_start: 0.8081 (ttpt) cc_final: 0.7850 (ttpp) REVERT: C 173 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8486 (tp) REVERT: D 69 ASN cc_start: 0.8139 (p0) cc_final: 0.7902 (p0) REVERT: E 13 LYS cc_start: 0.8766 (ttpp) cc_final: 0.8500 (ttpp) REVERT: E 26 GLU cc_start: 0.8105 (mp0) cc_final: 0.7616 (mp0) REVERT: E 79 ARG cc_start: 0.8342 (tpp80) cc_final: 0.8033 (ttm-80) REVERT: E 149 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8462 (p) REVERT: G 22 GLU cc_start: 0.7644 (tp30) cc_final: 0.7346 (tm-30) REVERT: G 33 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7685 (ttt180) REVERT: G 41 PHE cc_start: 0.7872 (t80) cc_final: 0.6774 (t80) REVERT: G 123 LYS cc_start: 0.7726 (mmmm) cc_final: 0.7389 (mmmt) REVERT: H 99 ASP cc_start: 0.8477 (t0) cc_final: 0.8229 (t0) REVERT: H 273 LYS cc_start: 0.8262 (tttt) cc_final: 0.7756 (ttpp) REVERT: H 297 ASN cc_start: 0.8188 (m-40) cc_final: 0.7772 (m110) REVERT: H 461 GLU cc_start: 0.7001 (pm20) cc_final: 0.6464 (pt0) REVERT: H 542 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7719 (tt0) REVERT: H 554 ARG cc_start: 0.8412 (ttm170) cc_final: 0.8121 (ttp80) REVERT: I 453 MET cc_start: 0.8539 (ttp) cc_final: 0.8070 (ttm) REVERT: I 488 GLN cc_start: 0.7065 (tp-100) cc_final: 0.6845 (tp-100) REVERT: J 87 CYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7491 (m) REVERT: K 456 SER cc_start: 0.7607 (p) cc_final: 0.7158 (p) REVERT: K 465 ARG cc_start: 0.7763 (mtp85) cc_final: 0.7384 (mtp180) REVERT: K 480 GLU cc_start: 0.7675 (tp30) cc_final: 0.7432 (tp30) REVERT: L 467 GLU cc_start: 0.7756 (pt0) cc_final: 0.7408 (pt0) REVERT: L 472 ASN cc_start: 0.6737 (OUTLIER) cc_final: 0.6384 (m-40) REVERT: L 476 MET cc_start: 0.8563 (tmt) cc_final: 0.8314 (tmt) REVERT: L 481 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: L 587 LEU cc_start: 0.6598 (OUTLIER) cc_final: 0.6278 (tt) outliers start: 101 outliers final: 42 residues processed: 394 average time/residue: 0.5724 time to fit residues: 256.4916 Evaluate side-chains 362 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 311 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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 73 THR 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 44 THR 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 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 G residue 95 SER Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain H residue 142 THR 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 430 LEU Chi-restraints excluded: chain H residue 436 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 170 ILE Chi-restraints excluded: chain K residue 197 THR 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 493 ASP Chi-restraints excluded: chain K residue 559 THR Chi-restraints excluded: chain K residue 579 LEU Chi-restraints excluded: chain L residue 472 ASN Chi-restraints excluded: chain L residue 481 GLU Chi-restraints excluded: chain L residue 587 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 73 optimal weight: 5.9990 chunk 140 optimal weight: 0.6980 chunk 241 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 201 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 211 optimal weight: 0.9980 chunk 162 optimal weight: 0.3980 chunk 68 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 ASN K 529 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.156205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.123215 restraints weight = 26779.831| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.54 r_work: 0.3223 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2945 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= 0.133 Angle : 0.602 16.610 28878 Z= 0.304 Chirality : 0.042 0.219 3387 Planarity : 0.004 0.047 3437 Dihedral : 14.938 171.453 3743 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.55 % Favored : 96.29 % Rotamer: Outliers : 4.29 % Allowed : 28.32 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.17), residues: 2425 helix: 1.42 (0.18), residues: 845 sheet: -1.08 (0.22), residues: 473 loop : -1.42 (0.17), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 95 TYR 0.020 0.001 TYR L 450 PHE 0.024 0.001 PHE B 167 TRP 0.019 0.001 TRP L 478 HIS 0.003 0.001 HIS H 62 Details of bonding type rmsd covalent geometry : bond 0.00298 (21113) covalent geometry : angle 0.58125 (28854) hydrogen bonds : bond 0.03584 ( 896) hydrogen bonds : angle 4.53625 ( 2589) metal coordination : bond 0.00518 ( 25) metal coordination : angle 5.42502 ( 24) *********************** 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 