Starting phenix.real_space_refine on Sun Aug 24 19:20:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gwg_34312/08_2025/8gwg_34312.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gwg_34312/08_2025/8gwg_34312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gwg_34312/08_2025/8gwg_34312.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gwg_34312/08_2025/8gwg_34312.map" model { file = "/net/cci-nas-00/data/ceres_data/8gwg_34312/08_2025/8gwg_34312.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gwg_34312/08_2025/8gwg_34312.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.029 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 8 6.06 5 P 55 5.49 5 S 158 5.16 5 C 13735 2.51 5 N 3694 2.21 5 O 4305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21955 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 7492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 931, 7492 Classifications: {'peptide': 931} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 900} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1396 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 600 Classifications: {'peptide': 78} Link IDs: {'TRANS': 77} Chain: "D" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1422 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 545 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 16, 'rna3p_pyr': 8} Link IDs: {'rna3p': 24} Chain: "J" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 565 Classifications: {'RNA': 27} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 25} Chain: "F" Number of atoms: 4513 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4598 Chain: "E" Number of atoms: 4513 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4598 Chain: "G" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 868 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' ZN': 2, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2465 SG CYS A 301 75.578 55.650 121.844 1.00 86.97 S ATOM 2506 SG CYS A 306 75.567 57.180 125.354 1.00 84.94 S ATOM 2538 SG CYS A 310 76.856 53.605 124.773 1.00 84.77 S ATOM 3946 SG CYS A 487 78.264 69.779 106.107 1.00 95.87 S ATOM 5199 SG CYS A 645 77.470 71.834 109.252 1.00 97.77 S ATOM 5205 SG CYS A 646 76.146 68.218 108.904 1.00 89.00 S ATOM 12129 SG CYS F 16 102.478 65.216 50.524 1.00183.45 S ATOM 12144 SG CYS F 19 103.212 62.542 47.852 1.00198.14 S ATOM 12047 SG CYS F 5 114.925 66.378 50.337 1.00183.01 S ATOM 12068 SG CYS F 8 115.808 69.235 47.969 1.00185.13 S ATOM 12206 SG CYS F 26 114.614 70.148 51.170 1.00172.26 S ATOM 12223 SG CYS F 29 112.090 68.304 48.775 1.00175.19 S ATOM 12388 SG CYS F 50 93.154 76.836 65.675 1.00158.72 S ATOM 12418 SG CYS F 55 89.756 76.042 64.216 1.00164.97 S ATOM 12551 SG CYS F 72 91.926 78.390 62.448 1.00168.17 S ATOM 16642 SG CYS E 16 61.349 74.627 65.591 1.00165.58 S ATOM 16657 SG CYS E 19 58.755 72.126 64.275 1.00179.24 S ATOM 16560 SG CYS E 5 70.232 70.535 57.925 1.00188.71 S ATOM 16581 SG CYS E 8 70.961 72.499 54.838 1.00197.10 S ATOM 16719 SG CYS E 26 72.392 73.907 58.159 1.00186.39 S ATOM 16736 SG CYS E 29 68.780 74.086 57.029 1.00167.57 S ATOM 16901 SG CYS E 50 66.240 87.403 79.620 1.00176.08 S ATOM 16931 SG CYS E 55 63.011 88.887 81.055 1.00192.48 S ATOM 17064 SG CYS E 72 65.078 90.922 78.545 1.00187.74 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AMET F 474 " occ=0.42 ... (14 atoms not shown) pdb=" CE BMET F 474 " occ=0.58 residue: pdb=" N AMET E 474 " occ=0.11 ... (14 atoms not shown) pdb=" CE BMET E 474 " occ=0.89 Time building chain proxies: 6.66, per 1000 atoms: 0.30 Number of scatterers: 21955 At special positions: 0 Unit cell: (154.98, 136.94, 186.14, 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 8 29.99 S 158 16.00 P 55 15.00 O 4305 8.00 N 3694 7.00 C 13735 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 19 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 16 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 29 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 5 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 26 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 55 " pdb=" ZN F 701 " pdb="ZN ZN F 701 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F 701 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 19 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 16 " pdb=" ZN F 702 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 8 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 26 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 5 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 29 " pdb=" ZN F 703 " pdb="ZN ZN F 703 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 72 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 55 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 50 " Number of angles added : 27 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5094 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 30 sheets defined 39.9% alpha, 10.3% beta 21 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 2.69 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 removed outlier: 3.974A pdb=" N ASN A 9 " --> pdb=" O GLN A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 91 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.649A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.622A pdb=" N TYR A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.815A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A 159 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.630A pdb=" N ASN A 209 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 206 through 210' Processing helix chain 'A' and resid 234 through 242 removed outlier: 3.528A pdb=" N TYR A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.865A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.569A pdb=" N HIS A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 removed outlier: 3.558A pdb=" N ARG A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 280 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.616A pdb=" N CYS A 301 " --> pdb=" O CYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.645A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.554A pdb=" N SER A 325 " --> pdb=" O PRO A 322 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 322 through 326' Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.506A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 425 Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 4.154A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.622A pdb=" N TRP A 509 " --> pdb=" O PHE A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.867A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 removed outlier: 3.610A pdb=" N THR A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 580 removed outlier: 4.033A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 removed outlier: 3.589A pdb=" N SER A 607 " --> pdb=" O LYS A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 removed outlier: 3.572A pdb=" N ARG A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 647 through 663 removed outlier: 3.586A pdb=" N ARG A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.525A pdb=" N ALA A 690 " --> pdb=" O THR A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 733 removed outlier: 3.504A pdb=" N ARG A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.792A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 851 through 855 Processing helix chain 'A' and resid 856 through 866 Processing helix chain 'A' and resid 867 through 872 removed outlier: 3.581A pdb=" N LYS A 871 " --> pdb=" O PRO A 868 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS A 872 " --> pdb=" O LEU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 903 removed outlier: 4.388A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N MET A 902 " --> pdb=" O HIS A 898 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR A 903 " --> pdb=" O MET A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 917 removed outlier: 3.678A pdb=" N GLU A 917 " --> pdb=" O ARG A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 923 removed outlier: 3.608A pdb=" N ALA A 923 " --> pdb=" O GLU A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 11 through 28 Processing helix chain 'B' and resid 31 through 96 removed outlier: 3.645A pdb=" N LEU B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP