Starting phenix.real_space_refine on Thu Sep 18 22:18:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z9e_39861/09_2025/8z9e_39861_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z9e_39861/09_2025/8z9e_39861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z9e_39861/09_2025/8z9e_39861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z9e_39861/09_2025/8z9e_39861.map" model { file = "/net/cci-nas-00/data/ceres_data/8z9e_39861/09_2025/8z9e_39861_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z9e_39861/09_2025/8z9e_39861_neut.cif" } resolution = 3.13 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= 0.002 sd= 0.040 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 73 5.49 5 S 83 5.16 5 C 12844 2.51 5 N 3586 2.21 5 O 4177 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 97 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: 20770 Number of models: 1 Model: "" Number of chains: 20 Chain: "B" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1230 Classifications: {'peptide': 170} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 165} Chain breaks: 3 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1525 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1543 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1524 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 192} 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: "F" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1468 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 188} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1248 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 5, 'TRANS': 169} Chain breaks: 6 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ASP:plan': 3, 'PHE:plan': 1, 'TYR:plan': 2, 'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "H" Number of atoms: 4388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4388 Classifications: {'peptide': 553} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 18, 'TRANS': 534} Chain breaks: 8 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 4, 'TYR:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "I" Number of atoms: 1297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1297 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 148} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1538 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 192} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 2379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2379 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 11, 'TRANS': 293} Chain breaks: 12 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 4, 'ASP:plan': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 68 Chain: "L" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1082 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain breaks: 5 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 4, 'ASN:plan1': 4, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "M" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 817 Classifications: {'RNA': 39} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 13, 'rna3p_pur': 12, 'rna3p_pyr': 7} Link IDs: {'rna2p': 19, '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': 3, 'rna2p_pyr': 1, 'rna3p_pur': 16, 'rna3p_pyr': 14} Link IDs: {'rna2p': 4, 'rna3p': 29} 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 429 SG CYS B 71 31.958 56.533 158.201 1.00142.25 S ATOM 503 SG CYS B 81 29.903 57.904 155.962 1.00132.05 S ATOM 524 SG CYS B 84 29.770 59.703 159.348 1.00133.41 S ATOM 544 SG CYS B 87 32.263 60.501 156.963 1.00136.05 S ATOM 1778 SG CYS C 71 24.638 81.252 134.547 1.00 88.56 S ATOM 1852 SG CYS C 81 22.492 83.525 132.351 1.00 88.83 S ATOM 1873 SG CYS C 84 24.056 85.021 135.457 1.00 80.73 S ATOM 1893 SG CYS C 87 26.308 84.046 132.749 1.00 81.38 S ATOM 3307 SG CYS D 71 63.428 99.841 86.453 1.00 50.81 S ATOM 3381 SG CYS D 81 65.653 102.138 83.164 1.00 90.28 S ATOM 3402 SG CYS D 84 66.286 100.670 86.383 1.00 79.97 S ATOM 3422 SG CYS D 87 65.431 97.633 84.526 1.00 54.63 S ATOM 4841 SG CYS E 71 77.334 78.958 63.355 1.00 94.43 S ATOM 4909 SG CYS E 81 80.031 78.655 60.373 1.00 82.30 S ATOM 4930 SG CYS E 84 80.049 77.016 63.221 1.00 99.36 S ATOM 4950 SG CYS E 87 76.864 76.324 61.322 1.00 61.14 S ATOM 6363 SG CYS F 71 69.066 55.163 40.438 1.00104.12 S ATOM 6431 SG CYS F 81 69.274 52.304 38.146 1.00116.08 S ATOM 6452 SG CYS F 84 67.054 52.084 41.370 1.00105.68 S ATOM 6472 SG CYS F 87 65.819 54.006 38.666 1.00 93.76 S ATOM 14770 SG CYS J 71 39.317 100.365 110.759 1.00 77.62 S ATOM 14844 SG CYS J 81 39.030 103.461 108.459 1.00 63.23 S ATOM 14865 SG CYS J 84 41.764 103.462 111.124 1.00 76.92 S ATOM 14885 SG CYS J 87 41.924 101.016 108.358 1.00 63.27 S Time building chain proxies: 4.89, per 1000 atoms: 0.24 Number of scatterers: 20770 At special positions: 0 Unit cell: (94.05, 125.4, 190.95, 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 83 16.00 P 73 15.00 O 4177 8.00 N 3586 7.00 C 12844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS H 29 " - pdb=" SG CYS H 58 " distance=2.78 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: 1.42 Conformation dependent library (CDL) restraints added in 826.8 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 81 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 84 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 87 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 71 " pdb=" ZN C 301 " 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 71 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 81 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 84 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 71 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 87 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 81 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 71 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 84 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 81 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 87 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 84 " 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 81 " 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 87 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 81 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 84 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 71 " Number of angles added : 36 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4674 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 35 sheets defined 36.6% alpha, 21.3% beta 18 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'B' and resid 51 through 66 Processing helix chain 'B' and resid 84 through 90 Processing helix chain 'B' and resid 156 through 172 Processing helix chain 'B' and resid 176 through 180 removed outlier: 3.509A pdb=" N LYS B 179 " --> pdb=" O TRP B 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 30 Processing helix chain 'C' and resid 53 through 67 Processing helix chain 'C' and resid 84 through 90 Processing helix chain 'C' and resid 109 through 113 removed outlier: 3.722A 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 124 through 127 Processing helix chain 'C' and resid 157 through 172 Processing helix chain 'D' and resid 24 through 32 Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 109 through 113 removed outlier: 3.526A pdb=" N ILE D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 109 through 113' Processing helix chain 'D' and resid 156 through 172 removed outlier: 3.661A pdb=" N LEU D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 32 Processing helix chain 'E' and resid 51 through 67 Processing helix chain 'E' and resid 84 through 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: 3.588A pdb=" N GLY E 180 " --> pdb=" O LEU E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 198 No H-bonds generated for 'chain 'E' and resid 196 through 198' Processing helix chain 'F' and resid 24 through 32 Processing helix chain 'F' and resid 52 through 67 removed outlier: 3.563A pdb=" N GLY F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 90 Processing helix chain 'F' and resid 109 through 113 removed outlier: 3.678A 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 28 through 43 removed outlier: 3.698A pdb=" N LEU G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 53 removed outlier: 4.100A pdb=" N LYS G 50 " --> pdb=" O PRO G 46 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP G 53 " --> pdb=" O SER G 49 " (cutoff:3.500A) 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 127 through 141 Processing helix chain 'H' and resid 41 through 53 removed outlier: 3.637A 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 107 Processing helix chain 'H' and resid 114 through 124 removed outlier: 3.843A pdb=" N ILE H 124 " --> pdb=" O SER H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 220 Processing helix chain 'H' and resid 233 through 245 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 277 Processing helix chain 'H' and resid 295 through 305 Processing helix chain 'H' and resid 322 through 333 removed outlier: 4.107A pdb=" N HIS H 326 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU H 328 " --> pdb=" O LEU H 324 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLN H 329 " --> pdb=" O ASN H 325 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP H 333 " --> pdb=" O GLN H 329 " (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 471 through 478 Processing helix chain 'H' and resid 509 through 523 Processing helix chain 'H' and resid 527 through 541 Processing helix chain 'H' and resid 541 through 554 Processing helix chain 'H' and resid 572 through 592 Processing helix chain 'H' and resid 594 through 606 removed outlier: 4.235A pdb=" N ASN H 604 " --> pdb=" O ASN H 600 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N PHE H 605 " --> pdb=" O ILE H 601 " (cutoff:3.500A) Processing helix chain 'I' and resid 470 through 489 removed outlier: 3.807A pdb=" N PHE I 474 " --> pdb=" O ASP I 470 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU I 480 " --> pdb=" O MET I 476 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ARG I 486 " --> pdb=" O TYR I 482 " (cutoff:3.500A) Processing helix chain 'I' and resid 509 through 523 Processing helix chain 'I' and resid 527 through 540 Processing helix chain 'I' and resid 541 through 554 Processing helix chain 'I' and resid 572 through 593 removed outlier: 3.872A pdb=" N