422 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 338 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: B 59 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7437 (mt) REVERT: B 170 GLU cc_start: 0.6166 (OUTLIER) cc_final: 0.5886 (pp20) REVERT: B 196 ASP cc_start: 0.7367 (p0) cc_final: 0.7071 (p0) REVERT: B 198 PHE cc_start: 0.6467 (m-80) cc_final: 0.6050 (m-80) REVERT: C 13 LYS cc_start: 0.7848 (tptt) cc_final: 0.7643 (tptt) REVERT: C 41 LYS cc_start: 0.7991 (mttt) cc_final: 0.7626 (mttt) REVERT: C 134 LYS cc_start: 0.8002 (ttpt) cc_final: 0.7742 (ttpt) REVERT: C 173 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8409 (tp) REVERT: D 69 ASN cc_start: 0.8095 (p0) cc_final: 0.7887 (p0) REVERT: E 13 LYS cc_start: 0.8672 (ttpp) cc_final: 0.8401 (ttpp) REVERT: E 79 ARG cc_start: 0.8255 (tpp80) cc_final: 0.7981 (mtm-85) REVERT: E 110 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.8022 (ptmm) REVERT: E 149 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8309 (p) REVERT: F 152 ASN cc_start: 0.8359 (m-40) cc_final: 0.7709 (t0) REVERT: G 22 GLU cc_start: 0.7692 (tp30) cc_final: 0.7376 (tm-30) REVERT: G 41 PHE cc_start: 0.7833 (t80) cc_final: 0.6781 (t80) REVERT: G 57 ASP cc_start: 0.7772 (t0) cc_final: 0.7291 (t70) REVERT: G 123 LYS cc_start: 0.7690 (mmmm) cc_final: 0.7418 (mmmt) REVERT: G 131 MET cc_start: 0.8813 (mmp) cc_final: 0.8430 (mmm) REVERT: H 52 ILE cc_start: 0.8286 (mt) cc_final: 0.8018 (mp) REVERT: H 99 ASP cc_start: 0.8413 (t0) cc_final: 0.8154 (t0) REVERT: H 273 LYS cc_start: 0.8243 (tttt) cc_final: 0.7748 (ttpp) REVERT: H 297 ASN cc_start: 0.8174 (m-40) cc_final: 0.7772 (m-40) REVERT: H 378 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7453 (mt-10) REVERT: H 389 THR cc_start: 0.8890 (OUTLIER) cc_final: 0.8633 (m) REVERT: H 461 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6365 (pt0) REVERT: H 554 ARG cc_start: 0.8341 (ttm170) cc_final: 0.8092 (ttp80) REVERT: H 568 GLU cc_start: 0.8224 (tt0) cc_final: 0.7937 (mm-30) REVERT: I 529 ASN cc_start: 0.8335 (t0) cc_final: 0.7759 (m-40) REVERT: J 87 CYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7356 (m) REVERT: J 150 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.7986 (mt) REVERT: K 157 ILE cc_start: 0.7053 (OUTLIER) cc_final: 0.6580 (pt) REVERT: K 456 SER cc_start: 0.7712 (p) cc_final: 0.7237 (p) REVERT: K 465 ARG cc_start: 0.7765 (mtp85) cc_final: 0.7375 (mtp180) REVERT: L 467 GLU cc_start: 0.7666 (pt0) cc_final: 0.7219 (pt0) REVERT: L 470 ASP cc_start: 0.8150 (p0) cc_final: 0.7937 (p0) REVERT: L 476 MET cc_start: 0.8590 (tmt) cc_final: 0.8154 (tmt) REVERT: L 481 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7321 (mp0) outliers start: 84 outliers final: 32 residues processed: 390 average time/residue: 0.5311 time to fit residues: 235.8412 Evaluate side-chains 351 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 308 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 39 VAL Chi-restraints excluded: chain D residue 73 THR 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 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 F residue 108 ASP Chi-restraints excluded: chain G residue 25 LEU 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 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 493 ASP Chi-restraints excluded: chain K residue 514 ILE Chi-restraints excluded: chain K residue 559 THR Chi-restraints excluded: chain K residue 579 LEU 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 155 optimal weight: 7.9990 chunk 149 optimal weight: 0.9990 chunk 182 optimal weight: 4.9990 chunk 246 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 chunk 166 optimal weight: 2.9990 chunk 217 optimal weight: 0.5980 chunk 77 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 245 optimal weight: 20.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 125 GLN D 178 ASN F 125 GLN I 488 GLN J 45 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.152293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.117656 restraints weight = 26596.723| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.74 r_work: 0.3145 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 21138 Z= 0.226 Angle : 0.661 20.633 28878 Z= 0.330 Chirality : 0.044 0.199 3387 Planarity : 0.004 0.049 3437 Dihedral : 14.881 170.639 3743 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.92 % Favored : 95.96 % Rotamer: Outliers : 4.45 % Allowed : 27.66 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.17), residues: 2425 helix: 1.49 (0.18), residues: 841 sheet: -0.98 (0.23), residues: 463 loop : -1.38 (0.17), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 95 TYR 0.019 0.001 TYR L 450 PHE 0.024 0.002 PHE B 167 TRP 0.018 0.002 TRP L 478 HIS 0.002 0.001 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00518 (21113) covalent geometry : angle 0.63498 (28854) hydrogen bonds : bond 0.03663 ( 896) hydrogen bonds : angle 4.55012 ( 2589) metal coordination : bond 0.00897 ( 25) metal coordination : angle 6.43810 ( 24) *********************** 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 402 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 315 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: B 59 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7464 (mt) REVERT: B 93 MET cc_start: 0.7489 (tpp) cc_final: 0.6844 (tpt) REVERT: B 170 GLU cc_start: 0.6236 (OUTLIER) cc_final: 0.5985 (pp20) REVERT: B 196 ASP cc_start: 0.7568 (p0) cc_final: 0.7195 (p0) REVERT: B 198 PHE cc_start: 0.6533 (m-80) cc_final: 0.6228 (m-80) REVERT: C 3 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8702 (mtmt) REVERT: C 13 LYS cc_start: 0.7913 (tptt) cc_final: 0.7703 (tptt) REVERT: C 41 LYS cc_start: 0.8129 (mttt) cc_final: 0.7765 (mttt) REVERT: C 173 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8444 (tp) REVERT: D 69 ASN cc_start: 0.8161 (p0) cc_final: 0.7931 (p0) REVERT: D 157 ASP cc_start: 0.7978 (m-30) cc_final: 0.7712 (m-30) REVERT: E 79 ARG cc_start: 0.8344 (tpp80) cc_final: 0.8082 (mtm-85) REVERT: E 110 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8161 (ptmm) REVERT: E 149 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8408 (p) REVERT: G 9 GLU cc_start: 0.8186 (tp30) cc_final: 0.7590 (tp30) REVERT: G 22 GLU cc_start: 0.7769 (tp30) cc_final: 0.7487 (tm-30) REVERT: G 33 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7701 (ttt-90) REVERT: G 41 PHE cc_start: 0.7903 (t80) cc_final: 0.6754 (t80) REVERT: G 57 ASP cc_start: 0.7726 (t0) cc_final: 0.7290 (t70) REVERT: G 123 LYS cc_start: 0.7613 (mmmm) cc_final: 0.7320 (mmmt) REVERT: G 163 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.6756 (pt) 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: 0.7762 (m-40) REVERT: H 328 GLU cc_start: 0.7268 (tp30) cc_final: 0.6938 (mm-30) REVERT: H 378 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7477 (mt-10) REVERT: H 389 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8737 (m) REVERT: H 461 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6416 (pt0) REVERT: H 542 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7656 (tt0) REVERT: H 554 ARG cc_start: 0.8385 (ttm170) cc_final: 0.8107 (ttp80) REVERT: H 568 GLU cc_start: 0.8327 (tt0) cc_final: 0.7923 (mm-30) REVERT: I 453 MET cc_start: 0.8607 (ttp) cc_final: 0.8233 (ttm) REVERT: I 551 GLN cc_start: 0.8083 (tt0) cc_final: 0.7289 (tp-100) REVERT: J 87 CYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7492 (m) REVERT: K 157 ILE cc_start: 0.7004 (OUTLIER) cc_final: 0.6531 (pt) REVERT: K 189 VAL cc_start: 0.8522 (t) cc_final: 0.8250 (p) REVERT: K 387 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8285 (tttt) REVERT: K 456 SER cc_start: 0.7811 (p) cc_final: 0.7370 (p) REVERT: K 465 ARG cc_start: 0.7755 (mtp85) cc_final: 0.7390 (mtp180) REVERT: L 470 ASP cc_start: 0.8090 (p0) cc_final: 0.7837 (p0) REVERT: L 476 MET cc_start: 0.8596 (tmt) cc_final: 0.8391 (tmt) REVERT: L 481 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7365 (mp0) outliers start: 87 outliers final: 38 residues processed: 365 average time/residue: 0.5528 time to fit residues: 229.4223 Evaluate side-chains 351 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 298 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU 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 5 MET Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 73 THR 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 192 ASP Chi-restraints excluded: chain E residue 44 THR 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 108 ASP Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 33 ARG Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 163 ILE 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 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 K residue 157 ILE Chi-restraints excluded: chain K residue 170 ILE Chi-restraints excluded: chain K residue 387 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 219 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 164 optimal weight: 4.9990 chunk 166 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 chunk 241 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 234 