B 52 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 109 removed outlier: 3.763A pdb=" N ASN B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.619A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 25 through 41 removed outlier: 3.665A pdb=" N LEU C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 61 removed outlier: 3.681A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 73 Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 31 through 80 removed outlier: 3.885A pdb=" N LEU D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA D 45 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP D 52 " --> pdb=" O GLU D 48 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA D 54 " --> pdb=" O ASP D 50 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 99 removed outlier: 3.842A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 134 through 142 removed outlier: 3.570A pdb=" N TYR D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'F' and resid 26 through 36 Processing helix chain 'F' and resid 104 through 110 Processing helix chain 'F' and resid 116 through 125 removed outlier: 4.231A pdb=" N TYR F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 147 Processing helix chain 'F' and resid 265 through 275 Processing helix chain 'F' and resid 290 through 299 Processing helix chain 'F' and resid 310 through 325 removed outlier: 3.684A pdb=" N ALA F 316 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU F 317 " --> pdb=" O ALA F 313 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N LYS F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU F 322 " --> pdb=" O CYS F 318 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N LYS F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 328 No H-bonds generated for 'chain 'F' and resid 326 through 328' Processing helix chain 'F' and resid 381 through 391 removed outlier: 3.632A pdb=" N LEU F 391 " --> pdb=" O VAL F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 433 removed outlier: 3.999A pdb=" N LYS F 430 " --> pdb=" O CYS F 426 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR F 431 " --> pdb=" O ARG F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 456 removed outlier: 3.616A pdb=" N VAL F 449 " --> pdb=" O PRO F 445 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR F 451 " --> pdb=" O GLU F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 501 Processing helix chain 'F' and resid 503 through 507 removed outlier: 3.912A pdb=" N TRP F 506 " --> pdb=" O ASN F 503 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG F 507 " --> pdb=" O PRO F 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 503 through 507' Processing helix chain 'F' and resid 516 through 523 Processing helix chain 'E' and resid 26 through 36 Processing helix chain 'E' and resid 103 through 112 Processing helix chain 'E' and resid 116 through 124 removed outlier: 4.094A pdb=" N TYR E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 148 Processing helix chain 'E' and resid 264 through 273 Processing helix chain 'E' and resid 290 through 299 removed outlier: 3.748A pdb=" N LEU E 297 " --> pdb=" O ILE E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 325 removed outlier: 4.509A pdb=" N LYS E 320 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ALA E 321 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU E 322 " --> pdb=" O CYS E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 391 Processing helix chain 'E' and resid 418 through 422 Processing helix chain 'E' and resid 423 through 432 removed outlier: 3.864A pdb=" N LYS E 430 " --> pdb=" O CYS E 426 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE E 432 " --> pdb=" O LEU E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 456 removed outlier: 4.497A pdb=" N VAL E 449 " --> pdb=" O PRO E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 494 Processing helix chain 'E' and resid 494 through 500 Processing helix chain 'E' and resid 505 through 509 removed outlier: 4.422A pdb=" N LYS E 508 " --> pdb=" O ALA E 505 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA E 509 " --> pdb=" O TRP E 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 505 through 509' Processing helix chain 'E' and resid 515 through 526 Processing helix chain 'E' and resid 560 through 565 removed outlier: 4.014A pdb=" N ALA E 564 " --> pdb=" O ARG E 560 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 5.374A pdb=" N TYR A 69 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 114 " --> pdb=" O LYS A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.687A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 355 removed outlier: 3.551A pdb=" N ILE A 333 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 9.675A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 355 removed outlier: 3.551A pdb=" N ILE A 333 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.970A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA8, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AA9, first strand: chain 'A' and resid 816 through 822 Processing sheet with id=AB1, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.344A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU D 189 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 15 through 16 Processing sheet with id=AB3, first strand: chain 'F' and resid 64 through 65 Processing sheet with id=AB4, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AB5, first strand: chain 'F' and resid 152 through 154 Processing sheet with id=AB6, first strand: chain 'F' and resid 186 through 187 Processing sheet with id=AB7, first strand: chain 'F' and resid 200 through 202 Processing sheet with id=AB8, first strand: chain 'F' and resid 304 through 305 removed outlier: 5.091A pdb=" N VAL F 305 " --> pdb=" O VAL F 372 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 330 through 331 removed outlier: 3.532A pdb=" N SER F 331 " --> pdb=" O TYR F 355 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 472 through 473 Processing sheet with id=AC2, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AC3, first strand: chain 'E' and resid 24 through 25 removed outlier: 4.432A pdb=" N LEU E 14 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 69 through 71 Processing sheet with id=AC5, first strand: chain 'E' and resid 152 through 154 removed outlier: 3.672A pdb=" N PHE E 225 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 182 through 187 removed outlier: 6.958A pdb=" N PHE E 182 " --> pdb=" O GLU E 197 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLU E 197 " --> pdb=" O PHE E 182 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLY E 184 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE E 195 " --> pdb=" O GLY E 184 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 330 through 332 removed outlier: 6.593A pdb=" N SER E 331 " --> pdb=" O PHE E 357 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL E 356 " --> pdb=" O ILE E 304 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL E 305 " --> pdb=" O VAL E 372 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 481 through 482 removed outlier: 3.854A pdb=" N THR E 481 " --> pdb=" O ILE E 488 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 511 through 512 removed outlier: 6.087A pdb=" N PHE E 511 " --> pdb=" O GLN E 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'E' and resid 544 through 546 removed outlier: 3.552A pdb=" N LEU E 573 " --> pdb=" O VAL E 544 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 16 through 17 removed outlier: 3.737A pdb=" N ALA G 54 " --> pdb=" O THR G 67 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE G 56 " --> pdb=" O ILE G 65 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE G 65 " --> pdb=" O PHE G 56 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 29 through 31 removed outlier: 3.535A pdb=" N SER G 46 " --> pdb=" O TYR G 87 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS G 86 " --> pdb=" O PHE G 75 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE G 75 " --> pdb=" O LYS G 86 " (cutoff:3.500A) 799 hydrogen bonds defined for protein. 