LYS I 592 " --> pdb=" O LEU I 588 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR I 593 " --> pdb=" O SER I 589 " (cutoff:3.500A) Processing helix chain 'I' and resid 594 through 603 removed outlier: 3.547A pdb=" N LEU I 602 " --> pdb=" O VAL I 598 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 32 Processing helix chain 'J' and resid 51 through 67 Processing helix chain 'J' and resid 84 through 90 Processing helix chain 'J' and resid 109 through 113 Processing helix chain 'J' and resid 156 through 172 Processing helix chain 'K' and resid 377 through 385 Processing helix chain 'K' and resid 399 through 412 removed outlier: 3.701A pdb=" N ARG K 403 " --> pdb=" O GLU K 399 " (cutoff:3.500A) Processing helix chain 'K' and resid 446 through 450 removed outlier: 3.916A pdb=" N SER K 449 " --> pdb=" O ASN K 446 " (cutoff:3.500A) Processing helix chain 'K' and resid 470 through 487 removed outlier: 3.648A pdb=" N PHE K 474 " --> pdb=" O ASP K 470 " (cutoff:3.500A) Processing helix chain 'K' and resid 509 through 523 removed outlier: 3.508A pdb=" N ILE K 523 " --> pdb=" O TYR K 519 " (cutoff:3.500A) Processing helix chain 'K' and resid 527 through 540 removed outlier: 3.584A pdb=" N LYS K 540 " --> pdb=" O GLU K 536 " (cutoff:3.500A) Processing helix chain 'K' and resid 541 through 554 removed outlier: 3.681A pdb=" N ALA K 545 " --> pdb=" O GLY K 541 " (cutoff:3.500A) Processing helix chain 'K' and resid 572 through 591 Processing helix chain 'K' and resid 594 through 603 Processing helix chain 'L' and resid 470 through 488 removed outlier: 3.627A pdb=" N PHE L 474 " --> pdb=" O ASP L 470 " (cutoff:3.500A) Processing helix chain 'L' and resid 511 through 523 removed outlier: 3.911A pdb=" N ASN L 522 " --> pdb=" O GLU L 518 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE L 523 " --> pdb=" O TYR L 519 " (cutoff:3.500A) Processing helix chain 'L' and resid 527 through 535 removed outlier: 4.123A pdb=" N GLU L 533 " --> pdb=" O ASN L 529 " (cutoff:3.500A) Processing helix chain 'L' and resid 546 through 554 Processing helix chain 'L' and resid 572 through 590 Processing helix chain 'L' and resid 595 through 600 Processing helix chain 'L' and resid 601 through 606 Processing sheet with id=AA1, first strand: chain 'B' and resid 48 through 49 removed outlier: 3.756A pdb=" N ILE B 49 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 48 through 49 removed outlier: 3.756A pdb=" N ILE B 49 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS B 7 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 114 through 115 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 99 through 101 Processing sheet with id=AA6, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AA7, first strand: chain 'C' and resid 119 through 122 Processing sheet with id=AA8, first strand: chain 'D' and resid 99 through 100 Processing sheet with id=AA9, first strand: chain 'D' and resid 99 through 100 Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 122 removed outlier: 3.781A pdb=" N ASP D 131 " --> pdb=" O ARG D 121 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 99 through 100 Processing sheet with id=AB3, first strand: chain 'E' and resid 99 through 100 Processing sheet with id=AB4, first strand: chain 'E' and resid 114 through 122 Processing sheet with id=AB5, first strand: chain 'F' and resid 48 through 49 Processing sheet with id=AB6, first strand: chain 'F' and resid 48 through 49 Processing sheet with id=AB7, first strand: chain 'F' and resid 114 through 122 Processing sheet with id=AB8, first strand: chain 'G' and resid 115 through 120 removed outlier: 6.813A pdb=" N LYS G 5 " --> pdb=" O TYR G 161 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TYR G 161 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE G 7 " --> pdb=" O LYS G 159 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 17 through 18 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: 6.556A pdb=" N SER H 14 " --> pdb=" O CYS H 29 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N CYS H 29 " --> pdb=" O SER H 14 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LYS H 24 " --> pdb=" O ALA H 55 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE H 57 " --> pdb=" O LYS H 24 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ASP H 56 " --> pdb=" O VAL H 80 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS H 82 " --> pdb=" O ASP H 56 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE H 84 " --> pdb=" O CYS H 58 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ASP H 126 " --> pdb=" O ASN H 81 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ILE H 83 " --> pdb=" O ASP H 126 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 134 through 136 removed outlier: 8.689A pdb=" N VAL H 153 " --> pdb=" O GLY H 168 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N GLY H 168 " --> pdb=" O VAL H 153 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU H 192 " --> pdb=" O PHE H 394 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 226 through 229 removed outlier: 5.505A pdb=" N TYR H 252 " --> pdb=" O ILE H 312 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ALA H 314 " --> pdb=" O TYR H 252 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 338 through 340 Processing sheet with id=AC7, first strand: chain 'H' and resid 445 through 446 Processing sheet with id=AC8, first strand: chain 'H' and resid 445 through 446 removed outlier: 4.296A pdb=" N ARG H 451 " --> pdb=" O GLU K 461 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE K 455 " --> pdb=" O GLY H 457 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL K 435 " --> pdb=" O ILE K 466 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ILE K 468 " --> pdb=" O VAL K 435 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU K 437 " --> pdb=" O ILE K 468 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 436 through 437 removed outlier: 7.503A pdb=" N VAL I 436 " --> pdb=" O ILE I 468 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 436 through 437 removed outlier: 7.503A pdb=" N VAL I 436 " --> pdb=" O ILE I 468 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG I 451 " --> pdb=" O GLU L 461 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 99 through 100 Processing sheet with id=AD3, first strand: chain 'J' and resid 99 through 100 Processing sheet with id=AD4, first strand: chain 'J' and resid 114 through 122 Processing sheet with id=AD5, first strand: chain 'K' and resid 2 through 3 Processing sheet with id=AD6, first strand: chain 'K' and resid 56 through 57 Processing sheet with id=AD7, first strand: chain 'K' and resid 133 through 134 removed outlier: 6.612A pdb=" N ASN K 163 " --> pdb=" O TYR K 191 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ILE K 193 " --> pdb=" O ASN K 163 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU K 165 " --> pdb=" O ILE K 193 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N GLU K 195 " --> pdb=" O LEU K 165 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 445 through 447 891 hydrogen bonds defined for protein. 2544 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 3.78 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5502 1.33 - 1.46: 4508 1.46 - 1.58: 10947 1.58 - 1.70: 146 1.70 - 1.82: 129 Bond restraints: 21232 Sorted by residual: bond pdb=" C ASP K 381 " pdb=" N TYR K 382 " ideal model delta sigma weight residual 1.335 1.496 -0.160 1.34e-02 5.57e+03 1.43e+02 bond pdb=" C ILE H 57 " pdb=" N CYS H 58 " ideal model delta sigma weight residual 1.333 1.464 -0.130 1.33e-02 5.65e+03 9.59e+01 bond pdb=" C LYS I 528 " pdb=" N ASN I 529 " ideal model delta sigma weight residual 1.335 1.437 -0.103 1.31e-02 5.83e+03 6.13e+01 bond pdb=" C CYS H 58 " pdb=" N ILE H 59 " ideal model delta sigma weight residual 1.335 1.424 -0.089 1.16e-02 7.43e+03 5.85e+01 bond pdb=" C ILE E 139 " pdb=" N GLU E 140 " ideal model delta sigma weight residual 1.329 1.403 -0.074 1.36e-02 5.41e+03 2.95e+01 ... (remaining 21227 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 27810 2.45 - 4.90: 994 4.90 - 7.35: 139 7.35 - 9.80: 26 9.80 - 12.25: 8 Bond angle restraints: 28977 Sorted by residual: angle pdb=" O ILE H 57 " pdb=" C ILE H 57 " pdb=" N CYS H 58 " ideal model delta sigma weight residual 123.19 129.85 -6.66 9.60e-01 1.09e+00 4.82e+01 angle pdb=" C ASP K 381 " pdb=" N TYR K 382 " pdb=" CA TYR K 382 " ideal model delta sigma weight residual 120.28 110.90 9.38 1.44e+00 4.82e-01 4.24e+01 angle pdb=" C ASN L 600 " pdb=" N ILE L 601 " pdb=" CA ILE L 601 " ideal model delta sigma weight residual 121.97 133.67 -11.70 1.80e+00 3.09e-01 4.23e+01 angle pdb=" N SER K 456 " pdb=" CA SER K 456 " pdb=" C SER K 456 " ideal model delta sigma weight residual 109.40 99.25 10.15 1.63e+00 3.76e-01 3.88e+01 angle pdb=" O LYS I 528 " pdb=" C LYS I 528 " pdb=" N ASN I 529 " ideal model delta sigma weight residual 122.15 128.94 -6.79 1.14e+00 7.69e-01 3.55e+01 ... (remaining 28972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 12381 35.52 - 71.04: 495 71.04 - 106.56: 46 106.56 - 142.07: 1 142.07 - 177.59: 4 Dihedral angle restraints: 12927 sinusoidal: 5736 harmonic: 7191 Sorted by residual: dihedral pdb=" CB CYS H 29 " pdb=" SG CYS H 29 " pdb=" SG CYS H 58 " pdb=" CB CYS H 58 " ideal model delta sinusoidal sigma weight residual 93.00 21.00 72.00 1 1.00e+01 1.00e-02 6.63e+01 dihedral pdb=" O4' C M 29 " pdb=" C1' C M 29 " pdb=" N1 C M 29 " pdb=" C2 C M 29 " ideal model delta sinusoidal sigma weight residual -128.00 39.17 -167.17 1 1.70e+01 3.46e-03 6.56e+01 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 -128.00 39.09 -167.09 1 1.70e+01 3.46e-03 6.56e+01 ... (remaining 12924 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2909 0.089 - 0.177: 402 0.177 - 0.266: 34 0.266 - 0.355: 7 0.355 - 0.443: 7 Chirality restraints: 3359 Sorted by residual: chirality pdb=" P C M 29 " pdb=" OP1 C M 29 " pdb=" OP2 C M 29 " pdb=" O5' C M 29 " both_signs ideal model delta sigma weight residual True 2.41 -2.85 -0.44 2.00e-01 2.50e+01 4.91e+00 chirality pdb=" P C N 11 " pdb=" OP1 C N 11 " pdb=" OP2 C N 11 " pdb=" O5' C N 11 " both_signs ideal model delta sigma weight residual True 2.41 -2.83 -0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" CB ILE H 214 " pdb=" CA ILE H 214 " pdb=" CG1 ILE H 214 " pdb=" CG2 ILE H 214 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.28e+00 ... (remaining 3356 not shown) Planarity restraints: 