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 175 GLN I 488 GLN J 45 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.151649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.117204 restraints weight = 26866.123| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.79 r_work: 0.3129 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 21138 Z= 0.228 Angle : 0.665 21.434 28878 Z= 0.331 Chirality : 0.045 0.202 3387 Planarity : 0.004 0.049 3437 Dihedral : 14.892 170.689 3743 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.71 % Favored : 96.12 % Rotamer: Outliers : 4.50 % Allowed : 28.02 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.17), residues: 2425 helix: 1.51 (0.18), residues: 841 sheet: -1.01 (0.23), residues: 470 loop : -1.34 (0.17), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 34 TYR 0.018 0.001 TYR L 450 PHE 0.024 0.002 PHE H 474 TRP 0.025 0.002 TRP L 478 HIS 0.003 0.001 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00524 (21113) covalent geometry : angle 0.63720 (28854) hydrogen bonds : bond 0.03677 ( 896) hydrogen bonds : angle 4.60131 ( 2589) metal coordination : bond 0.00934 ( 25) metal coordination : angle 6.60231 ( 24) *********************** 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 398 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 310 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: B 59 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7451 (mt) REVERT: B 93 MET cc_start: 0.7676 (tpp) cc_final: 0.7212 (tpt) REVERT: B 170 GLU cc_start: 0.6090 (OUTLIER) cc_final: 0.5735 (pp20) REVERT: B 198 PHE cc_start: 0.6534 (m-80) cc_final: 0.6189 (m-80) REVERT: C 3 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8767 (mtmt) REVERT: C 173 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8439 (tp) REVERT: D 69 ASN cc_start: 0.8086 (p0) cc_final: 0.7873 (p0) REVERT: D 157 ASP cc_start: 0.8065 (m-30) cc_final: 0.7723 (m-30) REVERT: E 79 ARG cc_start: 0.8315 (tpp80) cc_final: 0.8061 (mtm-85) REVERT: E 149 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8385 (p) REVERT: F 152 ASN cc_start: 0.8588 (m-40) cc_final: 0.7800 (t0) REVERT: G 9 GLU cc_start: 0.8286 (tp30) cc_final: 0.7651 (tp30) REVERT: G 22 GLU cc_start: 0.7792 (tp30) cc_final: 0.7493 (tm-30) REVERT: G 33 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7764 (ttt-90) REVERT: G 41 PHE cc_start: 0.7888 (t80) cc_final: 0.6766 (t80) REVERT: G 57 ASP cc_start: 0.7773 (t0) cc_final: 0.7364 (t70) REVERT: G 58 ASP cc_start: 0.7362 (m-30) cc_final: 0.7089 (m-30) REVERT: G 65 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7552 (mm) REVERT: G 123 LYS cc_start: 0.7585 (mmmm) cc_final: 0.7313 (mmpt) REVERT: G 131 MET cc_start: 0.8797 (mmp) cc_final: 0.8367 (mmm) REVERT: G 163 ILE cc_start: 0.7682 (OUTLIER) cc_final: 0.6836 (pt) REVERT: H 99 ASP cc_start: 0.8439 (t0) cc_final: 0.8209 (t0) REVERT: H 273 LYS cc_start: 0.8264 (tttt) cc_final: 0.7775 (ttpp) REVERT: H 297 ASN cc_start: 0.8171 (m-40) cc_final: 0.7787 (m-40) REVERT: H 328 GLU cc_start: 0.7238 (tp30) cc_final: 0.6870 (mm-30) REVERT: H 389 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8764 (m) REVERT: H 461 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6313 (pt0) REVERT: H 542 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7677 (tt0) REVERT: H 554 ARG cc_start: 0.8373 (ttm170) cc_final: 0.8106 (ttp80) REVERT: I 472 ASN cc_start: 0.8357 (OUTLIER) cc_final: 0.8127 (m110) REVERT: I 551 GLN cc_start: 0.8091 (tt0) cc_final: 0.7307 (tp-100) REVERT: J 87 CYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7504 (m) REVERT: J 150 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8096 (mt) REVERT: K 387 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8275 (tttt) REVERT: K 456 SER cc_start: 0.7810 (p) cc_final: 0.7375 (p) REVERT: K 465 ARG cc_start: 0.7810 (mtp85) cc_final: 0.7453 (mtp180) REVERT: K 508 MET cc_start: 0.7332 (OUTLIER) cc_final: 0.7067 (ttp) REVERT: L 470 ASP cc_start: 0.8009 (p0) cc_final: 0.7699 (p0) REVERT: L 476 MET cc_start: 0.8596 (tmt) cc_final: 0.8377 (tmt) REVERT: L 481 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7317 (mp0) outliers start: 88 outliers final: 43 residues processed: 366 average time/residue: 0.5663 time to fit residues: 235.2564 Evaluate side-chains 353 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 293 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 143 THR 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 162 GLN Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 73 THR 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 44 THR 