2226 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 4.58 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.45 - 0.72: 1 0.72 - 1.00: 0 1.00 - 1.27: 3471 1.27 - 1.54: 18641 1.54 - 1.82: 414 Warning: very small bond lengths. Bond restraints: 22527 Sorted by residual: bond pdb=" CG PRO F 491 " pdb=" CD PRO F 491 " ideal model delta sigma weight residual 1.503 0.448 1.055 3.40e-02 8.65e+02 9.63e+02 bond pdb=" N PRO F 491 " pdb=" CD PRO F 491 " ideal model delta sigma weight residual 1.473 1.632 -0.159 1.40e-02 5.10e+03 1.29e+02 bond pdb=" CG PRO E 364 " pdb=" CD PRO E 364 " ideal model delta sigma weight residual 1.503 1.264 0.239 3.40e-02 8.65e+02 4.94e+01 bond pdb=" N PRO E 364 " pdb=" CD PRO E 364 " ideal model delta sigma weight residual 1.473 1.569 -0.096 1.40e-02 5.10e+03 4.66e+01 bond pdb=" N ALA G 15 " pdb=" CA ALA G 15 " ideal model delta sigma weight residual 1.458 1.541 -0.083 1.27e-02 6.20e+03 4.32e+01 ... (remaining 22522 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.85: 30820 6.85 - 13.71: 47 13.71 - 20.56: 6 20.56 - 27.41: 4 27.41 - 34.27: 2 Bond angle restraints: 30879 Sorted by residual: angle pdb=" N PRO F 491 " pdb=" CD PRO F 491 " pdb=" CG PRO F 491 " ideal model delta sigma weight residual 103.20 68.93 34.27 1.50e+00 4.44e-01 5.22e+02 angle pdb=" CA PRO E 364 " pdb=" N PRO E 364 " pdb=" CD PRO E 364 " ideal model delta sigma weight residual 112.00 89.87 22.13 1.40e+00 5.10e-01 2.50e+02 angle pdb=" CA PRO F 491 " pdb=" N PRO F 491 " pdb=" CD PRO F 491 " ideal model delta sigma weight residual 112.00 90.72 21.28 1.40e+00 5.10e-01 2.31e+02 angle pdb=" N TYR G 32 " pdb=" CA TYR G 32 " pdb=" C TYR G 32 " ideal model delta sigma weight residual 110.80 138.73 -27.93 2.13e+00 2.20e-01 1.72e+02 angle pdb=" CA PRO F 491 " pdb=" CB PRO F 491 " pdb=" CG PRO F 491 " ideal model delta sigma weight residual 104.50 80.58 23.92 1.90e+00 2.77e-01 1.58e+02 ... (remaining 30874 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.29: 12788 33.29 - 66.58: 741 66.58 - 99.87: 35 99.87 - 133.16: 0 133.16 - 166.45: 2 Dihedral angle restraints: 13566 sinusoidal: 5672 harmonic: 7894 Sorted by residual: dihedral pdb=" N CYS G 14 " pdb=" C CYS G 14 " pdb=" CA CYS G 14 " pdb=" CB CYS G 14 " ideal model delta harmonic sigma weight residual 122.80 159.42 -36.62 0 2.50e+00 1.60e-01 2.15e+02 dihedral pdb=" C CYS G 14 " pdb=" N CYS G 14 " pdb=" CA CYS G 14 " pdb=" CB CYS G 14 " ideal model delta harmonic sigma weight residual -122.60 -158.49 35.89 0 2.50e+00 1.60e-01 2.06e+02 dihedral pdb=" N TYR G 32 " pdb=" C TYR G 32 " pdb=" CA TYR G 32 " pdb=" CB TYR G 32 " ideal model delta harmonic sigma weight residual 122.80 147.41 -24.61 0 2.50e+00 1.60e-01 9.69e+01 ... (remaining 13563 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.321: 3575 0.321 - 0.642: 2 0.642 - 0.963: 0 0.963 - 1.284: 2 1.284 - 1.605: 2 Chirality restraints: 3581 Sorted by residual: chirality pdb=" CA CYS G 14 " pdb=" N CYS G 14 " pdb=" C CYS G 14 " pdb=" CB CYS G 14 " both_signs ideal model delta sigma weight residual False 2.51 0.91 1.61 2.00e-01 2.50e+01 6.44e+01 chirality pdb=" CA TYR G 32 " pdb=" N TYR G 32 " pdb=" C TYR G 32 " pdb=" CB TYR G 32 " both_signs ideal model delta sigma weight residual False 2.51 1.18 1.33 2.00e-01 2.50e+01 4.42e+01 chirality pdb=" CA GLN G 11 " pdb=" N GLN G 11 " pdb=" C GLN G 11 " pdb=" CB GLN G 11 " both_signs ideal model delta sigma weight residual False 2.51 1.49 1.02 2.00e-01 2.50e+01 2.60e+01 ... (remaining 3578 not shown) Planarity restraints: 3748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 72 " -0.030 2.00e-02 2.50e+03 5.97e-02 3.57e+01 pdb=" C VAL A 72 " 0.103 2.00e-02 2.50e+03 pdb=" O VAL A 72 " -0.039 2.00e-02 2.50e+03 pdb=" N LYS A 73 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 363 " 0.106 5.00e-02 4.00e+02 1.40e-01 3.15e+01 pdb=" N PRO E 364 " -0.241 5.00e-02 4.00e+02 pdb=" CA PRO E 364 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO E 364 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 490 " 0.092 5.00e-02 4.00e+02 1.20e-01 2.31e+01 pdb=" N PRO F 491 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO F 491 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO F 491 " 0.062 5.00e-02 4.00e+02 ... (remaining 3745 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 299 2.62 - 3.19: 18637 3.19 - 3.76: 34097 3.76 - 4.33: 46279 4.33 - 4.90: 74396 Nonbonded interactions: 173708 Sorted by model distance: nonbonded pdb=" O SER D 173 " pdb=" OG SER D 177 " model vdw 2.045 3.040 nonbonded pdb=" OD1 ASN F 381 " pdb=" OG SER F 424 " model vdw 2.140 3.040 nonbonded pdb=" O PRO E 77 " pdb=" OG SER E 80 " model vdw 2.141 3.040 nonbonded pdb=" N2 G I 12 " pdb=" O2 C J 48 " model vdw 2.148 2.496 nonbonded pdb=" O CYS E 471 " pdb=" OG1 THR E 588 " model vdw 2.171 3.040 ... (remaining 173703 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 6 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 192)) selection = (chain 'D' and (resid 6 through 21 or (resid 22 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 42 or (resid 43 and (name N or name CA or name C or na \ me O or name CB )) or resid 44 through 46 or (resid 47 and (name N or name CA or \ name C or name O or name CB )) or resid 48 through 192)) } ncs_group { reference = (chain 'E' and (resid 1 through 473 or resid 475 through 703)) selection = (chain 'F' and (resid 1 through 473 or resid 475 through 703)) } 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=0.11 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: 8.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 28.760 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1795 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 1.055 22559 Z= 0.327 Angle : 0.952 34.266 30906 Z= 0.546 Chirality : 0.063 1.605 3581 Planarity : 0.006 0.140 3748 Dihedral : 18.826 166.450 8472 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.43 % Favored : 91.19 % Rotamer: Outliers : 5.14 % Allowed : 33.58 % Favored : 61.28 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -1.94 (0.16), residues: 2650 helix: 0.34 (0.18), residues: 947 sheet: -1.60 (0.35), residues: 218 loop : -2.47 (0.15), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 303 TYR 0.022 0.001 TYR F 299 PHE 0.017 0.001 PHE F 437 TRP 0.037 0.002 TRP G 53 HIS 0.007 0.001 HIS A 928 Details of bonding type rmsd covalent geometry : bond 0.00855 (22527) covalent geometry : angle 0.93982 (30879) hydrogen bonds : bond 0.18370 ( 842) hydrogen bonds : angle 6.41261 ( 2324) metal coordination : bond 0.01942 ( 32) metal coordination : angle 5.22093 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 347 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: -0.2328 (OUTLIER) cc_final: -0.2780 (t) REVERT: A 520 SER cc_start: -0.0143 (OUTLIER) cc_final: -0.0412 (t) REVERT: A 629 MET cc_start: 0.0013 (mmm) cc_final: -0.0275 (pmm) REVERT: A 835 SER cc_start: 0.1783 (OUTLIER) cc_final: 0.1238 (m) REVERT: D 62 MET cc_start: 0.1578 (tmm) cc_final: 0.1267 (ppp) REVERT: D 179 ASN cc_start: 0.3873 (OUTLIER) cc_final: 0.2321 (m-40) REVERT: D 187 THR cc_start: 0.4711 (OUTLIER) cc_final: 0.3903 (p) REVERT: D 189 LEU cc_start: 0.6175 (mp) cc_final: 0.5881 (mt) REVERT: F 43 LEU cc_start: 0.7239 (mt) cc_final: 0.6989 (tt) REVERT: F 247 VAL cc_start: 0.4141 (t) cc_final: 0.2619 (t) REVERT: F 248 ARG cc_start: 0.5941 (tmm160) cc_final: 0.5060 (ptt-90) REVERT: F 274 MET cc_start: 0.2108 (ppp) cc_final: 0.1751 (pmm) REVERT: F 305 VAL cc_start: 0.7848 (t) cc_final: 0.7422 (t) REVERT: F 453 SER cc_start: -0.2824 (OUTLIER) cc_final: -0.3137 (m) REVERT: F 539 SER cc_start: 0.3734 (m) cc_final: 0.3234 (p) REVERT: F 561 PHE cc_start: 0.2848 (p90) cc_final: 0.2497 (m-10) REVERT: E 315 ASP cc_start: 0.6714 (OUTLIER) cc_final: 0.6448 (p0) REVERT: E 430 LYS cc_start: 0.5031 (tmtm) cc_final: 0.4704 (mmtt) outliers start: 116 outliers final: 22 residues processed: 448 average time/residue: 0.1431 time to fit residues: 100.1434 Evaluate side-chains 224 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain F residue 453 SER Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 84 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.0000 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 408 GLN A 459 ASN A 492 GLN A 534 ASN B 65 GLN B 100 ASN ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN D 176 ASN F 46 ASN F 164 HIS ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 492 GLN E 275 GLN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5359 r_free = 0.5359 target = 0.206536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5035 r_free = 0.5035 target = 0.173474 restraints weight = 138115.885| |-----------------------------------------------------------------------------| r_work (start): 0.4987 rms_B_bonded: 11.15 r_work: 0.4829 rms_B_bonded: 7.06 restraints_weight: 2.0000 r_work (final): 0.4829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4826 r_free = 0.4826 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4826 r_free = 0.4826 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2821 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 22559 Z= 0.174 Angle : 0.801 11.710 30906 Z= 0.402 Chirality : 0.046 0.288 3581 Planarity : 0.006 0.060 3748 Dihedral : 13.015 149.804 3779 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.59 % Favored : 91.15 % Rotamer: Outliers : 4.87 % Allowed : 30.86 % Favored : 64.