3456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE L 477 " -0.022 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C ILE L 477 " 0.073 2.00e-02 2.50e+03 pdb=" O ILE L 477 " -0.027 2.00e-02 2.50e+03 pdb=" N TRP L 478 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU K 505 " -0.068 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO K 506 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO K 506 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO K 506 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 16 " 0.066 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO G 17 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO G 17 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO G 17 " 0.054 5.00e-02 4.00e+02 ... (remaining 3453 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 678 2.69 - 3.24: 18793 3.24 - 3.79: 34130 3.79 - 4.35: 45386 4.35 - 4.90: 73981 Nonbonded interactions: 172968 Sorted by model distance: nonbonded pdb=" OD2 ASP H 169 " pdb="ZN ZN H 701 " model vdw 2.136 2.230 nonbonded pdb=" O LEU D 120 " pdb=" O2' U M 16 " model vdw 2.241 3.040 nonbonded pdb=" OG SER K 527 " pdb=" OP1 A N 29 " model vdw 2.260 3.040 nonbonded pdb=" O SER E 92 " pdb=" O2' U M 2 " model vdw 2.279 3.040 nonbonded pdb=" O LEU H 136 " pdb=" OG1 THR H 139 " model vdw 2.297 3.040 ... (remaining 172963 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 'B' and ((resid 3 through 4 and (name N or name CA or name C or name O or \ name CB )) or resid 5 through 76 or (resid 77 through 78 and (name N or name CA \ or name C or name O or name CB )) or resid 79 through 94 or (resid 95 through 9 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 97 through 1 \ 54 or (resid 155 through 156 and (name N or name CA or name C or name O or name \ CB )) or resid 157 through 194 or (resid 195 through 196 and (name N or name CA \ or name C or name O or name CB )) or resid 301)) selection = (chain 'C' and ((resid 3 through 4 and (name N or name CA or name C or name O or \ name CB )) or resid 5 or (resid 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 15 or resid 19 through 26 or resid 3 \ 6 through 45 or (resid 46 and (name N or name CA or name C or name O or name CB \ )) or resid 47 through 59 or (resid 60 and (name N or name CA or name C or name \ O or name CB )) or resid 61 through 62 or (resid 63 through 65 and (name N or na \ me CA or name C or name O or name CB )) or resid 66 through 68 or (resid 69 and \ (name N or name CA or name C or name O or name CB )) or resid 70 through 76 or ( \ resid 77 through 78 and (name N or name CA or name C or name O or name CB )) or \ resid 79 through 94 or (resid 95 through 96 and (name N or name CA or name C or \ name O or name CB )) or resid 97 through 109 or (resid 110 through 111 and (name \ N or name CA or name C or name O or name CB )) or resid 112 through 114 or (res \ id 115 through 116 and (name N or name CA or name C or name O or name CB )) or r \ esid 117 or resid 135 or (resid 136 and (name N or name CA or name C or name O o \ r name CB )) or resid 137 or (resid 138 and (name N or name CA or name C or name \ O or name CB )) or resid 139 through 154 or (resid 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 or name CB )) or resid 167 or (re \ sid 168 and (name N or name CA or name C or name O or name CB )) or resid 169 th \ rough 178 or (resid 179 and (name N or name CA or name C or name O or name CB )) \ or resid 180 through 182 or (resid 183 and (name N or name CA or name C or name \ O or name CB )) or resid 184 through 186 or (resid 187 and (name N or name CA o \ r 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 194 or (resid 195 thro \ ugh 196 and (name N or name CA or name C or name O or name CB )) or resid 301)) selection = (chain 'D' and ((resid 3 through 4 and (name N or name CA or name C or name O or \ name CB )) or resid 5 or (resid 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 15 or resid 19 through 26 or resid 3 \ 6 through 45 or (resid 46 and (name N or name CA or name C or name O or name CB \ )) or resid 47 through 59 or (resid 60 and (name N or name CA or name C or name \ O or name CB )) or resid 61 through 62 or (resid 63 through 65 and (name N or na \ me CA or name C or name O or name CB )) or resid 66 through 68 or (resid 69 and \ (name N or name CA or name C or name O or name CB )) or resid 70 through 76 or ( \ resid 77 through 78 and (name N or name CA or name C or name O or name CB )) or \ resid 79 through 94 or (resid 95 through 96 and (name N or name CA or name C or \ name O or name CB )) or resid 97 through 109 or (resid 110 through 111 and (name \ N or name CA or name C or name O or name CB )) or resid 112 through 114 or (res \ id 115 through 116 and (name N or name CA or name C or name O or name CB )) or r \ esid 117 or resid 135 or (resid 136 and (name N or name CA or name C or name O o \ r name CB )) or resid 137 or (resid 138 and (name N or name CA or name C or name \ O or name CB )) or resid 139 through 154 or (resid 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 or name CB )) or resid 167 or (re \ sid 168 and (name N or name CA or name C or name O or name CB )) or resid 169 th \ rough 178 or (resid 179 and (name N or name CA or name C or name O or name CB )) \ or resid 180 through 182 or (resid 183 and (name N or name CA or name C or name \ O or name CB )) or resid 184 through 186 or (resid 187 and (name N or name CA o \ r 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 194 or (resid 195 thro \ ugh 196 and (name N or name CA or name C or name O or name CB )) or resid 301)) selection = (chain 'E' and ((resid 3 through 4 and (name N or name CA or name C or name O or \ name CB )) or resid 5 or (resid 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 15 or resid 19 through 26 or resid 3 \ 6 through 45 or (resid 46 and (name N or name CA or name C or name O or name CB \ )) or resid 47 through 59 or (resid 60 and (name N or name CA or name C or name \ O or name CB )) or resid 61 through 62 or (resid 63 through 65 and (name N or na \ me CA or name C or name O or name CB )) or resid 66 through 68 or (resid 69 and \ (name N or name CA or name C or name O or name CB )) or resid 70 through 94 or ( \ resid 95 through 96 and (name N or name CA or name C or name O or name CB )) or \ resid 97 through 109 or (resid 110 through 111 and (name N or name CA or name C \ or name O or name CB )) or resid 112 through 114 or (resid 115 through 116 and ( \ name N or name CA or name C or name O or name CB )) or resid 117 or resid 135 or \ (resid 136 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 7 or (resid 138 and (name N or name CA or name C or name O or name CB )) or resi \ d 139 through 154 or (resid 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 or name CB )) or resid 167 or (resid 168 and (name N or n \ ame CA or name C or name O or name CB )) or resid 169 through 178 or (resid 179 \ and (name N or name CA or name C or name O or name CB )) or resid 180 through 18 \ 2 or (resid 183 and (name N or name CA or name C or name O or name CB )) or resi \ d 184 through 186 or (resid 187 and (name N or name CA or name C or name O or na \ me CB )) or resid 188 or (resid 189 and (name N or name CA or name C or name O o \ r name CB )) or resid 190 through 194 or (resid 195 through 196 and (name N or n \ ame CA or name C or name O or name CB )) or resid 301)) selection = (chain 'F' and (resid 3 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB )) or resid 7 through 12 or (resid 13 and (name N or name CA \ or name C or name O or name CB )) or resid 14 through 15 or resid 19 through 26 \ or resid 36 through 45 or (resid 46 and (name N or name CA or name C or name O \ or name CB )) or resid 47 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 62 or (resid 63 through 65 and (n \ ame N or name CA or name C or name O or name CB )) or resid 66 through 68 or (re \ sid 69 and (name N or name CA or name C or name O or name CB )) or resid 70 thro \ ugh 109 or (resid 110 through 111 and (name N or name CA or name C or name O or \ name CB )) or resid 112 through 114 or (resid 115 through 116 and (name N or nam \ e CA or name C or name O or name CB )) or resid 117 or resid 135 or (resid 136 a \ nd (name N or name CA or name C or name O or name CB )) or resid 137 or (resid 1 \ 38 and (name N or name CA or name C or name O or name CB )) or resid 139 through \ 165 or (resid 166 and (name N or name CA or name C or name O or name CB )) or r \ esid 167 or (resid 168 and (name N or name CA or name C or name O or name CB )) \ or resid 169 through 178 or (resid 179 and (name N or name CA or name C or name \ O or name CB )) or resid 180 through 182 or (resid 183 and (name N or name CA or \ name C or name O or name CB )) or resid 184 through 188 or (resid 189 and (name \ N or name CA or name C or name O or name CB )) or resid 190 through 301)) selection = (chain 'J' and ((resid 3 through 4 and (name N or name CA or name C or name O or \ name CB )) or resid 5 or (resid 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 15 or resid 19 through 26 or resid 3 \ 6 through 45 or (resid 46 and (name N or name CA or name C or name O or name CB \ )) or resid 47 through 59 or (resid 60 and (name N or name CA or name C or name \ O or name CB )) or resid 61 through 62 or (resid 63 through 65 and (name N or na \ me CA or name C or name O or name CB )) or resid 66 through 68 or (resid 69 and \ (name N or name CA or name C or name O or name CB )) or resid 70 through 76 or ( \ resid 77 through 78 and (name N or name CA or name C or name O or name CB )) or \ resid 79 through 94 or (resid 95 through 96 and (name N or name CA or name C or \ name O or name CB )) or resid 97 through 109 or (resid 110 through 111 and (name \ N or name CA or name C or name O or name CB )) or resid 112 through 114 or (res \ id 115 through 116 and (name N or name CA or name C or name O or name CB )) or r \ esid 117 or resid 135 or (resid 136 and (name N or name CA or name C or name O o \ r name CB )) or resid 137 or (resid 138 and (name N or name CA or name C or name \ O or name CB )) or resid 139 through 154 or (resid 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 or name CB )) or resid 167 or (re \ sid 168 and (name N or name CA or name C or name O or name CB )) or resid 169 th \ rough 178 or (resid 179 and (name N or name CA or name C or name O or name CB )) \ or resid 180 through 182 or (resid 183 and (name N or name CA