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 108 ASP Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain G residue 33 ARG Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 163 ILE 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 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 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 542 GLN Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain I residue 461 GLU Chi-restraints excluded: chain I residue 472 ASN 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 197 THR 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 476 MET Chi-restraints excluded: chain K residue 508 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 240 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 chunk 123 optimal weight: 0.7980 chunk 197 optimal weight: 1.9990 chunk 200 optimal weight: 0.5980 chunk 193 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 203 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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** H 221 ASN H 335 ASN I 443 ASN I 488 GLN I 596 ASN J 45 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.153703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.119391 restraints weight = 26757.662| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.72 r_work: 0.3170 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3394 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= 0.167 Angle : 0.628 18.019 28878 Z= 0.316 Chirality : 0.043 0.207 3387 Planarity : 0.004 0.055 3437 Dihedral : 14.882 171.520 3743 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.84 % Favored : 96.04 % Rotamer: Outliers : 4.04 % Allowed : 29.19 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.17), residues: 2425 helix: 1.61 (0.18), residues: 843 sheet: -0.94 (0.23), residues: 470 loop : -1.27 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 95 TYR 0.019 0.001 TYR L 450 PHE 0.024 0.002 PHE H 474 TRP 0.028 0.002 TRP L 478 HIS 0.002 0.001 HIS H 326 Details of bonding type rmsd covalent geometry : bond 0.00382 (21113) covalent geometry : angle 0.60648 (28854) hydrogen bonds : bond 0.03504 ( 896) hydrogen bonds : angle 4.49002 ( 2589) metal coordination : bond 0.00675 ( 25) metal coordination : angle 5.74875 ( 24) *********************** 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 396 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 317 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: B 93 MET cc_start: 0.7610 (tpp) cc_final: 0.7179 (tpt) REVERT: B 170 GLU cc_start: 0.6084 (OUTLIER) cc_final: 0.5768 (pp20) REVERT: B 198 PHE cc_start: 0.6480 (m-80) cc_final: 0.6210 (m-80) REVERT: C 173 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8405 (tp) REVERT: D 157 ASP cc_start: 0.8056 (m-30) cc_final: 0.7804 (m-30) REVERT: E 149 THR cc_start: 0.8742 (OUTLIER) cc_final: 0.8387 (p) REVERT: G 22 GLU cc_start: 0.7767 (tp30) cc_final: 0.7473 (tm-30) REVERT: G 41 PHE cc_start: 0.7875 (t80) cc_final: 0.6744 (t80) REVERT: G 57 ASP cc_start: 0.7760 (t0) cc_final: 0.7467 (t70) REVERT: G 123 LYS cc_start: 0.7551 (mmmm) cc_final: 0.7043 (mmpt) REVERT: G 131 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8354 (mmm) REVERT: G 147 ASN cc_start: 0.8880 (p0) cc_final: 0.8675 (p0) REVERT: G 163 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.6800 (pt) REVERT: G 188 ASP cc_start: 0.8299 (m-30) cc_final: 0.7898 (m-30) REVERT: H 99 ASP cc_start: 0.8444 (t0) cc_final: 0.8174 (t0) REVERT: H 273 LYS cc_start: 0.8263 (tttt) cc_final: 0.7803 (ttpp) REVERT: H 297 ASN cc_start: 0.8159 (m-40) cc_final: 0.7783 (m-40) REVERT: H 328 GLU cc_start: 0.7103 (tp30) cc_final: 0.6723 (mm-30) REVERT: H 389 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8690 (m) REVERT: H 461 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6380 (pt0) REVERT: H 542 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7568 (tt0) REVERT: H 568 GLU cc_start: 0.8396 (tt0) cc_final: 0.7942 (mm-30) REVERT: I 453 MET cc_start: 0.8495 (ttp) cc_final: 0.8109 (ttm) REVERT: I 472 ASN cc_start: 0.8345 (t0) cc_final: 0.8128 (m110) REVERT: I 551 GLN cc_start: 0.8073 (tt0) cc_final: 0.7298 (tp-100) REVERT: J 87 CYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7526 (m) REVERT: K 157 ILE cc_start: 0.7035 (OUTLIER) cc_final: 0.6565 (pt) REVERT: K 439 ILE cc_start: 0.7336 (OUTLIER) cc_final: 0.7005 (mt) REVERT: K 456 SER cc_start: 0.7834 (p) cc_final: 0.7470 (p) REVERT: K 465 ARG cc_start: 0.7876 (mtp85) cc_final: 0.7490 (mtp180) REVERT: K 470 ASP cc_start: 0.7165 (t0) cc_final: 0.6576 (p0) REVERT: L 467 GLU cc_start: 0.7546 (pt0) cc_final: 0.7298 (pt0) REVERT: L 470 ASP cc_start: 0.7998 (p0) cc_final: 0.7695 (p0) REVERT: L 476 MET cc_start: 0.8587 (tmt) cc_final: 0.8351 (tmt) REVERT: L 481 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7304 (mp0) outliers start: 79 outliers final: 39 residues processed: 369 average time/residue: 0.5881 time to fit residues: 248.1250 Evaluate side-chains 357 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 306 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 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 73 THR 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 187 GLU 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 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 E residue 195 THR Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 163 ILE 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 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 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 542 GLN Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain I residue 488 GLN Chi-restraints excluded: chain I residue 513 ILE 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 412 SER Chi-restraints excluded: chain K residue 417 VAL Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain K residue 514 ILE 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: 0.0970 chunk 108 optimal weight: 9.9990 chunk 95 optimal weight: 0.0770 chunk 8 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 13 optimal weight: 30.0000 chunk 227 optimal weight: 0.7980 overall best weight: 0.7938 ------------------------------------------------------------------------------- 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 E 171 ASN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 ASN I 483 ASN I 488 GLN J 45 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.155447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.121143 restraints weight = 26740.637| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.64 r_work: 0.3215 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 21138 Z= 0.138 Angle : 0.612 16.618 28878 Z= 0.310 Chirality : 0.042 0.205 3387 Planarity : 0.004 0.050 3437 Dihedral : 14.879 172.114 3743 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.46 % Favored : 96.41 % Rotamer: Outliers : 3.22 % Allowed : 30.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.17), residues: 2425 helix: 1.69 (0.18), residues: 844 sheet: -0.96 (0.23), residues: 489 loop : -1.23 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 95 TYR 0.021 0.001 TYR I 599 PHE 0.024 0.002 PHE H 474 TRP 0.030 0.001 TRP L 478 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00315 (21113) covalent geometry : angle 0.59264 (28854) hydrogen bonds : bond 0.03431 ( 896) hydrogen bonds : angle 4.42357 ( 2589) metal coordination : bond 0.00549 ( 25) metal coordination : angle 5.31115 ( 24) *********************** 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 386 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 323 time to evaluate : 0.800 Fit side-chains REVERT: B 93 MET cc_start: 0.7553 (tpp) cc_final: 0.7107 (tpt) REVERT: B 104 LEU cc_start: 0.7449 (mm) cc_final: 0.6997 (mm) REVERT: B 170 GLU cc_start: 0.6260 (OUTLIER) cc_final: 0.5957 (pp20) REVERT: C 173 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8370 (tp) REVERT: D 69 ASN cc_start: 0.8100 (p0) cc_final: 0.7855 (p0) REVERT: D 157 ASP cc_start: 0.7957 (m-30) cc_final: 0.7714 (m-30) REVERT: E 149 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8371 (p) REVERT: G 22 GLU cc_start: 0.7846 (tp30) cc_final: 0.7550 (tm-30) REVERT: G 41 PHE cc_start: 0.7825 (t80) cc_final: 0.6680 (t80) REVERT: G 57 ASP cc_start: 0.7831 (t0) cc_final: 0.7485 (t70) REVERT: G 127 TYR cc_start: 0.6981 (m-80) cc_final: 0.6613 (m-80) REVERT: H 52 ILE cc_start: 0.8363 (mt) cc_final: 0.8122 (mp) REVERT: H 99 ASP cc_start: 0.8422 (t0) cc_final: 0.8161 (t0) REVERT: H 273 LYS cc_start: 0.8272 (tttt) cc_final: 0.7823 (ttpp) REVERT: H 297 ASN cc_start: 0.8153 (m-40) cc_final: 0.7773 (m-40) REVERT: H 326 HIS cc_start: 0.8108 (m-70) cc_final: 0.7886 (m-70) REVERT: H 328 GLU cc_start: 0.7056 (tp30) cc_final: 0.6695 (mm-30) REVERT: H 347 ASN cc_start: 0.7455 (t0) cc_final: 0.6841 (t0) REVERT: H 389 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.8626 (m) REVERT: H 461 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6345 (pt0) REVERT: H 554 ARG cc_start: 0.8545 (ttp80) cc_final: 0.8047 (ttt90) REVERT: H 568 GLU cc_start: 0.8353 (tt0) cc_final: 0.7953 (mm-30) REVERT: I 453 MET cc_start: 0.8545 (ttp) cc_final: 0.8190 (ttm) REVERT: I 508 MET cc_start: 0.6254 (ptp) cc_final: 0.5686 (ptp) REVERT: I 529 ASN cc_start: 0.8353 (t0) cc_final: 0.7685 (m-40) REVERT: I 551 GLN cc_start: 0.8019 (tt0) cc_final: 0.7281 (tp-100) REVERT: J 87 CYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7410 (m) REVERT: K 157 ILE cc_start: 0.6978 (OUTLIER) cc_final: 0.6502 (pt) REVERT: K 439 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.7183 (mt) REVERT: K 456 SER cc_start: 0.7853 (p) cc_final: 0.7498 (p) REVERT: K 465 ARG cc_start: 0.7875 (mtp85) cc_final: 0.7488 (mtp180) REVERT: K 470 ASP cc_start: 0.7136 (t0) cc_final: 0.6581 (p0) REVERT: L 467 GLU cc_start: 0.7616 (pt0) cc_final: 0.7330 (pt0) REVERT: L 470 ASP cc_start: 0.7994 (p0) cc_final: 0.7688 (p0) REVERT: L 481 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7317 (mp0) outliers start: 63 outliers final: 40 residues processed: 361 average time/residue: 0.5367 time to fit residues: 222.1180 Evaluate side-chains 357 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 308 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 THR 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 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 73 THR 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 E residue 44 THR 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 72 ASP Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain H residue 5 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 I residue 435 VAL Chi-restraints excluded: chain I residue 488 GLN Chi-restraints excluded: chain I residue 513 ILE 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 412 SER Chi-restraints excluded: chain K residue 417 VAL Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain K residue 514 ILE Chi-restraints excluded: chain K residue 559 THR Chi-restraints excluded: chain L residue 481 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 32 optimal weight: 4.9990 chunk 227 optimal weight: 0.9990 chunk 211 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 182 optimal weight: 4.9990 chunk 246 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 111 optimal weight: 0.0020 chunk 53 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- 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 I 488 GLN J 45 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.156011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.123046 restraints weight = 26717.349| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.41 r_work: 0.3235 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 21138 Z= 0.134 Angle : 0.612 15.784 28878 Z= 0.310 Chirality : 0.042 0.200 3387 Planarity : 0.004 0.048 3437 Dihedral : 14.845 172.397 3743 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.67 % Favored : 96.21 % Rotamer: Outliers : 3.07 % Allowed : 30.47 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.17), residues: 2425 helix: 1.78 (0.18), residues: 843 sheet: -0.92 (0.23), residues: 493 loop : -1.18 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 95 TYR 0.022 0.001 TYR L 450 PHE 0.025 0.002 PHE H 474 TRP 0.030 0.001 TRP L 478 HIS 0.003 0.001 HIS H 326 Details of bonding type rmsd covalent geometry : bond 0.00306 (21113) covalent geometry : angle 0.59329 (28854) hydrogen bonds : bond 0.03385 ( 896) hydrogen bonds : angle 4.36749 ( 2589) metal coordination : bond 0.00518 ( 25) metal coordination : angle 5.17658 ( 24) ********************** 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 385 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 325 time to evaluate : 0.743 Fit side-chains revert: symmetry clash REVERT: B 93 MET cc_start: 0.7828 (tpp) cc_final: 0.7393 (tpt) REVERT: B 104 LEU cc_start: 0.7420 (mm) cc_final: 0.6955 (mm) REVERT: B 170 GLU cc_start: 0.6274 (OUTLIER) cc_final: 0.5969 (pp20) REVERT: C 173 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8430 (tp) REVERT: D 69 ASN cc_start: 0.8200 (p0) cc_final: 0.7936 (p0) REVERT: D 157 ASP cc_start: 0.8074 (m-30) cc_final: 0.7840 (m-30) REVERT: E 149 THR cc_start: 0.8829 (OUTLIER) cc_final: 0.8489 (p) REVERT: E 171 ASN cc_start: 0.8296 (m-40) cc_final: 0.8095 (m110) REVERT: F 83 ARG cc_start: 0.7885 (mtm180) cc_final: 0.7680 (mmm160) REVERT: G 22 GLU cc_start: 0.7923 (tp30) cc_final: 0.7619 (tm-30) REVERT: G 33 ARG cc_start: 0.8214 (ttt-90) cc_final: 0.7911 (tmm-80) REVERT: G 41 PHE cc_start: 0.7855 (t80) cc_final: 0.6640 (t80) REVERT: G 57 ASP cc_start: 0.7826 (t0) cc_final: 0.7467 (t70) REVERT: H 52 ILE cc_start: 0.8295 (mt) cc_final: 0.8022 (mp) REVERT: H 99 ASP cc_start: 0.8447 (t0) cc_final: 0.8177 (t0) REVERT: H 273 