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.04 % 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: -2.08 (0.16), residues: 2650 helix: -0.03 (0.17), residues: 967 sheet: -1.36 (0.33), residues: 235 loop : -2.44 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 569 TYR 0.021 0.002 TYR A 746 PHE 0.030 0.002 PHE D 92 TRP 0.029 0.003 TRP C 29 HIS 0.008 0.002 HIS F 39 Details of bonding type rmsd covalent geometry : bond 0.00374 (22527) covalent geometry : angle 0.78828 (30879) hydrogen bonds : bond 0.05315 ( 842) hydrogen bonds : angle 5.39876 ( 2324) metal coordination : bond 0.03392 ( 32) metal coordination : angle 4.93823 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 232 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 LYS cc_start: 0.4559 (OUTLIER) cc_final: 0.4320 (mtpt) REVERT: A 484 ASP cc_start: 0.2423 (p0) cc_final: 0.2211 (p0) REVERT: A 629 MET cc_start: 0.1224 (mmm) cc_final: 0.0601 (pmm) REVERT: A 746 TYR cc_start: 0.1312 (t80) cc_final: 0.0716 (t80) REVERT: B 38 LEU cc_start: 0.1178 (OUTLIER) cc_final: 0.0873 (mt) REVERT: B 103 LEU cc_start: 0.4081 (OUTLIER) cc_final: 0.3735 (mm) REVERT: D 87 MET cc_start: 0.5048 (mmt) cc_final: 0.4789 (mmm) REVERT: F 539 SER cc_start: 0.3870 (m) cc_final: 0.3364 (p) REVERT: E 15 ARG cc_start: 0.8018 (mtm180) cc_final: 0.7627 (mpp80) REVERT: E 92 LEU cc_start: 0.1040 (mt) cc_final: 0.0759 (mt) REVERT: E 359 THR cc_start: -0.3744 (OUTLIER) cc_final: -0.4106 (m) REVERT: E 430 LYS cc_start: 0.5180 (tmtm) cc_final: 0.4934 (mmtt) REVERT: G 35 THR cc_start: 0.1124 (OUTLIER) cc_final: 0.0919 (m) outliers start: 110 outliers final: 35 residues processed: 329 average time/residue: 0.1320 time to fit residues: 67.4378 Evaluate side-chains 214 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 694 PHE Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 801 THR Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 436 MET Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 91 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 264 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 255 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 118 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN A 209 ASN ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 HIS A 408 GLN A 414 ASN A 725 HIS A 791 ASN B 118 ASN D 136 ASN F 46 ASN F 516 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 482 HIS ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 2 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5195 r_free = 0.5195 target = 0.195309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.159309 restraints weight = 143099.347| |-----------------------------------------------------------------------------| r_work (start): 0.4723 rms_B_bonded: 10.98 r_work: 0.4536 rms_B_bonded: 7.59 restraints_weight: 2.0000 r_work (final): 0.4536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4523 r_free = 0.4523 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4523 r_free = 0.4523 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4459 moved from start: 0.5949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 22559 Z= 0.273 Angle : 0.975 21.809 30906 Z= 0.495 Chirality : 0.052 0.380 3581 Planarity : 0.008 0.103 3748 Dihedral : 13.073 133.680 3742 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 19.95 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.81 % Favored : 90.89 % Rotamer: Outliers : 6.15 % Allowed : 29.54 % Favored : 64.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.04 % 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: -2.71 (0.15), residues: 2650 helix: -0.93 (0.16), residues: 972 sheet: -1.70 (0.36), residues: 192 loop : -2.50 (0.14), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 183 TYR 0.036 0.003 TYR A 516 PHE 0.061 0.004 PHE D 15 TRP 0.030 0.004 TRP A 916 HIS 0.017 0.002 HIS A 642 Details of bonding type rmsd covalent geometry : bond 0.00592 (22527) covalent geometry : angle 0.96498 (30879) hydrogen bonds : bond 0.05958 ( 842) hydrogen bonds : angle 6.16228 ( 2324) metal coordination : bond 0.02212 ( 32) metal coordination : angle 4.80724 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 232 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.4479 (OUTLIER) cc_final: 0.4037 (mtt-85) REVERT: A 103 LYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6936 (mtpp) REVERT: A 484 ASP cc_start: 0.3617 (p0) cc_final: 0.3387 (p0) REVERT: A 515 TYR cc_start: 0.3202 (m-80) cc_final: 0.1910 (m-80) REVERT: A 579 ILE cc_start: 0.7371 (mt) cc_final: 0.6939 (mt) REVERT: A 613 HIS cc_start: 0.5898 (OUTLIER) cc_final: 0.5661 (m90) REVERT: A 618 ASP cc_start: 0.4729 (OUTLIER) cc_final: 0.4011 (t70) REVERT: A 629 MET cc_start: 0.3213 (mmm) cc_final: 0.2725 (pmm) REVERT: A 861 SER cc_start: 0.7989 (m) cc_final: 0.7544 (p) REVERT: B 97 LYS cc_start: 0.0533 (pttm) cc_final: -0.1999 (tmtt) REVERT: B 103 LEU cc_start: 0.4711 (mm) cc_final: 0.4445 (mm) REVERT: B 153 LEU cc_start: 0.7841 (tp) cc_final: 0.7606 (mt) REVERT: B 174 MET cc_start: 0.6866 (tpp) cc_final: 0.6620 (tpp) REVERT: C 1 SER cc_start: 0.4412 (OUTLIER) cc_final: 0.4056 (p) REVERT: C 63 GLN cc_start: 0.5471 (mm110) cc_final: 0.5182 (mm-40) REVERT: D 160 VAL cc_start: 0.7769 (OUTLIER) cc_final: 0.7529 (t) REVERT: D 161 ASP cc_start: 0.7205 (OUTLIER) cc_final: 0.6742 (m-30) REVERT: F 57 VAL cc_start: -0.1699 (OUTLIER) cc_final: -0.1916 (m) REVERT: F 307 THR cc_start: 0.4893 (OUTLIER) cc_final: 0.3549 (m) REVERT: F 373 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.8082 (t80) REVERT: F 490 ARG cc_start: -0.1091 (OUTLIER) cc_final: -0.1607 (tpt170) REVERT: F 539 SER cc_start: 0.4417 (m) cc_final: 0.4062 (p) REVERT: E 15 ARG cc_start: 0.8001 (mtm180) cc_final: 0.7672 (mpp80) REVERT: E 62 GLN cc_start: 0.4284 (OUTLIER) cc_final: 0.3714 (pp30) REVERT: E 68 MET cc_start: 0.8369 (mmt) cc_final: 0.7197 (pmm) REVERT: E 131 LYS cc_start: 0.5190 (OUTLIER) cc_final: 0.4660 (tttm) REVERT: E 359 THR cc_start: -0.3742 (OUTLIER) cc_final: -0.4197 (m) REVERT: E 575 ILE cc_start: -0.0626 (OUTLIER) cc_final: -0.1316 (tp) REVERT: G 2 ASN cc_start: 0.4685 (OUTLIER) cc_final: 0.4049 (m-40) REVERT: G 23 CYS cc_start: 0.1256 (OUTLIER) cc_final: 0.0463 (m) outliers start: 137 outliers final: 49 residues processed: 344 average time/residue: 0.1419 time to fit residues: 76.3058 Evaluate side-chains 249 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 183 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 694 PHE Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 36 HIS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 373 PHE Chi-restraints excluded: chain F residue 490 ARG Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain E residue 575 ILE Chi-restraints excluded: chain G residue 2 ASN Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 70 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 240 optimal weight: 4.9990 chunk 153 optimal weight: 8.9990 chunk 236 optimal weight: 30.0000 chunk 70 optimal weight: 0.9990 chunk 137 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 237 optimal weight: 10.0000 chunk 261 optimal weight: 4.9990 chunk 242 optimal weight: 9.9990 chunk 220 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN A 599 HIS ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 ASN ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN E 88 GLN E 116 ASN ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 1 ASN G 2 ASN G 33 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5156 r_free = 0.5156 target = 0.185858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.150315 restraints weight = 126338.269| |-----------------------------------------------------------------------------| r_work (start): 0.4693 rms_B_bonded: 8.41 r_work: 0.4404 rms_B_bonded: 7.19 restraints_weight: 2.0000 r_work: 0.4515 rms_B_bonded: 5.32 restraints_weight: 4.0000 r_work (final): 0.4515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4552 r_free = 0.4552 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4552 r_free = 0.4552 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5804 moved from start: 1.0697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.163 22559 Z= 0.457 Angle : 1.330 31.142 30906 Z= 0.676 Chirality : 0.064 0.480 3581 Planarity : 0.010 0.184 3748 Dihedral : 14.095 115.921 3739 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 33.02 Ramachandran Plot: Outliers : 0.45 % Allowed : 11.42 % Favored : 88.12 % Rotamer: Outliers : 7.81 % Allowed : 30.03 % Favored : 62.16 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.43 % 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: -3.54 (0.14), residues: 2650 helix: -1.88 (0.14), residues: 945 sheet: -1.90 (0.35), residues: 216 loop : -2.82 (0.14), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.002 ARG A 285 TYR 0.067 0.005 TYR A 217 PHE 0.054 0.005 PHE A 694 TRP 0.082 0.005 TRP A 617 HIS 0.015 0.003 HIS A 810 Details of bonding type rmsd covalent geometry : bond 0.00965 (22527) covalent geometry : angle 1.30793 (30879) hydrogen bonds : bond 0.08661 ( 842) hydrogen bonds : angle 7.70346 ( 2324) metal coordination : bond 0.01983 ( 32) metal coordination : angle 8.22918 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 256 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.7023 (OUTLIER) cc_final: 0.6562 (mtt-85) REVERT: A 98 LYS cc_start: 0.7629 (mtmm) cc_final: 0.7397 (mtmm) REVERT: A 153 ASP cc_start: 0.3128 (OUTLIER) cc_final: 0.1974 (m-30) REVERT: A 181 ARG cc_start: 0.1534 (OUTLIER) cc_final: 0.0341 (ttp80) REVERT: A 238 TYR cc_start: 0.5922 (m-80) cc_final: 0.5722 (m-80) REVERT: A 289 TYR cc_start: 0.3510 (m-80) cc_final: 0.1812 (m-80) REVERT: A 357 GLN cc_start: 0.5840 (mt0) cc_final: 0.5187 (mt0) REVERT: A 408 GLN cc_start: 0.0031 (OUTLIER) cc_final: -0.0344 (pm20) REVERT: A 493 VAL cc_start: 0.8485 (OUTLIER) cc_final: 0.8243 (p) REVERT: A 724 GLN cc_start: 0.6551 (OUTLIER) cc_final: 0.6327 (tt0) REVERT: A 788 TYR cc_start: 0.1723 (OUTLIER) cc_final: 0.1294 (p90) REVERT: A 818 MET cc_start: 0.7583 (ptp) cc_final: 0.7322 (ptp) REVERT: A 884 TYR cc_start: 0.8779 (OUTLIER) cc_final: 0.7806 (m-80) REVERT: A 899 MET cc_start: 0.9380 (tmm) cc_final: 0.9167 (tmm) REVERT: A 924 MET cc_start: 0.8069 (mmt) cc_final: 0.7396 (mmt) REVERT: B 62 MET cc_start: 0.6649 (ptp) cc_final: 0.6445 (mpp) REVERT: B 103 LEU cc_start: 0.5440 (OUTLIER) cc_final: 0.5060 (mm) REVERT: B 129 MET cc_start: 0.1712 (OUTLIER) cc_final: 0.0649 (mmm) REVERT: B 153 LEU cc_start: 0.8156 (tp) cc_final: 0.7738 (mt) REVERT: B 174 MET cc_start: 0.6736 (tpp) cc_final: 0.6337 (tpp) REVERT: C 34 GLN cc_start: 0.7323 (pp30) cc_final: 0.7115 (tp-100) REVERT: C 74 GLU cc_start: 0.7015 (tm-30) cc_final: 0.5665 (mp0) REVERT: D 49 PHE cc_start: 0.6606 (OUTLIER) cc_final: 0.6383 (t80) REVERT: D 70 MET cc_start: 0.7337 (ppp) cc_final: 0.7116 (ppp) REVERT: D 87 MET cc_start: 0.6545 (mmt) cc_final: 0.6343 (mmp) REVERT: D 185 ILE cc_start: 0.6966 (mt) cc_final: 0.6727 (mm) REVERT: D 187 THR cc_start: 0.7262 (p) cc_final: 0.6845 (p) REVERT: F 440 THR cc_start: 0.6533 (m) cc_final: 0.4694 (p) REVERT: F 442 ARG cc_start: 0.0758 (mmt180) cc_final: -0.0407 (ptt180) REVERT: F 539 SER cc_start: 0.4504 (m) cc_final: 0.4269 (p) REVERT: E 15 ARG cc_start: 0.7885 (mtm180) cc_final: 0.7548 (mpp80) REVERT: E 51 ASN cc_start: 0.7250 (OUTLIER) cc_final: 0.6992 (t0) REVERT: E 131 LYS cc_start: 0.6055 (OUTLIER) cc_final: 0.5396 (tmmt) REVERT: E 359 THR cc_start: -0.4417 (OUTLIER) cc_final: -0.4637 (m) REVERT: E 575 ILE cc_start: -0.0775 (OUTLIER) cc_final: -0.1159 (tp) REVERT: G 31 TYR cc_start: 0.7500 (m-10) cc_final: 0.7282 (m-80) REVERT: G 52 LYS cc_start: 0.6687 (OUTLIER) cc_final: 0.6155 (tptp) REVERT: G 77 THR cc_start: 0.1514 (OUTLIER) cc_final: 0.1285 (m) REVERT: G 97 LEU cc_start: 0.6256 (OUTLIER) cc_final: 0.6023 (mp) outliers start: 175 outliers final: 79 residues processed: 405 average time/residue: 0.1231 time to fit residues: 77.8804 Evaluate side-chains 294 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 197 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 788 TYR Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 884 TYR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 373 PHE Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 382 TYR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 423 ASN Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 575 ILE Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 163 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 143 optimal weight: 0.0970 chunk 199 optimal weight: 0.5980 chunk 263 optimal weight: 5.9990 chunk 176 optimal weight: 10.0000 chunk 231 optimal weight: 40.0000 chunk 82 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 210 GLN A 312 ASN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 ASN ** A 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 ASN F 381 ASN ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN E 116 ASN ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 2 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5222 r_free = 0.5222 target = 0.191703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.156018 restraints weight = 122541.954| |-----------------------------------------------------------------------------| r_work (start): 0.4752 rms_B_bonded: 8.71 r_work: 0.4488 rms_B_bonded: 7.61 restraints_weight: 2.0000 r_work: 0.4612 rms_B_bonded: 5.42 restraints_weight: 4.0000 r_work (final): 0.4612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4629 r_free = 0.4629 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4629 r_free = 0.4629 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5606 moved from start: 1.0768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 22559 Z= 0.159 Angle : 0.814 23.343 30906 Z= 0.405 Chirality : 0.047 0.261 3581 Planarity : 0.006 0.101 3748 Dihedral : 13.344 128.330 3738 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.41 % Favored : 92.36 % Rotamer: Outliers : 4.13 % Allowed : 32.79 % Favored : 63.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.77 (0.15), residues: 2650 helix: -1.06 (0.16), residues: 943 sheet: -1.53 (0.36), residues: 207 loop : -2.50 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 75 TYR 0.037 0.002 TYR E 382 PHE 0.025 0.002 PHE A 157 TRP 0.028 0.002 TRP D 182 HIS 0.014 0.001 HIS A 613 Details of bonding type rmsd covalent geometry : bond 0.00336 (22527) covalent geometry : angle 0.79254 (30879) hydrogen bonds : bond 0.05155 ( 842) hydrogen bonds : angle 6.16787 ( 2324) metal coordination : bond 0.01942 ( 32) metal coordination : angle 6.27019 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 219 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: -0.2173 (OUTLIER) cc_final: -0.2639 (t) REVERT: A 91 LYS cc_start: 0.7257 (tmmt) cc_final: 0.6743 (tppt) REVERT: A 129 TYR cc_start: 0.1891 (t80) cc_final: 0.1496 (t80) REVERT: A 304 ASP cc_start: 0.6417 (p0) cc_final: 0.6178 (p0) REVERT: A 380 MET cc_start: 0.2221 (ptp) cc_final: 0.1576 (pmm) REVERT: A 571 PHE cc_start: 0.7478 (t80) cc_final: 0.7017 (t80) REVERT: A 724 GLN cc_start: 0.6382 (tp40) cc_final: 0.6131 (tt0) REVERT: A 726 ARG cc_start: 0.7345 (mmm160) cc_final: 0.7068 (mmm160) REVERT: A 729 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7203 (mt-10) REVERT: A 788 TYR cc_start: 0.1708 (OUTLIER) cc_final: 0.1387 (p90) REVERT: A 792 VAL cc_start: 0.3935 (OUTLIER) cc_final: 0.3591 (p) REVERT: A 884 TYR cc_start: 0.8931 (OUTLIER) cc_final: 0.7896 (m-80) REVERT: B 94 MET cc_start: 0.4079 (ptt) cc_final: 0.3671 (ptt) REVERT: B 174 MET cc_start: 0.6562 (tpp) cc_final: 0.6145 (tpp) REVERT: D 80 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7664 (ttp80) REVERT: D 96 ARG cc_start: 0.7737 (tmm-80) cc_final: 0.7506 (tmm-80) REVERT: F 539 SER cc_start: 0.4581 (m) cc_final: 0.4345 (p) REVERT: E 15 ARG