or name C or name \ O or name CB )) or resid 184 through 186 or (resid 187 and (name N or name CA o \ r 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 194 or (resid 195 thro \ ugh 196 and (name N or name CA or name C or name O or name CB )) or resid 301)) } ncs_group { reference = (chain 'I' and (resid 435 through 470 or (resid 471 and (name N or name CA or na \ me C or name O or name CB )) or resid 472 through 488 or resid 510 or (resid 511 \ through 512 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 13 or (resid 514 through 516 and (name N or name CA or name C or name O or name \ CB )) or resid 517 or (resid 518 and (name N or name CA or name C or name O or n \ ame CB )) or resid 519 or (resid 520 and (name N or name CA or name C or name O \ or name CB )) or resid 521 or (resid 522 and (name N or name CA or name C or nam \ e O or name CB )) or resid 523 through 531 or (resid 532 and (name N or name CA \ or name C or name O or name CB )) or resid 533 through 535 or resid 545 through \ 553 or (resid 554 and (name N or name CA or name C or name O or name CB )) or re \ sid 555 through 569 or resid 571 through 572 or (resid 573 and (name N or name C \ A or name C or name O or name CB )) or resid 574 or (resid 575 through 576 and ( \ name N or name CA or name C or name O or name CB )) or resid 577 or (resid 578 a \ nd (name N or name CA or name C or name O or name CB )) or resid 579 through 580 \ or (resid 581 through 583 and (name N or name CA or name C or name O or name CB \ )) or resid 584 through 587 or (resid 588 and (name N or name CA or name C or n \ ame O or name CB )) or resid 589 through 590 or (resid 594 through 597 and (name \ N or name CA or name C or name O or name 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 604 and (name N or name CA or name C or name O or name CB )) \ or resid 605 through 606)) selection = (chain 'L' and (resid 435 through 462 or resid 466 or (resid 467 and (name N or \ name CA or name C or name O or name CB )) or resid 468 through 475 or (resid 476 \ and (name N or name CA or name C or name O or name CB )) or resid 477 through 6 \ 06)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 22.360 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 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 : 0.009 0.751 21260 Z= 0.458 Angle : 1.182 57.661 29015 Z= 0.643 Chirality : 0.063 0.443 3359 Planarity : 0.008 0.102 3456 Dihedral : 18.264 177.592 8250 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.31 % Favored : 95.31 % Rotamer: Outliers : 0.69 % Allowed : 21.58 % Favored : 77.73 % 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: -2.57 (0.14), residues: 2390 helix: -1.49 (0.14), residues: 812 sheet: -0.75 (0.23), residues: 464 loop : -2.26 (0.15), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 183 TYR 0.024 0.002 TYR K 482 PHE 0.030 0.003 PHE F 133 TRP 0.026 0.003 TRP H 478 HIS 0.017 0.002 HIS L 553 Details of bonding type rmsd covalent geometry : bond 0.00627 (21232) covalent geometry : angle 1.05502 (28977) SS BOND : bond 0.75122 ( 1) SS BOND : angle 42.26848 ( 2) hydrogen bonds : bond 0.15716 ( 916) hydrogen bonds : angle 7.55264 ( 2636) metal coordination : bond 0.11124 ( 27) metal coordination : angle 11.39799 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 366 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 MET cc_start: 0.5121 (mmm) cc_final: 0.3260 (tpp) REVERT: C 116 GLU cc_start: 0.7266 (tt0) cc_final: 0.7025 (tt0) REVERT: C 123 GLU cc_start: 0.6790 (mm-30) cc_final: 0.6517 (mm-30) REVERT: D 93 MET cc_start: 0.8707 (tpp) cc_final: 0.8489 (tpp) REVERT: E 95 ARG cc_start: 0.7531 (ttm110) cc_final: 0.7010 (mtp-110) REVERT: F 34 ARG cc_start: 0.7581 (mtm-85) cc_final: 0.7343 (mtm-85) REVERT: G 57 ASP cc_start: 0.8026 (m-30) cc_final: 0.7541 (t70) REVERT: G 98 ARG cc_start: 0.8322 (mpt90) cc_final: 0.7734 (mmt180) REVERT: G 202 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7351 (pt0) REVERT: H 126 ASP cc_start: 0.8088 (t0) cc_final: 0.7754 (t0) REVERT: H 331 LYS cc_start: 0.8022 (mtpt) cc_final: 0.7250 (tptt) REVERT: I 450 TYR cc_start: 0.7229 (m-80) cc_final: 0.6485 (m-10) REVERT: I 509 SER cc_start: 0.8029 (m) cc_final: 0.7419 (p) REVERT: J 83 ARG cc_start: 0.8134 (mtm110) cc_final: 0.7907 (mtm-85) REVERT: K 379 LEU cc_start: 0.8533 (mt) cc_final: 0.8301 (mt) REVERT: K 465 ARG cc_start: 0.7818 (ptp-170) cc_final: 0.7480 (ptp-170) REVERT: K 482 TYR cc_start: 0.8286 (t80) cc_final: 0.8068 (t80) REVERT: L 444 MET cc_start: 0.5116 (tpp) cc_final: 0.4434 (tpp) REVERT: L 465 ARG cc_start: 0.7050 (ptt-90) cc_final: 0.6323 (ptt180) REVERT: L 472 ASN cc_start: 0.8128 (m-40) cc_final: 0.7902 (m-40) REVERT: L 600 ASN cc_start: 0.7678 (m-40) cc_final: 0.6210 (p0) outliers start: 14 outliers final: 6 residues processed: 374 average time/residue: 0.1743 time to fit residues: 93.9475 Evaluate side-chains 338 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 332 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 110 LYS Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain L residue 479 ASN Chi-restraints excluded: chain L residue 488 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 0.0270 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 0.9980 chunk 247 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 7.9990 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 152 ASN D 178 ASN G 147 ASN H 329 GLN H 422 ASN I 469 ASN J 112 GLN J 125 GLN K 469 ASN L 529 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.159501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.122515 restraints weight = 26104.350| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.16 r_work: 0.3237 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21260 Z= 0.173 Angle : 0.659 19.567 29015 Z= 0.326 Chirality : 0.044 0.306 3359 Planarity : 0.005 0.072 3456 Dihedral : 15.547 175.379 3752 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.80 % Favored : 97.03 % Rotamer: Outliers : 2.18 % Allowed : 20.68 % Favored : 77.13 % 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: -1.36 (0.16), residues: 2390 helix: 0.22 (0.17), residues: 820 sheet: -0.70 (0.23), residues: 464 loop : -1.85 (0.16), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 121 TYR 0.010 0.001 TYR H 180 PHE 0.016 0.002 PHE G 41 TRP 0.011 0.001 TRP H 564 HIS 0.005 0.001 HIS L 553 Details of bonding type rmsd covalent geometry : bond 0.00384 (21232) covalent geometry : angle 0.59998 (28977) SS BOND : bond 0.02598 ( 1) SS BOND : angle 5.49416 ( 2) hydrogen bonds : bond 0.03756 ( 916) hydrogen bonds : angle 5.05858 ( 2636) metal coordination : bond 0.01241 ( 27) metal coordination : angle 7.63959 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 359 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: B 55 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6735 (mp) REVERT: B 75 GLU cc_start: 0.6235 (tp30) cc_final: 0.5663 (mm-30) REVERT: B 93 MET cc_start: 0.5680 (mmm) cc_final: 0.5209 (mmm) REVERT: B 137 GLU cc_start: 0.4909 (pm20) cc_final: 0.3754 (mt-10) REVERT: B 191 GLU cc_start: 0.6677 (tp30) cc_final: 0.6369 (tm-30) REVERT: C 69 ASN cc_start: 0.8195 (p0) cc_final: 0.7820 (p0) REVERT: C 123 GLU cc_start: 0.6373 (mm-30) cc_final: 0.5695 (mm-30) REVERT: C 162 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8294 (mt0) REVERT: D 6 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8084 (tptt) REVERT: D 154 GLN cc_start: 0.8213 (mp10) cc_final: 0.7943 (mp10) REVERT: E 4 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.7882 (t) REVERT: G 25 LEU cc_start: 0.8599 (mt) cc_final: 0.8394 (mt) REVERT: G 57 ASP cc_start: 0.8260 (m-30) cc_final: 0.7757 (t70) REVERT: G 103 ARG cc_start: 0.7918 (mmm-85) cc_final: 0.7611 (mmm-85) REVERT: H 116 ASP cc_start: 0.7154 (t70) cc_final: 0.6931 (t0) REVERT: H 119 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7755 (mm-30) REVERT: H 123 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8043 (mp0) REVERT: H 126 ASP cc_start: 0.8148 (t0) cc_final: 0.7775 (t0) REVERT: H 127 GLU cc_start: 0.8375 (pm20) cc_final: 0.8171 (pm20) REVERT: H 301 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7986 (tp30) REVERT: H 331 LYS cc_start: 0.8081 (mtpt) cc_final: 0.7450 (tppt) REVERT: H 461 GLU cc_start: 0.7858 (tt0) cc_final: 0.7200 (mt-10) REVERT: I 469 ASN cc_start: 0.8119 (OUTLIER) cc_final: 0.7812 (m-40) REVERT: K 25 ILE cc_start: 0.6553 (mp) cc_final: 0.6281 (mt) REVERT: K 165 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7288 (tm) REVERT: K 444 MET cc_start: 0.6545 (mmm) cc_final: 0.5732 (mmm) REVERT: K 451 ARG cc_start: 0.6366 (mmm160) cc_final: 0.6143 (mmm160) REVERT: K 561 ARG cc_start: 0.7523 (ptm-80) cc_final: 0.6993 (mtm110) REVERT: K 601 ILE cc_start: 0.8151 (mm) cc_final: 0.7810 (mt) REVERT: L 529 ASN cc_start: 0.7712 (m-40) cc_final: 0.6665 (t0) REVERT: L 600 ASN cc_start: 0.7944 (m-40) cc_final: 0.6476 (p0) outliers start: 44 outliers final: 24 residues processed: 391 average time/residue: 0.1680 time to fit residues: 96.5042 Evaluate side-chains 345 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 314 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 162 GLN Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 110 LYS Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 369 SER Chi-restraints excluded: chain H residue 446 ASN Chi-restraints excluded: chain H residue 549 ILE Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain I residue 469 ASN Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 453 MET Chi-restraints excluded: chain L residue 439 ILE Chi-restraints excluded: chain L residue 568 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 37 optimal weight: 0.9980 chunk 151 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 178 optimal weight: 0.7980 chunk 169 optimal weight: 6.9990 chunk 193 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN H 438 ASN H 469 ASN I 522 ASN I 542 GLN I 600 ASN J 125 GLN K 510 HIS K 529 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.156208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.119397 restraints weight = 26396.695| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.24 r_work: 0.3170 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 21260 Z= 0.195 Angle : 0.635 19.017 29015 Z= 0.312 Chirality : 0.044 0.272 3359 Planarity : 0.004 0.056 3456 Dihedral : 15.400 178.307 3745 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.47 % Favored : 96.40 % Rotamer: Outliers : 3.32 % Allowed : 21.08 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.16), residues: 2390 helix: 0.98 (0.18), residues: 826 sheet: -0.61 (0.23), residues: 454 loop : -1.66 (0.16), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 95 TYR 0.024 0.001 TYR I 599 PHE 0.015 0.002 PHE C 133 TRP 0.013 0.001 TRP H 125 HIS 0.004 0.001 HIS L 553 Details of bonding type rmsd covalent geometry : bond 0.00448 (21232) covalent geometry : angle 0.57977 (28977) SS BOND : bond 0.00291 ( 1) SS BOND : angle 4.37811 ( 2) hydrogen bonds : bond 0.03569 ( 916) hydrogen bonds : angle 4.69670 ( 2636) metal coordination : bond 0.01052 ( 27) metal coordination : angle 7.27562 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 323 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: B 55 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6815 (mp) REVERT: B 75 GLU cc_start: 0.6375 (tp30) cc_final: 0.5929 (mm-30) REVERT: B 77 ARG cc_start: 0.6413 (mtm180) cc_final: 0.5389 (mtt180) REVERT: B 93 MET cc_start: 0.5649 (mmm) cc_final: 0.5402 (mmm) REVERT: B 137 GLU cc_start: 0.4925 (pm20) cc_final: 0.3744 (mt-10) REVERT: B 191 GLU cc_start: 0.6657 (tp30) cc_final: 0.6333 (tm-30) REVERT: C 5 MET cc_start: 0.8584 (mtm) cc_final: 0.8330 (mtm) REVERT: C 69 ASN cc_start: 0.8321 (p0) cc_final: 0.8003 (p0) REVERT: C 123 GLU cc_start: 0.6476 (mm-30) cc_final: 0.5818 (mm-30) REVERT: C 162 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8381 (mt0) REVERT: D 154 GLN cc_start: 0.8180 (mp10) cc_final: 0.7805 (mp10) REVERT: E 62 MET cc_start: 0.9258 (mtm) cc_final: 0.8962 (mtm) REVERT: E 69 ASN cc_start: 0.7428 (p0) cc_final: 0.7014 (m110) REVERT: G 57 ASP cc_start: 0.8315 (m-30) cc_final: 0.7776 (t70) REVERT: G 98 ARG cc_start: 0.8658 (mmt-90) cc_final: 0.8323 (mmt-90) REVERT: G 103 ARG cc_start: 0.7989 (mmm-85) cc_final: 0.7746 (mmm-85) REVERT: H 79 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7320 (mmpt) REVERT: H 116 ASP cc_start: 0.7346 (t70) cc_final: 0.7075 (t0) REVERT: H 119 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7708 (mm-30) REVERT: H 123 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7827 (mp0) REVERT: H 126 ASP cc_start: 0.8254 (t0) cc_final: 0.7849 (t0) REVERT: H 184 MET cc_start: 0.8581 (mtm) cc_final: 0.8200 (mtm) REVERT: H 331 LYS cc_start: 0.8085 (mtpt) cc_final: 0.7461 (tptt) REVERT: H 461 GLU cc_start: 0.7887 (tt0) cc_final: 0.7367 (mt-10) REVERT: I 469 ASN cc_start: 0.7646 (m110) cc_final: 0.7221 (m-40) REVERT: I 588 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7991 (mp) REVERT: I 599 TYR cc_start: 0.8623 (t80) cc_final: 0.8411 (t80) REVERT: J 140 GLU cc_start: 0.9255 (mp0) cc_final: 0.9031 (mp0) REVERT: K 444 MET cc_start: 0.6548 (mmm) cc_final: 0.5941 (mmm) REVERT: K 561 ARG cc_start: 0.7591 (ptm-80) cc_final: 0.6916 (mtm110) REVERT: L 462 LYS cc_start: 0.7247 (mptt) cc_final: 0.7040 (mptt) REVERT: L 529 ASN cc_start: 0.7694 (m-40) cc_final: 0.6737 (t0) outliers start: 67 outliers final: 34 residues processed: 372 average time/residue: 0.1790 time to fit residues: 96.7150 Evaluate side-chains 336 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 297 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 162 GLN Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 110 LYS Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 257 MET Chi-restraints excluded: chain H residue 259 SER Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 369 SER Chi-restraints excluded: chain H residue 549 ILE Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain I residue 552 VAL Chi-restraints excluded: chain I residue 588 LEU Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 62 HIS Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain L residue 439 ILE Chi-restraints excluded: chain L residue 523 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 33 optimal weight: 0.7980 chunk 128 optimal weight: 0.4980 chunk 167 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 145 optimal weight: 0.5980 chunk 159 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 24 optimal weight: 0.0970 chunk 163 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 510 HIS I 542 GLN J 112 GLN J 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.159627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.122880 restraints weight = 26350.537| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.13 r_work: 0.3245 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 21260 Z= 0.112 Angle : 0.557 15.436 29015 Z= 0.278 Chirality : 0.042 0.339 3359 Planarity : 0.003 0.048 3456 Dihedral : 15.350 177.808 3745 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.47 % Favored : 97.41 % Rotamer: Outliers : 2.58 % Allowed : 21.68 % Favored : 75.74 % 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: -0.40 (0.16), residues: 2390 helix: 1.53 (0.18), residues: 823 sheet: -0.60 (0.23), residues: 458 loop : -1.53 (0.17), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 95 TYR 0.012 0.001 TYR I 599 PHE 0.014 0.001 PHE C 133 TRP 0.014 0.001 TRP H 478 HIS 0.004 0.001 HIS L 553 Details of bonding type rmsd covalent geometry : bond 0.00244 (21232) covalent geometry : angle 0.51356 (28977) SS BOND : bond 0.00469 ( 1) SS BOND : angle 3.70284 ( 2) hydrogen bonds : bond 0.03209 ( 916) hydrogen bonds : angle 4.39577 ( 2636) metal coordination : bond 0.00644 ( 27) metal coordination : angle 6.10376 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 328 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 75 GLU cc_start: 0.6283 (tp30) cc_final: 0.5788 (mm-30) REVERT: B 77 ARG cc_start: 0.6205 (mtm180) cc_final: 0.5440 (mtt180) REVERT: B 140 GLU cc_start: 0.3650 (mm-30) cc_final: 0.3163 (mm-30) REVERT: B 191 GLU cc_start: 0.6487 (tp30) cc_final: 0.6178 (tm-30) REVERT: C 5 MET cc_start: 0.8586 (mtm) cc_final: 0.8385 (mtm) REVERT: C 69 ASN cc_start: 0.8326 (p0) cc_final: 0.7974 (p0) REVERT: C 112 GLN cc_start: 0.8533 (mm-40) cc_final: 0.8257 (mm-40) REVERT: C 123 GLU cc_start: 0.6582 (mm-30) cc_final: 0.5957 (mm-30) REVERT: D 93 MET cc_start: 0.8600 (tpp) cc_final: 0.8281 (tpp) REVERT: D 154 GLN cc_start: 0.8142 (mp10) cc_final: 0.7734 (mp10) REVERT: E 62 MET cc_start: 0.9201 (mtm) cc_final: 0.8957 (mtm) REVERT: E 69 ASN cc_start: 0.7282 (p0) cc_final: 0.6939 (m110) REVERT: E 112 GLN cc_start: 0.8684 (mt0) cc_final: 0.8361 (mt0) REVERT: G 57 ASP cc_start: 0.8268 (m-30) cc_final: 0.7744 (t70) REVERT: G 98 ARG cc_start: 0.8622 (mmt-90) cc_final: 0.8246 (mmt-90) REVERT: H 116 ASP cc_start: 0.7286 (t70) cc_final: 0.7061 (t0) REVERT: H 119 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7565 (mm-30) REVERT: H 123 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7756 (mp0) REVERT: H 126 ASP cc_start: 0.8147 (t0) cc_final: 0.7776 (t0) REVERT: H 127 GLU cc_start: 0.8338 (pm20) cc_final: 0.8102 (pm20) REVERT: H 184 MET cc_start: 0.8539 (mtm) cc_final: 0.8172 (mtm) REVERT: H 301 GLU cc_start: 0.8546 (tp30) cc_final: 0.8328 (tp30) REVERT: H 331 LYS cc_start: 0.7895 (mtpt) cc_final: 0.7388 (tptt) REVERT: H 461 GLU cc_start: 0.7801 (tt0) cc_final: 0.7338 (mt-10) REVERT: I 469 ASN cc_start: 0.8004 (m110) cc_final: 0.7651 (m-40) REVERT: I 522 ASN cc_start: 0.9086 (m-40) cc_final: 0.8839 (m110) REVERT: I 588 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7898 (mp) REVERT: I 599 TYR cc_start: 0.8632 (t80) cc_final: 0.8382 (t80) REVERT: J 62 MET cc_start: 0.8910 (mtm) cc_final: 0.8702 (mtp) REVERT: J 140 GLU cc_start: 0.9193 (mp0) cc_final: 0.8980 (mp0) REVERT: K 141 ILE cc_start: 0.7267 (mt) cc_final: 0.7052 (tt) REVERT: K 165 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7395 (tm) REVERT: K 444 MET cc_start: 0.6808 (mmm) cc_final: 0.5929 (mmm) REVERT: K 451 ARG cc_start: 0.6216 (mmm160) cc_final: 0.5878 (mmm160) REVERT: K 561 ARG cc_start: 0.7467 (ptm-80) cc_final: 0.6991 (mtm110) REVERT: L 529 ASN cc_start: 0.7716 (m-40) cc_final: 0.6646 (t0) REVERT: L 600 ASN cc_start: 0.7539 (m-40) cc_final: 0.6237 (p0) outliers start: 52 outliers final: 36 residues processed: 361 average time/residue: 0.1739 time to fit residues: 91.1261 Evaluate side-chains 346 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 307 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 110 LYS Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 257 MET Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 439 ILE Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain H residue 514 ILE Chi-restraints excluded: chain H residue 549 ILE Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain I residue 475 ASP Chi-restraints excluded: chain I residue 588 LEU Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 123 GLU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 62 HIS Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 453 MET Chi-restraints excluded: chain L residue 439 ILE Chi-restraints excluded: chain L residue 456 SER Chi-restraints excluded: chain L residue 523 ILE Chi-restraints excluded: chain L residue 568 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 7 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 231 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 HIS F 171 ASN H 516 ASN I 606 ASN J 112 GLN J 125 GLN K 529 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.151537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.113278 restraints weight = 26396.452| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.22 r_work: 0.3087 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 21260 Z= 0.308 Angle : 0.720 22.830 29015 Z= 0.349 Chirality : 0.047 0.238 3359 Planarity : 0.004 0.051 3456 Dihedral : 15.334 179.159 3745 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.64 % Favored : 96.28 % Rotamer: Outliers : 3.72 % Allowed : 21.68 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.17), residues: 2390 helix: 1.44 (0.18), residues: 826 sheet: -0.63 (0.24), residues: 440 loop : -1.53 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 95 TYR 0.017 0.002 TYR H 180 PHE 0.020 0.002 PHE L 458 TRP 0.020 0.002 TRP H 125 HIS 0.006 0.001 HIS L 553 Details of bonding type rmsd covalent geometry : bond 0.00717 (21232) covalent geometry : angle 0.65660 (28977) SS BOND : bond 0.00976 ( 1) SS BOND : angle 5.41337 ( 2) hydrogen bonds : bond 0.03850 ( 916) hydrogen bonds : angle 4.64588 ( 2636) metal coordination : bond 0.01484 ( 27) metal coordination : angle 8.29474 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 306 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 