LYS cc_start: 0.8281 (tttt) cc_final: 0.7731 (ttpp) REVERT: H 297 ASN cc_start: 0.8130 (m-40) cc_final: 0.7761 (m110) REVERT: H 326 HIS cc_start: 0.8105 (m-70) cc_final: 0.7892 (m-70) REVERT: H 328 GLU cc_start: 0.7117 (tp30) cc_final: 0.6704 (mm-30) REVERT: H 347 ASN cc_start: 0.7531 (t0) cc_final: 0.6983 (t0) REVERT: H 389 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8662 (m) REVERT: H 461 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6344 (pt0) REVERT: H 554 ARG cc_start: 0.8699 (ttp80) cc_final: 0.8217 (ttt90) REVERT: H 568 GLU cc_start: 0.8490 (tt0) cc_final: 0.7966 (mm-30) REVERT: I 444 MET cc_start: 0.8218 (mmm) cc_final: 0.7952 (mmm) REVERT: I 453 MET cc_start: 0.8539 (ttp) cc_final: 0.8274 (ttm) REVERT: I 508 MET cc_start: 0.6351 (ptp) cc_final: 0.5747 (ptp) REVERT: I 529 ASN cc_start: 0.8486 (t0) cc_final: 0.7791 (m-40) REVERT: J 87 CYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7677 (m) REVERT: K 157 ILE cc_start: 0.7180 (OUTLIER) cc_final: 0.6685 (pt) REVERT: K 439 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.7179 (mt) REVERT: K 456 SER cc_start: 0.7774 (p) cc_final: 0.7447 (p) REVERT: K 465 ARG cc_start: 0.7970 (mtp85) cc_final: 0.7630 (mtp180) REVERT: K 470 ASP cc_start: 0.7301 (t0) cc_final: 0.6653 (p0) REVERT: L 467 GLU cc_start: 0.7699 (pt0) cc_final: 0.7429 (pt0) REVERT: L 470 ASP cc_start: 0.8070 (p0) cc_final: 0.7768 (p0) REVERT: L 476 MET cc_start: 0.8672 (tmt) cc_final: 0.8458 (ppp) REVERT: L 481 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7346 (mp0) outliers start: 60 outliers final: 46 residues processed: 365 average time/residue: 0.5163 time to fit residues: 216.5610 Evaluate side-chains 366 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 311 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 THR 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 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 73 THR 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 187 GLU Chi-restraints excluded: chain E residue 44 THR 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 72 ASP Chi-restraints excluded: chain F residue 108 ASP 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 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 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 453 MET Chi-restraints excluded: chain H residue 456 SER Chi-restraints excluded: chain H residue 461 GLU Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain I residue 488 GLN Chi-restraints excluded: chain I residue 513 ILE 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 412 SER Chi-restraints excluded: chain K residue 417 VAL Chi-restraints excluded: chain K residue 435 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 529 ASN Chi-restraints excluded: chain K residue 559 THR Chi-restraints excluded: chain K residue 579 LEU Chi-restraints excluded: chain L residue 481 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 71 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 68 optimal weight: 0.0370 chunk 25 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 chunk 169 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 233 optimal weight: 10.0000 chunk 212 optimal weight: 30.0000 chunk 250 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 178 ASN H 22 ASN I 443 ASN I 472 ASN I 488 GLN I 596 ASN J 45 ASN ** L 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.149377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.114409 restraints weight = 26860.148| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.86 r_work: 0.3080 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 21138 Z= 0.305 Angle : 0.738 24.228 28878 Z= 0.368 Chirality : 0.047 0.210 3387 Planarity : 0.005 0.044 3437 Dihedral : 14.935 170.022 3743 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.21 % Favored : 95.63 % Rotamer: Outliers : 3.63 % Allowed : 30.21 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.17), residues: 2425 helix: 1.53 (0.18), residues: 842 sheet: -0.98 (0.24), residues: 455 loop : -1.30 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 95 TYR 0.024 0.002 TYR I 580 PHE 0.028 0.002 PHE H 474 TRP 0.033 0.002 TRP L 478 HIS 0.004 0.001 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00706 (21113) covalent geometry : angle 0.70625 (28854) hydrogen bonds : bond 0.03938 ( 896) hydrogen bonds : angle 4.71026 ( 2589) metal coordination : bond 0.01206 ( 25) metal coordination : angle 7.44675 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6534.00 seconds wall clock time: 112 minutes 13.94 seconds (6733.94 seconds total)