cc_start: 0.7849 (mtm180) cc_final: 0.7543 (mpp80) REVERT: E 131 LYS cc_start: 0.6137 (OUTLIER) cc_final: 0.5611 (ttmm) REVERT: E 274 MET cc_start: 0.8196 (tpp) cc_final: 0.6801 (ptt) REVERT: E 359 THR cc_start: -0.4585 (OUTLIER) cc_final: -0.4838 (m) REVERT: E 378 MET cc_start: 0.6932 (ppp) cc_final: 0.6441 (ppp) REVERT: E 575 ILE cc_start: -0.0449 (OUTLIER) cc_final: -0.1042 (tp) REVERT: G 12 MET cc_start: 0.7508 (mmm) cc_final: 0.7062 (mmm) REVERT: G 23 CYS cc_start: 0.1110 (OUTLIER) cc_final: 0.0402 (m) REVERT: G 31 TYR cc_start: 0.7548 (m-80) cc_final: 0.7330 (m-80) REVERT: G 52 LYS cc_start: 0.6653 (OUTLIER) cc_final: 0.6063 (tptp) REVERT: G 69 LEU cc_start: 0.3397 (tp) cc_final: 0.2891 (tp) outliers start: 93 outliers final: 46 residues processed: 298 average time/residue: 0.1365 time to fit residues: 63.4747 Evaluate side-chains 237 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 181 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 788 TYR Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 884 TYR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 80 ARG Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 373 PHE Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 423 ASN Chi-restraints excluded: chain E residue 575 ILE Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 52 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 23 optimal weight: 0.5980 chunk 191 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 263 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 196 optimal weight: 20.0000 chunk 64 optimal weight: 7.9990 chunk 225 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 204 optimal weight: 0.3980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 HIS A 713 ASN A 816 HIS A 898 HIS ** A 909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN E 275 GLN ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5158 r_free = 0.5158 target = 0.187423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.149402 restraints weight = 132167.830| |-----------------------------------------------------------------------------| r_work (start): 0.4654 rms_B_bonded: 9.29 r_work: 0.4389 rms_B_bonded: 7.53 restraints_weight: 2.0000 r_work: 0.4524 rms_B_bonded: 5.17 restraints_weight: 4.0000 r_work (final): 0.4524 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4515 r_free = 0.4515 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4515 r_free = 0.4515 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5786 moved from start: 1.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 22559 Z= 0.175 Angle : 0.799 20.238 30906 Z= 0.397 Chirality : 0.046 0.271 3581 Planarity : 0.005 0.097 3748 Dihedral : 13.074 125.238 3738 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.85 % Favored : 90.92 % Rotamer: Outliers : 3.86 % Allowed : 32.35 % Favored : 63.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.56 (0.15), residues: 2650 helix: -0.80 (0.16), residues: 943 sheet: -1.63 (0.37), residues: 196 loop : -2.39 (0.15), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 116 TYR 0.038 0.002 TYR E 382 PHE 0.034 0.002 PHE A 368 TRP 0.023 0.002 TRP B 182 HIS 0.011 0.002 HIS F 33 Details of bonding type rmsd covalent geometry : bond 0.00391 (22527) covalent geometry : angle 0.77879 (30879) hydrogen bonds : bond 0.05072 ( 842) hydrogen bonds : angle 6.05206 ( 2324) metal coordination : bond 0.01519 ( 32) metal coordination : angle 6.11067 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 205 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: -0.2228 (OUTLIER) cc_final: -0.2686 (t) REVERT: A 74 ARG cc_start: 0.6365 (OUTLIER) cc_final: 0.6129 (mtt-85) REVERT: A 91 LYS cc_start: 0.7422 (tmmt) cc_final: 0.6857 (tppt) REVERT: A 129 TYR cc_start: 0.2780 (t80) cc_final: 0.2045 (t80) REVERT: A 289 TYR cc_start: 0.3018 (m-80) cc_final: 0.1525 (m-80) REVERT: A 312 ASN cc_start: 0.5558 (t0) cc_final: 0.5314 (t0) REVERT: A 324 THR cc_start: 0.6763 (p) cc_final: 0.6266 (t) REVERT: A 792 VAL cc_start: 0.4822 (OUTLIER) cc_final: 0.4520 (p) REVERT: A 794 MET cc_start: 0.1941 (OUTLIER) cc_final: 0.1552 (mtm) REVERT: A 818 MET cc_start: 0.7559 (pmm) cc_final: 0.6967 (ptt) REVERT: A 884 TYR cc_start: 0.9068 (OUTLIER) cc_final: 0.7790 (m-80) REVERT: A 924 MET cc_start: 0.8049 (mmt) cc_final: 0.7608 (mmt) REVERT: B 174 MET cc_start: 0.6575 (tpp) cc_final: 0.6065 (tpp) REVERT: D 189 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6344 (mm) REVERT: F 57 VAL cc_start: -0.1594 (OUTLIER) cc_final: -0.1800 (m) REVERT: F 442 ARG cc_start: 0.0549 (mmt180) cc_final: -0.0644 (ptp90) REVERT: F 539 SER cc_start: 0.4703 (m) cc_final: 0.4483 (p) REVERT: E 65 LEU cc_start: 0.7182 (tp) cc_final: 0.6653 (pp) REVERT: E 131 LYS cc_start: 0.6344 (OUTLIER) cc_final: 0.5852 (ttmm) REVERT: E 359 THR cc_start: -0.4883 (OUTLIER) cc_final: -0.5108 (m) REVERT: E 378 MET cc_start: 0.6951 (ppp) cc_final: 0.6542 (ppp) REVERT: G 23 CYS cc_start: 0.1131 (OUTLIER) cc_final: -0.0261 (m) REVERT: G 31 TYR cc_start: 0.7751 (m-80) cc_final: 0.7394 (m-80) REVERT: G 52 LYS cc_start: 0.6622 (OUTLIER) cc_final: 0.6050 (tptp) REVERT: G 66 TYR cc_start: 0.5317 (m-80) cc_final: 0.4660 (p90) REVERT: G 69 LEU cc_start: 0.3867 (tp) cc_final: 0.3183 (tp) outliers start: 87 outliers final: 57 residues processed: 275 average time/residue: 0.1365 time to fit residues: 59.6571 Evaluate side-chains 249 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 181 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 884 TYR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain F residue 30 CYS Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 373 PHE Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 423 ASN Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 52 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 86 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 156 optimal weight: 40.0000 chunk 101 optimal weight: 0.7980 chunk 263 optimal weight: 0.4980 chunk 212 optimal weight: 2.9990 chunk 68 optimal weight: 0.2980 chunk 29 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 241 optimal weight: 20.0000 chunk 16 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 882 HIS ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5168 r_free = 0.5168 target = 0.188488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.152081 restraints weight = 127114.646| |-----------------------------------------------------------------------------| r_work (start): 0.4685 rms_B_bonded: 9.57 r_work: 0.4384 rms_B_bonded: 7.68 restraints_weight: 2.0000 r_work: 0.4525 rms_B_bonded: 5.28 restraints_weight: 4.0000 r_work (final): 0.4525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4526 r_free = 0.4526 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4526 r_free = 0.4526 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5782 moved from start: 1.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22559 Z= 0.139 Angle : 0.742 18.682 30906 Z= 0.366 Chirality : 0.044 0.427 3581 Planarity : 0.005 0.086 3748 Dihedral : 12.921 128.900 3738 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.83 % Favored : 91.98 % Rotamer: Outliers : 3.60 % Allowed : 32.53 % Favored : 63.