75 GLU cc_start: 0.6259 (tp30) cc_final: 0.5612 (mm-30) REVERT: B 77 ARG cc_start: 0.6437 (mtm180) cc_final: 0.5577 (mtt180) REVERT: B 191 GLU cc_start: 0.6540 (tp30) cc_final: 0.6289 (tm-30) REVERT: C 69 ASN cc_start: 0.8472 (p0) cc_final: 0.8173 (p0) REVERT: C 123 GLU cc_start: 0.6512 (mm-30) cc_final: 0.5675 (mm-30) REVERT: D 93 MET cc_start: 0.8810 (tpp) cc_final: 0.8473 (tpp) REVERT: D 154 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7573 (mp10) REVERT: E 152 ASN cc_start: 0.8679 (m-40) cc_final: 0.8462 (t0) REVERT: G 57 ASP cc_start: 0.8391 (m-30) cc_final: 0.7929 (t70) REVERT: G 98 ARG cc_start: 0.8674 (mmt-90) cc_final: 0.8474 (mmt-90) REVERT: G 99 ASN cc_start: 0.8444 (m110) cc_final: 0.8167 (m110) REVERT: H 78 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7367 (ttm110) REVERT: H 79 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7566 (mmpt) REVERT: H 119 GLU cc_start: 0.8485 (mm-30) cc_final: 0.7919 (mm-30) REVERT: H 123 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: H 126 ASP cc_start: 0.8316 (t0) cc_final: 0.7894 (t0) REVERT: H 184 MET cc_start: 0.8644 (mtm) cc_final: 0.8232 (mtt) REVERT: H 195 GLU cc_start: 0.8334 (mp0) cc_final: 0.7993 (mm-30) REVERT: H 275 LYS cc_start: 0.8836 (ttpt) cc_final: 0.8521 (tptt) REVERT: H 331 LYS cc_start: 0.7973 (mtpt) cc_final: 0.7471 (tppt) REVERT: H 341 VAL cc_start: 0.9338 (m) cc_final: 0.9032 (p) REVERT: H 461 GLU cc_start: 0.7881 (tt0) cc_final: 0.7303 (mt-10) REVERT: I 438 ASN cc_start: 0.6929 (m-40) cc_final: 0.6503 (m-40) REVERT: I 439 ILE cc_start: 0.7201 (OUTLIER) cc_final: 0.6954 (tp) REVERT: I 469 ASN cc_start: 0.8175 (m110) cc_final: 0.7479 (m-40) REVERT: I 599 TYR cc_start: 0.8694 (t80) cc_final: 0.8415 (t80) REVERT: K 165 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7509 (tm) REVERT: K 444 MET cc_start: 0.6638 (mmm) cc_final: 0.6153 (mmm) REVERT: K 451 ARG cc_start: 0.6557 (mmm160) cc_final: 0.6326 (mmm160) REVERT: L 529 ASN cc_start: 0.7821 (m-40) cc_final: 0.6815 (t0) outliers start: 75 outliers final: 49 residues processed: 359 average time/residue: 0.1864 time to fit residues: 96.8261 Evaluate side-chains 348 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 293 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 110 LYS Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 78 ARG Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 257 MET Chi-restraints excluded: chain H residue 259 SER Chi-restraints excluded: chain H residue 369 SER Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain H residue 514 ILE Chi-restraints excluded: chain H residue 523 ILE Chi-restraints excluded: chain H residue 549 ILE Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain I residue 439 ILE Chi-restraints excluded: chain I residue 475 ASP Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 62 HIS Chi-restraints excluded: chain K residue 80 VAL Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 146 ASN Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 513 ILE Chi-restraints excluded: chain K residue 514 ILE Chi-restraints excluded: chain L residue 439 ILE Chi-restraints excluded: chain L residue 456 SER Chi-restraints excluded: chain L residue 523 ILE Chi-restraints excluded: chain L residue 553 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 195 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 217 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 211 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 179 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 107 ASN F 171 ASN F 178 ASN H 326 HIS I 469 ASN I 542 GLN J 112 GLN J 125 GLN K 376 GLN K 402 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.156193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.118182 restraints weight = 26266.435| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.10 r_work: 0.3168 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21260 Z= 0.142 Angle : 0.586 18.358 29015 Z= 0.290 Chirality : 0.043 0.307 3359 Planarity : 0.003 0.049 3456 Dihedral : 15.318 177.275 3745 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.59 % Favored : 97.32 % Rotamer: Outliers : 3.08 % Allowed : 22.47 % Favored : 74.45 % 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: -0.20 (0.17), residues: 2390 helix: 1.75 (0.18), residues: 828 sheet: -0.49 (0.24), residues: 443 loop : -1.46 (0.17), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 197 TYR 0.010 0.001 TYR H 180 PHE 0.016 0.001 PHE L 458 TRP 0.012 0.001 TRP H 478 HIS 0.005 0.001 HIS L 553 Details of bonding type rmsd covalent geometry : bond 0.00320 (21232) covalent geometry : angle 0.53641 (28977) SS BOND : bond 0.00146 ( 1) SS BOND : angle 5.02831 ( 2) hydrogen bonds : bond 0.03281 ( 916) hydrogen bonds : angle 4.39388 ( 2636) metal coordination : bond 0.00838 ( 27) metal coordination : angle 6.58401 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 317 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: B 75 GLU cc_start: 0.6245 (tp30) cc_final: 0.5712 (mm-30) REVERT: B 77 ARG cc_start: 0.6370 (mtm180) cc_final: 0.5501 (mtt180) REVERT: B 93 MET cc_start: 0.5162 (tmm) cc_final: 0.2927 (tmm) REVERT: B 191 GLU cc_start: 0.6626 (tp30) cc_final: 0.6185 (tm-30) REVERT: C 69 ASN cc_start: 0.8299 (p0) cc_final: 0.8025 (p0) REVERT: C 123 GLU cc_start: 0.6558 (mm-30) cc_final: 0.5904 (mm-30) REVERT: D 154 GLN cc_start: 0.8162 (mp10) cc_final: 0.7782 (mp10) REVERT: E 62 MET cc_start: 0.9208 (mtm) cc_final: 0.8950 (mtm) REVERT: E 75 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7738 (pp20) REVERT: G 57 ASP cc_start: 0.8340 (m-30) cc_final: 0.7885 (t70) REVERT: G 99 ASN cc_start: 0.8374 (m110) cc_final: 0.8128 (m110) REVERT: H 78 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7391 (ttm110) REVERT: H 79 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7449 (mmpt) REVERT: H 119 GLU cc_start: 0.8452 (mm-30) cc_final: 0.7858 (mm-30) REVERT: H 123 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: H 126 ASP cc_start: 0.8175 (t0) cc_final: 0.7779 (t0) REVERT: H 184 MET cc_start: 0.8591 (mtm) cc_final: 0.8283 (mtm) REVERT: H 195 GLU cc_start: 0.8283 (mp0) cc_final: 0.7927 (mm-30) REVERT: H 331 LYS cc_start: 0.7938 (mtpt) cc_final: 0.7397 (tppt) REVERT: H 341 VAL cc_start: 0.9321 (m) cc_final: 0.8995 (p) REVERT: H 461 GLU cc_start: 0.7803 (tt0) cc_final: 0.7258 (mt-10) REVERT: I 469 ASN cc_start: 0.8296 (OUTLIER) cc_final: 0.7654 (m-40) REVERT: I 599 TYR cc_start: 0.8678 (t80) cc_final: 0.8380 (t80) REVERT: K 165 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7421 (tm) REVERT: K 444 MET cc_start: 0.6679 (mmm) cc_final: 0.5986 (mmm) REVERT: K 451 ARG cc_start: 0.6503 (mmm160) cc_final: 0.6249 (mmm160) REVERT: K 561 ARG cc_start: 0.7765 (ptm-80) cc_final: 0.7041 (mtm110) REVERT: L 529 ASN cc_start: 0.7755 (m-40) cc_final: 0.6837 (t0) REVERT: L 600 ASN cc_start: 0.7484 (m-40) cc_final: 0.6110 (p0) outliers start: 62 outliers final: 41 residues processed: 362 average time/residue: 0.1756 time to fit residues: 92.1008 Evaluate side-chains 348 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 301 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 110 LYS Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 78 ARG Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 257 MET Chi-restraints excluded: chain H residue 259 SER Chi-restraints excluded: chain H residue 369 SER Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain H residue 514 ILE Chi-restraints excluded: chain H residue 523 ILE Chi-restraints excluded: chain H residue 549 ILE Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain I residue 469 ASN Chi-restraints excluded: chain I residue 475 ASP Chi-restraints excluded: chain I residue 552 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 62 HIS Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 505 LEU Chi-restraints excluded: chain K residue 514 ILE Chi-restraints excluded: chain L residue 439 ILE Chi-restraints excluded: chain L residue 523 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 204 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 240 optimal weight: 10.0000 chunk 222 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 161 optimal weight: 0.0970 chunk 241 optimal weight: 5.9990 chunk 223 optimal weight: 0.6980 chunk 139 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 171 ASN I 469 ASN I 542 GLN J 112 GLN J 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.152652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.115405 restraints weight = 26497.866| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.11 r_work: 0.3129 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 21260 Z= 0.220 Angle : 0.631 19.919 29015 Z= 0.309 Chirality : 0.044 0.264 3359 Planarity : 0.004 0.048 3456 Dihedral : 15.267 177.129 3745 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.64 % Favored : 96.28 % Rotamer: Outliers : 3.52 % Allowed : 21.83 % Favored : 74.65 % 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: -0.24 (0.17), residues: 2390 helix: 1.70 (0.18), residues: 836 sheet: -0.58 (0.24), residues: 445 loop : -1.47 (0.17), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 95 TYR 0.013 0.001 TYR H 268 PHE 0.017 0.002 PHE L 458 TRP 0.011 0.001 TRP H 478 HIS 0.006 0.001 HIS L 553 Details of bonding type rmsd covalent geometry : bond 0.00512 (21232) covalent geometry : angle 0.57885 (28977) SS BOND : bond 0.00293 ( 1) SS BOND : angle 5.60401 ( 2) hydrogen bonds : bond 0.03409 ( 916) hydrogen bonds : angle 4.45078 ( 2636) metal coordination : bond 0.01088 ( 27) metal coordination : angle 7.06182 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 296 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: B 75 GLU cc_start: 0.6270 (tp30) cc_final: 0.5744 (mm-30) REVERT: B 77 ARG cc_start: 0.6384 (mtm180) cc_final: 0.5552 (mtt180) REVERT: B 93 MET cc_start: 0.5258 (tmm) cc_final: 0.3462 (tmm) REVERT: B 191 GLU cc_start: 0.6691 (tp30) cc_final: 0.6283 (tm-30) REVERT: C 69 ASN cc_start: 0.8504 (p0) cc_final: 0.8128 (p0) REVERT: C 123 GLU cc_start: 0.6569 (mm-30) cc_final: 0.5879 (mm-30) REVERT: D 154 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7826 (mp10) REVERT: E 62 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.8958 (mtm) REVERT: F 191 GLU cc_start: 0.7424 (tm-30) cc_final: 0.6892 (tm-30) REVERT: G 57 ASP cc_start: 0.8311 (m-30) cc_final: 0.7905 (t70) REVERT: G 99 ASN cc_start: 0.8447 (m110) cc_final: 0.8179 (m110) REVERT: H 78 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7396 (ttm110) REVERT: H 79 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7489 (mmpt) REVERT: H 119 GLU cc_start: 0.8469 (mm-30) cc_final: 0.7854 (mm-30) REVERT: H 123 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7605 (mp0) REVERT: H 126 ASP cc_start: 0.8249 (t0) cc_final: 0.7849 (t0) REVERT: H 184 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8288 (mtm) REVERT: H 195 GLU cc_start: 0.8370 (mp0) cc_final: 0.8000 (mm-30) REVERT: H 275 LYS cc_start: 0.8839 (ttpt) cc_final: 0.8521 (tptt) REVERT: H 331 LYS cc_start: 0.7969 (mtpt) cc_final: 0.7439 (tppt) REVERT: H 341 VAL cc_start: 0.9317 (m) cc_final: 0.8974 (p) REVERT: H 461 GLU cc_start: 0.7835 (tt0) cc_final: 0.7256 (mt-10) REVERT: I 438 ASN cc_start: 0.7004 (m-40) cc_final: 0.6577 (m-40) REVERT: I 469 ASN cc_start: 0.8268 (OUTLIER) cc_final: 0.7960 (m-40) REVERT: I 599 TYR cc_start: 0.8664 (t80) cc_final: 0.8387 (t80) REVERT: K 165 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7563 (tm) REVERT: K 444 MET cc_start: 0.6787 (mmm) cc_final: 0.6173 (mmm) REVERT: K 529 ASN cc_start: 0.8468 (m-40) cc_final: 0.8106 (m110) REVERT: K 561 ARG cc_start: 0.7856 (ptm-80) cc_final: 0.6960 (mtm110) REVERT: L 529 ASN cc_start: 0.7758 (m-40) cc_final: 0.6806 (t0) outliers start: 71 outliers final: 50 residues processed: 346 average time/residue: 0.1699 time to fit residues: 85.7405 Evaluate side-chains 351 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 293 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 110 LYS Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain G residue 56 PHE Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 78 ARG Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 184 MET Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 257 MET Chi-restraints excluded: chain H residue 259 SER Chi-restraints excluded: chain H residue 326 HIS Chi-restraints excluded: chain H residue 369 SER Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain H residue 514 ILE Chi-restraints excluded: chain H residue 523 ILE Chi-restraints excluded: chain H residue 549 ILE Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain I residue 469 ASN Chi-restraints excluded: chain I residue 475 ASP Chi-restraints excluded: chain I residue 552 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 62 HIS Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 146 ASN Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 505 LEU Chi-restraints excluded: chain K residue 514 ILE Chi-restraints excluded: chain L residue 439 ILE Chi-restraints excluded: chain L residue 456 SER Chi-restraints excluded: chain L residue 523 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 82 optimal weight: 7.9990 chunk 242 optimal weight: 8.9990 chunk 146 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 174 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 144 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 195 optimal weight: 0.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 171 ASN H 22 ASN I 488 GLN I 542 GLN J 112 GLN J 125 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.154829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.117267 restraints weight = 26236.987| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.17 r_work: 0.3156 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21260 Z= 0.174 Angle : 0.600 19.017 29015 Z= 0.295 Chirality : 0.043 0.277 3359 Planarity : 0.003 0.050 3456 Dihedral : 15.277 176.405 3745 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.39 % Favored : 96.57 % Rotamer: Outliers : 3.47 % Allowed : 22.17 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2390 helix: 1.83 (0.18), residues: 835 sheet: -0.54 (0.24), residues: 451 loop : -1.44 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 95 TYR 0.010 0.001 TYR H 180 PHE 0.021 0.002 PHE B 51 TRP 0.011 0.001 TRP H 478 HIS 0.006 0.001 HIS L 553 Details of bonding type rmsd covalent geometry : bond 0.00402 (21232) covalent geometry : angle 0.54998 (28977) SS BOND : bond 0.00043 ( 1) SS BOND : angle 5.53751 ( 2) hydrogen bonds : bond 0.03270 ( 916) hydrogen bonds : angle 4.39635 ( 2636) metal coordination : bond 0.00901 ( 27) metal coordination : angle 6.70086 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 309 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: B 75 GLU cc_start: 0.6287 (tp30) cc_final: 0.5747 (mm-30) REVERT: B 77 ARG cc_start: 0.6360 (mtm180) cc_final: 0.5501 (mtt180) REVERT: B 93 MET cc_start: 0.5281 (tmm) cc_final: 0.3522 (tmm) REVERT: B 140 GLU cc_start: 0.3936 (mm-30) cc_final: 0.2958 (mm-30) REVERT: B 191 GLU cc_start: 0.6559 (tp30) cc_final: 0.6172 (tm-30) REVERT: C 69 ASN cc_start: 0.8463 (p0) cc_final: 0.8069 (p0) REVERT: C 123 GLU cc_start: 0.6552 (mm-30) cc_final: 0.5862 (mm-30) REVERT: D 111 GLU cc_start: 0.9043 (mp0) cc_final: 0.8824 (mp0) REVERT: D 154 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7808 (mp10) REVERT: E 62 MET cc_start: 0.9196 (mtm) cc_final: 0.8933 (mtm) REVERT: F 191 GLU cc_start: 0.7406 (tm-30) cc_final: 0.6878 (tm-30) REVERT: G 57 ASP cc_start: 0.8291 (m-30) cc_final: 0.7913 (t70) REVERT: G 99 ASN cc_start: 0.8428 (m110) cc_final: 0.8159 (m110) REVERT: H 59 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8168 (mm) REVERT: H 78 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7415 (ttm110) REVERT: H 79 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7460 (mmpt) REVERT: H 116 ASP cc_start: 0.7201 (t70) cc_final: 0.6974 (t0) REVERT: H 119 GLU cc_start: 0.8446 (mm-30) cc_final: 0.7838 (mm-30) REVERT: H 123 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: H 126 ASP cc_start: 0.8207 (t0) cc_final: 0.7810 (t0) REVERT: H 184 MET cc_start: 0.8624 (mtm) cc_final: 0.8293 (mtm) REVERT: H 195 GLU cc_start: 0.8362 (mp0) cc_final: 0.7977 (mm-30) REVERT: H 275 LYS cc_start: 0.8827 (ttpt) cc_final: 0.8513 (tptt) REVERT: H 331 LYS cc_start: 0.7942 (mtpt) cc_final: 0.7470 (tppt) REVERT: H 341 VAL cc_start: 0.9304 (m) cc_final: 0.9017 (p) REVERT: H 461 GLU cc_start: 0.7806 (tt0) cc_final: 0.7224 (mt-10) REVERT: H 604 ASN cc_start: 0.8342 (t0) cc_final: 0.8133 (t0) REVERT: I 438 ASN cc_start: 0.6946 (m-40) cc_final: 0.6489 (m-40) REVERT: I 469 ASN cc_start: 0.7895 (m110) cc_final: 0.7646 (m-40) REVERT: I 599 TYR cc_start: 0.8665 (t80) cc_final: 0.8323 (t80) REVERT: K 165 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7528 (tm) REVERT: K 444 MET cc_start: 0.6573 (mmm) cc_final: 0.5921 (mmm) REVERT: K 561 ARG cc_start: 0.7849 (ptm-80) cc_final: 0.6966 (mtm110) REVERT: L 529 ASN cc_start: 0.7749 (m-40) cc_final: 0.6798 (t0) REVERT: L 600 ASN cc_start: 0.7379 (m-40) cc_final: 0.5950 (p0) outliers start: 70 outliers final: 56 residues processed: 360 average time/residue: 0.1814 time to fit residues: 95.2720 Evaluate side-chains 357 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 295 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 110 LYS Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain G residue 56 PHE Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 78 ARG Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 257 MET Chi-restraints excluded: chain H residue 259 SER Chi-restraints excluded: chain H residue 265 ILE Chi-restraints excluded: chain H residue 326 HIS Chi-restraints excluded: chain H residue 369 SER Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain H residue 514 ILE Chi-restraints excluded: chain H residue 523 ILE Chi-restraints excluded: chain H residue 549 ILE Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain I residue 475 ASP Chi-restraints excluded: chain I residue 505 LEU Chi-restraints excluded: chain I residue 513 ILE Chi-restraints excluded: chain I residue 552 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 62 HIS Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 146 ASN Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 514 ILE Chi-restraints excluded: chain L residue 439 ILE Chi-restraints excluded: chain L residue 456 SER Chi-restraints excluded: chain L residue 476 MET Chi-restraints excluded: chain L residue 523 ILE Chi-restraints excluded: chain L residue 568 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 64 optimal weight: 0.4980 chunk 61 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 193 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 206 optimal weight: 9.9990 chunk 95 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 166 optimal weight: 10.0000 chunk 231 optimal weight: 5.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 171 ASN H 22 ASN I 542 GLN J 112 GLN J 125 GLN K 529 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.154278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.116542 restraints weight = 26294.648| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.14 r_work: 0.3148 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21260 Z= 0.180 Angle : 0.606 18.728 29015 Z= 0.298 Chirality : 0.043 0.276 3359 Planarity : 0.004 0.051 3456 Dihedral : 15.270 175.803 3745 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.68 % Favored : 96.28 % Rotamer: Outliers : 3.42 % Allowed : 22.72 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.17), residues: 2390 helix: 1.92 (0.18), residues: 830 sheet: -0.53 (0.24), residues: 451 loop : -1.40 (0.17), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 95 TYR 0.010 0.001 TYR H 180 PHE 0.022 0.002 PHE H 474 TRP 0.011 0.001 TRP H 478 HIS 0.006 0.001 HIS L 553 Details of bonding type rmsd covalent geometry : bond 0.00418 (21232) covalent geometry : angle 0.55714 (28977) SS BOND : bond 0.00050 ( 1) SS BOND : angle 5.34294 ( 2) hydrogen bonds : bond 0.03262 ( 916) hydrogen bonds : angle 4.39548 ( 2636) metal coordination : bond 0.00918 ( 27) metal coordination : angle 6.64483 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 302 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: B 75 GLU cc_start: 0.6272 (tp30) cc_final: 0.5732 (mm-30) REVERT: B 77 ARG cc_start: 0.6333 (mtm180) cc_final: 0.5442 (mtt180) REVERT: B 93 MET cc_start: 0.5347 (tmm) cc_final: 0.3639 (tmm) REVERT: B 140 GLU cc_start: 0.4049 (mm-30) cc_final: 0.3034 (mm-30) REVERT: B 191 GLU cc_start: 0.6428 (tp30) cc_final: 0.6141 (tm-30) REVERT: C 69 ASN cc_start: 0.8498 (p0) cc_final: 0.8058 (p0) REVERT: C 123 GLU cc_start: 0.6594 (mm-30) cc_final: 0.5891 (mm-30) REVERT: D 154 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7811 (mp10) REVERT: E 62 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8937 (mtm) REVERT: E 192 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.8111 (m-30) REVERT: F 191 GLU cc_start: 0.7406 (tm-30) cc_final: 0.6887 (tm-30) REVERT: G 57 ASP cc_start: 0.8281 (m-30) cc_final: 0.7915 (t70) REVERT: G 99 ASN cc_start: 0.8448 (m110) cc_final: 0.8173 (m110) REVERT: H 59 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8172 (mm) REVERT: H 78 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7457 (ttm110) REVERT: H 79 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7431 (mmpt) REVERT: H 119 GLU cc_start: 0.8460 (mm-30) cc_final: 0.7876 (mm-30) REVERT: H 123 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: H 126 ASP cc_start: 0.8229 (t0) cc_final: 0.7848 (t0) REVERT: H 184 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8301 (mtm) REVERT: H 195 GLU cc_start: 0.8406 (mp0) cc_final: 0.7988 (mm-30) REVERT: H 275 LYS cc_start: 0.8824 (ttpt) cc_final: 0.8511 (tptt) REVERT: H 331 LYS cc_start: 0.7940 (mtpt) cc_final: 0.7467 (tppt) REVERT: H 341 VAL cc_start: 0.9282 (m) cc_final: 0.8917 (p) REVERT: H 461 GLU cc_start: 0.7816 (tt0) cc_final: 0.7314 (mt-10) REVERT: H 604 ASN cc_start: 0.8356 (t0) cc_final: 0.8144 (t0) REVERT: I 438 ASN cc_start: 0.6994 (m-40) cc_final: 0.6367 (m-40) REVERT: I 469 ASN cc_start: 0.8047 (m110) cc_final: 0.7779 (m-40) REVERT: I 599 TYR cc_start: 0.8687 (t80) cc_final: 0.8359 (t80) REVERT: K 165 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7606 (tm) REVERT: K 444 MET cc_start: 0.6564 (mmm) cc_final: 0.5711 (mmm) REVERT: K 451 ARG cc_start: 0.6574 (mmm160) cc_final: 0.6255 (mmm-85) REVERT: K 561 ARG cc_start: 0.7900 (ptm-80) cc_final: 0.6956 (mtm110) REVERT: L 529 ASN cc_start: 0.7790 (m-40) cc_final: 0.6764 (t0) REVERT: L 600 ASN cc_start: 0.7426 (m-40) cc_final: 0.5995 (p0) outliers start: 69 outliers final: 55 residues processed: 351 average time/residue: 0.1711 time to fit residues: 88.0284 Evaluate side-chains 356 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 292 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 110 LYS Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain G residue 56 PHE Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 22 ASN Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 78 ARG Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 184 MET Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 257 MET Chi-restraints excluded: chain H residue 259 SER Chi-restraints excluded: chain H residue 265 ILE Chi-restraints excluded: chain H residue 326 HIS Chi-restraints excluded: chain H residue 369 SER Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain H residue 514 ILE Chi-restraints excluded: chain H residue 523 ILE Chi-restraints excluded: chain H residue 549 ILE Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain I residue 475 ASP Chi-restraints excluded: chain I residue 505 LEU Chi-restraints excluded: chain I residue 513 ILE Chi-restraints excluded: chain I residue 552 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 62 HIS Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 146 ASN Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 514 ILE Chi-restraints excluded: chain L residue 439 ILE Chi-restraints excluded: chain L residue 456 SER Chi-restraints excluded: chain L residue 476 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 107 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 202 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 187 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 221 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 171 ASN H 22 ASN H 175 GLN I 542 GLN J 45 ASN J 125 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.155732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.118255 restraints weight = 26298.694| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.04 r_work: 0.3169 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21260 Z= 0.143 Angle : 0.592 17.741 29015 Z= 0.292 Chirality : 0.043 0.288 3359 Planarity : 0.003 0.052 3456 Dihedral : 15.280 175.234 3745 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.14 % Favored : 96.82 % Rotamer: Outliers : 3.37 % Allowed : 22.42 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.17), residues: 2390 helix: 2.00 (0.18), residues: 831 sheet: -0.42 (0.24), residues: 462 loop : -1.39 (0.17), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 95 TYR 0.016 0.001 TYR K 599 PHE 0.018 0.001 PHE G 41 TRP 0.011 0.001 TRP H 478 HIS 0.006 0.001 HIS L 553 Details of bonding type rmsd covalent geometry : bond 0.00329 (21232) covalent geometry : angle 0.54758 (28977) SS BOND : bond 0.00009 ( 1) SS BOND : angle 5.54625 ( 2) hydrogen bonds : bond 0.03176 ( 916) hydrogen bonds : angle 4.34076 ( 2636) metal coordination : bond 0.00762 ( 27) metal coordination : angle 6.26618 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 311 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 ARG cc_start: 0.5429 (ttt90) cc_final: 0.5214 (ttt90) REVERT: B 75 GLU cc_start: 0.6276 (tp30) cc_final: 0.5715 (mm-30) REVERT: B 77 ARG cc_start: 0.6350 (mtm180) cc_final: 0.5459 (mtt180) REVERT: B 93 MET cc_start: 0.5307 (tmm) cc_final: 0.3716 (tmm) REVERT: B 140 GLU cc_start: 0.4106 (mm-30) cc_final: 0.3096 (mm-30) REVERT: B 191 GLU cc_start: 0.6445 (tp30) cc_final: 0.6188 (tm-30) REVERT: C 69 ASN cc_start: 0.8523 (p0) cc_final: 0.8074 (p0) REVERT: C 123 GLU cc_start: 0.6645 (mm-30) cc_final: 0.5926 (mm-30) REVERT: D 154 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7664 (mp10) REVERT: E 62 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8940 (mtm) REVERT: E 111 GLU cc_start: 0.8148 (pm20) cc_final: 0.7885 (pm20) REVERT: E 192 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.8111 (m-30) REVERT: F 191 GLU cc_start: 0.7399 (tm-30) cc_final: 0.6900 (tm-30) REVERT: G 57 ASP cc_start: 0.8252 (m-30) cc_final: 0.7901 (t70) REVERT: G 99 ASN cc_start: 0.8415 (m110) cc_final: 0.8137 (m110) REVERT: H 59 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8165 (mm) REVERT: H 78 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7427 (ttm110) REVERT: H 79 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7356 (mmpt) REVERT: H 119 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7842 (mm-30) REVERT: H 123 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7598 (mp0) REVERT: H 126 ASP cc_start: 0.8187 (t0) cc_final: 0.7806 (t0) REVERT: H 184 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8311 (mtm) REVERT: H 195 GLU cc_start: 0.8374 (mp0) cc_final: 0.7948 (mm-30) REVERT: H 275 LYS cc_start: 0.8808 (ttpt) cc_final: 0.8497 (tptt) REVERT: H 331 LYS cc_start: 0.7832 (mtpt) cc_final: 0.7457 (tppt) REVERT: H 341 VAL cc_start: 0.9272 (m) cc_final: 0.8892 (p) REVERT: H 461 GLU cc_start: 0.7804 (tt0) cc_final: 0.7335 (mt-10) REVERT: H 604 ASN cc_start: 0.8339 (t0) cc_final: 0.8115 (t0) REVERT: I 469 ASN cc_start: 0.8066 (m110) cc_final: 0.7814 (m-40) REVERT: I 599 TYR cc_start: 0.8689 (t80) cc_final: 0.8353 (t80) REVERT: K 165 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7543 (tm) REVERT: K 451 ARG cc_start: 0.6600 (mmm160) cc_final: 0.6321 (mmm-85) REVERT: K 561 ARG cc_start: 0.7851 (ptm-80) cc_final: 0.6893 (mtm110) REVERT: L 529 ASN cc_start: 0.7784 (m-40) cc_final: 0.6800 (t0) REVERT: L 600 ASN cc_start: 0.7456 (m-40) cc_final: 0.5996 (p0) outliers start: 68 outliers final: 54 residues processed: 357 average time/residue: 0.1911 time to fit residues: 99.0946 Evaluate side-chains 368 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 305 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 110 LYS Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain G residue 56 PHE Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 78 ARG Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 184 MET Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 257 MET Chi-restraints excluded: chain H residue 259 SER Chi-restraints excluded: chain H residue 265 ILE Chi-restraints excluded: chain H residue 326 HIS Chi-restraints excluded: chain H residue 369 SER Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain H residue 514 ILE Chi-restraints excluded: chain H residue 523 ILE Chi-restraints excluded: chain H residue 549 ILE Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain I residue 475 ASP Chi-restraints excluded: chain I residue 509 SER Chi-restraints excluded: chain I residue 513 ILE Chi-restraints excluded: chain I residue 552 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 62 HIS Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 146 ASN Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 514 ILE Chi-restraints excluded: chain L residue 439 ILE Chi-restraints excluded: chain L residue 456 SER Chi-restraints excluded: chain L residue 476 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 15 optimal weight: 9.9990 chunk 230 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 151 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 235 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 110 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 171 ASN J 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.155352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.117813 restraints weight = 26203.469| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.06 r_work: 0.3161 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21260 Z= 0.148 Angle : 0.586 17.264 29015 Z= 0.291 Chirality : 0.042 0.284 3359 Planarity : 0.003 0.051 3456 Dihedral : 15.248 175.619 3745 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.35 % Favored : 96.61 % Rotamer: Outliers : 3.17 % Allowed : 22.77 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.17), residues: 2390 helix: 2.05 (0.18), residues: 836 sheet: -0.40 (0.24), residues: 462 loop : -1.39 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 95 TYR 0.023 0.001 TYR K 482 PHE 0.017 0.001 PHE G 41 TRP 0.011 0.001 TRP H 478 HIS 0.006 0.001 HIS L 553 Details of bonding type rmsd covalent geometry : bond 0.00340 (21232) covalent geometry : angle 0.54367 (28977) SS BOND : bond 0.00044 ( 1) SS BOND : angle 5.09375 ( 2) hydrogen bonds : bond 0.03155 ( 916) hydrogen bonds : angle 4.28651 ( 2636) metal coordination : bond 0.00773 ( 27) metal coordination : angle 6.11878 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5989.50 seconds wall clock time: 103 minutes 9.08 seconds (6189.08 seconds total)