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.20 (0.16), residues: 2650 helix: -0.44 (0.17), residues: 930 sheet: -1.34 (0.39), residues: 186 loop : -2.22 (0.15), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 15 TYR 0.028 0.002 TYR A 217 PHE 0.021 0.002 PHE A 368 TRP 0.023 0.002 TRP B 182 HIS 0.012 0.001 HIS A 572 Details of bonding type rmsd covalent geometry : bond 0.00301 (22527) covalent geometry : angle 0.72495 (30879) hydrogen bonds : bond 0.04644 ( 842) hydrogen bonds : angle 5.75305 ( 2324) metal coordination : bond 0.01669 ( 32) metal coordination : angle 5.37544 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 200 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: -0.1941 (OUTLIER) cc_final: -0.2386 (t) REVERT: A 91 LYS cc_start: 0.7327 (tmmt) cc_final: 0.6724 (tppt) REVERT: A 124 MET cc_start: 0.1396 (mtp) cc_final: -0.1291 (ttm) REVERT: A 129 TYR cc_start: 0.2270 (t80) cc_final: 0.1646 (t80) REVERT: A 571 PHE cc_start: 0.7223 (t80) cc_final: 0.6908 (t80) REVERT: A 633 MET cc_start: 0.7179 (mtt) cc_final: 0.6631 (ttt) REVERT: A 654 ARG cc_start: 0.6148 (mmm160) cc_final: 0.5905 (mmm160) REVERT: A 755 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7672 (tmm) REVERT: A 756 MET cc_start: 0.7309 (tmm) cc_final: 0.6608 (ttp) REVERT: A 884 TYR cc_start: 0.9026 (OUTLIER) cc_final: 0.7852 (m-80) REVERT: B 174 MET cc_start: 0.6575 (tpp) cc_final: 0.6056 (tpp) REVERT: D 75 ARG cc_start: 0.6277 (mmp80) cc_final: 0.5917 (tpt90) REVERT: D 189 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6212 (mm) REVERT: F 442 ARG cc_start: 0.0554 (mmt180) cc_final: -0.0605 (ptp90) REVERT: F 539 SER cc_start: 0.4864 (m) cc_final: 0.4662 (p) REVERT: E 65 LEU cc_start: 0.7268 (tp) cc_final: 0.6797 (pp) REVERT: E 131 LYS cc_start: 0.6348 (OUTLIER) cc_final: 0.5898 (tttt) REVERT: E 359 THR cc_start: -0.4920 (OUTLIER) cc_final: -0.5152 (m) REVERT: E 378 MET cc_start: 0.6840 (ppp) cc_final: 0.6453 (ppp) REVERT: E 475 PHE cc_start: 0.5101 (OUTLIER) cc_final: 0.4706 (p90) REVERT: G 12 MET cc_start: 0.7563 (mmm) cc_final: 0.6166 (mmm) REVERT: G 23 CYS cc_start: 0.1131 (OUTLIER) cc_final: -0.0138 (m) REVERT: G 31 TYR cc_start: 0.7730 (m-80) cc_final: 0.7272 (m-80) REVERT: G 39 ARG cc_start: 0.4007 (ttt180) cc_final: 0.3484 (tpt-90) REVERT: G 52 LYS cc_start: 0.6573 (OUTLIER) cc_final: 0.5999 (tptp) REVERT: G 66 TYR cc_start: 0.5233 (m-80) cc_final: 0.4581 (p90) REVERT: G 69 LEU cc_start: 0.3677 (tp) cc_final: 0.3032 (tp) outliers start: 80 outliers final: 58 residues processed: 265 average time/residue: 0.1344 time to fit residues: 57.1425 Evaluate side-chains 250 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 183 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 781 ASN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 884 TYR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 373 PHE Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 423 ASN Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 475 PHE Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 52 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 252 optimal weight: 8.9990 chunk 204 optimal weight: 3.9990 chunk 216 optimal weight: 30.0000 chunk 190 optimal weight: 0.8980 chunk 103 optimal weight: 0.3980 chunk 78 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 240 optimal weight: 0.6980 chunk 193 optimal weight: 7.9990 chunk 189 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 HIS A 691 ASN ** A 909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5115 r_free = 0.5115 target = 0.184828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.146535 restraints weight = 136628.941| |-----------------------------------------------------------------------------| r_work (start): 0.4616 rms_B_bonded: 9.69 r_work: 0.4305 rms_B_bonded: 8.22 restraints_weight: 2.0000 r_work: 0.4446 rms_B_bonded: 5.22 restraints_weight: 4.0000 r_work (final): 0.4446 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4453 r_free = 0.4453 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4453 r_free = 0.4453 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6000 moved from start: 1.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 22559 Z= 0.169 Angle : 0.790 17.078 30906 Z= 0.392 Chirality : 0.045 0.229 3581 Planarity : 0.006 0.114 3748 Dihedral : 12.997 136.451 3738 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.28 % Favored : 91.53 % Rotamer: Outliers : 3.78 % Allowed : 32.66 % Favored : 63.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.21 (0.16), residues: 2650 helix: -0.49 (0.17), residues: 944 sheet: -1.48 (0.39), residues: 183 loop : -2.19 (0.15), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 96 TYR 0.036 0.002 TYR A 38 PHE 0.022 0.002 PHE A 368 TRP 0.039 0.003 TRP B 182 HIS 0.009 0.002 HIS F 33 Details of bonding type rmsd covalent geometry : bond 0.00369 (22527) covalent geometry : angle 0.77460 (30879) hydrogen bonds : bond 0.05001 ( 842) hydrogen bonds : angle 5.91792 ( 2324) metal coordination : bond 0.01661 ( 32) metal coordination : angle 5.29985 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 200 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: -0.2125 (OUTLIER) cc_final: -0.2621 (t) REVERT: A 91 LYS cc_start: 0.7347 (tmmt) cc_final: 0.6793 (tppt) REVERT: A 124 MET cc_start: 0.1214 (mtp) cc_final: -0.1737 (ttm) REVERT: A 211 ASP cc_start: 0.6537 (OUTLIER) cc_final: 0.4600 (p0) REVERT: A 289 TYR cc_start: 0.3495 (m-80) cc_final: 0.1805 (m-80) REVERT: A 324 THR cc_start: 0.6624 (p) cc_final: 0.6101 (t) REVERT: A 818 MET cc_start: 0.7603 (pmm) cc_final: 0.7001 (ptt) REVERT: A 884 TYR cc_start: 0.9015 (OUTLIER) cc_final: 0.7922 (m-80) REVERT: B 174 MET cc_start: 0.6502 (tpp) cc_final: 0.6230 (tpp) REVERT: C 34 GLN cc_start: 0.7433 (pp30) cc_final: 0.6838 (tp-100) REVERT: D 75 ARG cc_start: 0.6473 (mmp80) cc_final: 0.6214 (tpt90) REVERT: D 93 THR cc_start: 0.8458 (m) cc_final: 0.8244 (m) REVERT: D 142 CYS cc_start: -0.0162 (OUTLIER) cc_final: -0.0409 (t) REVERT: D 182 TRP cc_start: 0.3892 (OUTLIER) cc_final: 0.2529 (m-10) REVERT: D 189 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6535 (mm) REVERT: E 65 LEU cc_start: 0.7241 (tp) cc_final: 0.6911 (pp) REVERT: E 131 LYS cc_start: 0.6385 (OUTLIER) cc_final: 0.5892 (tttm) REVERT: E 378 MET cc_start: 0.6883 (ppp) cc_final: 0.6512 (ppp) REVERT: G 12 MET cc_start: 0.7532 (mmm) cc_final: 0.6650 (mmm) REVERT: G 23 CYS cc_start: 0.1616 (OUTLIER) cc_final: 0.0104 (m) REVERT: G 31 TYR cc_start: 0.7745 (m-80) cc_final: 0.7293 (m-80) REVERT: G 39 ARG cc_start: 0.4284 (ttt180) cc_final: 0.3906 (tpt-90) REVERT: G 52 LYS cc_start: 0.6573 (OUTLIER) cc_final: 0.6020 (tptp) REVERT: G 66 TYR cc_start: 0.5163 (m-80) cc_final: 0.4405 (p90) REVERT: G 69 LEU cc_start: 0.3920 (tp) cc_final: 0.3022 (tp) outliers start: 85 outliers final: 54 residues processed: 270 average time/residue: 0.1505 time to fit residues: 63.7527 Evaluate side-chains 241 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 178 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 725 HIS Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 781 ASN Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 884 TYR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 423 ASN Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 52 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 131 optimal weight: 0.7980 chunk 117 optimal weight: 6.9990 chunk 256 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 166 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 chunk 245 optimal weight: 4.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 GLN A 215 ASN A 300 ASN A 312 ASN A 414 ASN A 909 ASN B 69 GLN D 88 GLN F 388 ASN ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5086 r_free = 0.5086 target = 0.180386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.138289 restraints weight = 108885.008| |-----------------------------------------------------------------------------| r_work (start): 0.4464 rms_B_bonded: 8.88 r_work: 0.4227 rms_B_bonded: 7.05 restraints_weight: 2.0000 r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4227 r_free = 0.4227 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4227 r_free = 0.4227 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 moved from start: 1.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.181 22559 Z= 0.267 Angle : 0.922 29.032 30906 Z= 0.460 Chirality : 0.051 0.616 3581 Planarity : 0.006 0.097 3748 Dihedral : 13.326 146.543 3738 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.38 % Favored : 90.43 % Rotamer: Outliers : 3.73 % Allowed : 32.53 % Favored : 63.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.52 (0.15), residues: 2650 helix: -0.83 (0.16), residues: 940 sheet: -1.63 (0.38), residues: 184 loop : -2.31 (0.15), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 392 TYR 0.040 0.003 TYR A 38 PHE 0.043 0.003 PHE A 101 TRP 0.042 0.003 TRP B 182 HIS 0.014 0.002 HIS A 810 Details of bonding type rmsd covalent geometry : bond 0.00579 (22527) covalent geometry : angle 0.90140 (30879) hydrogen bonds : bond 0.05880 ( 842) hydrogen bonds : angle 6.47510 ( 2324) metal coordination : bond 0.02071 ( 32) metal coordination : angle 6.62112 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 213 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: -0.1631 (OUTLIER) cc_final: -0.2243 (t) REVERT: A 31 VAL cc_start: 0.3569 (OUTLIER) cc_final: 0.3365 (m) REVERT: A 124 MET cc_start: 0.1691 (mtp) cc_final: -0.2545 (ttm) REVERT: A 211 ASP cc_start: 0.7037 (OUTLIER) cc_final: 0.5148 (p0) REVERT: A 289 TYR cc_start: 0.5274 (m-80) cc_final: 0.3070 (m-80) REVERT: A 389 LEU cc_start: 0.6568 (pp) cc_final: 0.6271 (mp) REVERT: A 405 VAL cc_start: 0.8045 (t) cc_final: 0.7750 (p) REVERT: A 610 GLU cc_start: 0.7926 (tp30) cc_final: 0.7722 (mm-30) REVERT: A 654 ARG cc_start: 0.8473 (mmp80) cc_final: 0.7799 (mmp80) REVERT: A 728 TYR cc_start: 0.7004 (t80) cc_final: 0.6582 (t80) REVERT: A 818 MET cc_start: 0.7834 (pmm) cc_final: 0.7154 (ptt) REVERT: A 884 TYR cc_start: 0.8966 (OUTLIER) cc_final: 0.7797 (m-80) REVERT: B 182 TRP cc_start: 0.3549 (m100) cc_final: 0.3110 (t60) REVERT: C 34 GLN cc_start: 0.7906 (pp30) cc_final: 0.7427 (tp-100) REVERT: C 38 ASP cc_start: 0.8566 (m-30) cc_final: 0.8164 (t0) REVERT: D 75 ARG cc_start: 0.6745 (mmp80) cc_final: 0.6445 (tpt90) REVERT: D 128 LEU cc_start: 0.2717 (OUTLIER) cc_final: 0.2356 (tp) REVERT: D 142 CYS cc_start: 0.0707 (OUTLIER) cc_final: -0.0339 (t) REVERT: D 189 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7198 (mm) REVERT: E 65 LEU cc_start: 0.7037 (tp) cc_final: 0.6698 (pp) REVERT: E 131 LYS cc_start: 0.6499 (OUTLIER) cc_final: 0.5956 (tttp) REVERT: E 378 MET cc_start: 0.6918 (ppp) cc_final: 0.6509 (ppp) REVERT: E 475 PHE cc_start: 0.4974 (OUTLIER) cc_final: 0.4415 (p90) REVERT: G 12 MET cc_start: 0.7635 (mmm) cc_final: 0.7147 (mmm) REVERT: G 23 CYS cc_start: 0.1895 (OUTLIER) cc_final: 0.0355 (m) REVERT: G 31 TYR cc_start: 0.7734 (m-80) cc_final: 0.7417 (m-80) REVERT: G 52 LYS cc_start: 0.6861 (OUTLIER) cc_final: 0.6194 (tptp) REVERT: G 66 TYR cc_start: 0.5283 (m-80) cc_final: 0.4612 (p90) REVERT: G 69 LEU cc_start: 0.4649 (tp) cc_final: 0.3640 (tp) outliers start: 84 outliers final: 49 residues processed: 284 average time/residue: 0.1404 time to fit residues: 61.3131 Evaluate side-chains 240 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 180 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 884 TYR Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 373 PHE Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 475 PHE Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 52 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 89 optimal weight: 0.9980 chunk 203 optimal weight: 0.9990 chunk 265 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 140 optimal weight: 20.0000 chunk 173 optimal weight: 0.0050 chunk 197 optimal weight: 0.9980 chunk 260 optimal weight: 0.2980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN A 534 ASN A 572 HIS B 136 ASN ** F 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5086 r_free = 0.5086 target = 0.182258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.144721 restraints weight = 134931.073| |-----------------------------------------------------------------------------| r_work (start): 0.4607 rms_B_bonded: 10.87 r_work: 0.4275 rms_B_bonded: 7.73 restraints_weight: 2.0000 r_work: 0.4416 rms_B_bonded: 5.02 restraints_weight: 4.0000 r_work (final): 0.4416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4404 r_free = 0.4404 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4404 r_free = 0.4404 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4404 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 moved from start: 1.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22559 Z= 0.146 Angle : 0.791 18.464 30906 Z= 0.392 Chirality : 0.045 0.254 3581 Planarity : 0.005 0.083 3748 Dihedral : 13.102 145.011 3738 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.83 % Favored : 92.02 % Rotamer: Outliers : 2.55 % Allowed : 33.71 % Favored : 63.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.23 (0.16), residues: 2650 helix: -0.49 (0.16), residues: 941 sheet: -1.47 (0.39), residues: 173 loop : -2.21 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 96 TYR 0.021 0.002 TYR G 32 PHE 0.026 0.002 PHE A 101 TRP 0.028 0.002 TRP A 509 HIS 0.012 0.001 HIS E 290 Details of bonding type rmsd covalent geometry : bond 0.00321 (22527) covalent geometry : angle 0.77454 (30879) hydrogen bonds : bond 0.04838 ( 842) hydrogen bonds : angle 5.98149 ( 2324) metal coordination : bond 0.01882 ( 32) metal coordination : angle 5.52800 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 195 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: -0.2066 (OUTLIER) cc_final: -0.2539 (t) REVERT: A 31 VAL cc_start: 0.3018 (OUTLIER) cc_final: 0.2774 (m) REVERT: A 91 LYS cc_start: 0.7166 (tmmt) cc_final: 0.6600 (tppt) REVERT: A 124 MET cc_start: 0.0775 (mtp) cc_final: -0.2175 (ttm) REVERT: A 129 TYR cc_start: 0.2261 (t80) cc_final: 0.1257 (t80) REVERT: A 251 LEU cc_start: 0.3208 (pt) cc_final: 0.2478 (mp) REVERT: A 519 MET cc_start: 0.3969 (pmm) cc_final: 0.3437 (pmm) REVERT: A 665 GLU cc_start: 0.7347 (pm20) cc_final: 0.6943 (pm20) REVERT: A 728 TYR cc_start: 0.6193 (t80) cc_final: 0.5573 (t80) REVERT: A 818 MET cc_start: 0.7597 (pmm) cc_final: 0.7289 (ptt) REVERT: A 884 TYR cc_start: 0.9003 (OUTLIER) cc_final: 0.7737 (m-80) REVERT: B 87 MET cc_start: 0.5561 (mtp) cc_final: 0.4091 (tpt) REVERT: C 34 GLN cc_start: 0.7724 (pp30) cc_final: 0.6700 (tp-100) REVERT: C 51 LYS cc_start: 0.8533 (ttpt) cc_final: 0.8240 (ttpp) REVERT: D 138 TYR cc_start: 0.5577 (t80) cc_final: 0.5202 (t80) REVERT: D 142 CYS cc_start: 0.0549 (OUTLIER) cc_final: -0.0264 (t) REVERT: D 182 TRP cc_start: 0.4105 (OUTLIER) cc_final: 0.2797 (m-10) REVERT: D 189 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6803 (mm) REVERT: E 131 LYS cc_start: 0.6263 (OUTLIER) cc_final: 0.5707 (tttp) REVERT: E 378 MET cc_start: 0.6723 (ppp) cc_final: 0.6404 (ppp) REVERT: G 12 MET cc_start: 0.7396 (mmm) cc_final: 0.6979 (mmm) REVERT: G 23 CYS cc_start: 0.1764 (OUTLIER) cc_final: 0.0245 (m) REVERT: G 31 TYR cc_start: 0.7747 (m-80) cc_final: 0.7368 (m-80) REVERT: G 52 LYS cc_start: 0.6559 (OUTLIER) cc_final: 0.5945 (tptp) REVERT: G 66 TYR cc_start: 0.5075 (m-80) cc_final: 0.4345 (p90) REVERT: G 69 LEU cc_start: 0.4301 (tp) cc_final: 0.3415 (tp) outliers start: 57 outliers final: 37 residues processed: 246 average time/residue: 0.1646 time to fit residues: 62.2340 Evaluate side-chains 223 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 177 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 884 TYR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 52 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.1835 > 50: distance: 27 - 32: 17.058 distance: 32 - 33: 11.312 distance: 33 - 34: 12.301 distance: 34 - 35: 24.146 distance: 34 - 36: 13.240 distance: 36 - 37: 10.816 distance: 37 - 38: 14.519 distance: 37 - 40: 18.827 distance: 38 - 39: 17.799 distance: 38 - 45: 36.493 distance: 40 - 41: 18.209 distance: 41 - 42: 41.109 distance: 42 - 43: 11.240 distance: 43 - 44: 17.935 distance: 45 - 46: 14.820 distance: 45 - 51: 29.824 distance: 46 - 47: 29.646 distance: 46 - 49: 18.784 distance: 47 - 48: 39.125 distance: 47 - 52: 30.180 distance: 49 - 50: 32.076 distance: 50 - 51: 3.128 distance: 52 - 53: 23.451 distance: 53 - 54: 20.167 distance: 53 - 56: 20.886 distance: 54 - 55: 7.711 distance: 54 - 63: 10.037 distance: 56 - 57: 43.401 distance: 57 - 58: 4.306 distance: 58 - 59: 28.248 distance: 59 - 60: 41.044 distance: 60 - 61: 37.895 distance: 60 - 62: 37.911 distance: 63 - 64: 7.300 distance: 63 - 69: 25.005 distance: 64 - 65: 19.100 distance: 64 - 67: 15.416 distance: 65 - 66: 10.438 distance: 65 - 70: 11.883 distance: 67 - 68: 18.024 distance: 68 - 69: 18.654 distance: 70 - 71: 13.591 distance: 70 - 76: 8.452 distance: 71 - 74: 13.033 distance: 72 - 73: 8.600 distance: 72 - 77: 8.956 distance: 74 - 75: 14.202 distance: 75 - 76: 17.219 distance: 77 - 78: 4.824 distance: 78 - 79: 11.166 distance: 78 - 81: 7.041 distance: 79 - 80: 5.732 distance: 79 - 85: 5.653 distance: 81 - 82: 6.126 distance: 82 - 83: 12.865 distance: 82 - 84: 13.387 distance: 85 - 86: 12.193 distance: 86 - 87: 20.146 distance: 86 - 89: 5.815 distance: 87 - 88: 26.618 distance: 87 - 93: 5.178 distance: 89 - 90: 16.207 distance: 90 - 91: 11.017 distance: 90 - 92: 12.511 distance: 93 - 94: 31.326 distance: 94 - 95: 43.237 distance: 94 - 97: 18.098 distance: 95 - 96: 39.879 distance: 95 - 98: 5.241 distance: 98 - 99: 20.479 distance: 99 - 100: 17.695 distance: 99 - 102: 22.666 distance: 100 - 101: 27.583 distance: 100 - 106: 28.765 distance: 102 - 103: 40.813 distance: 103 - 104: 41.000 distance: 103 - 105: 49.943