Starting phenix.real_space_refine on Thu May 22 04:10:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gwi_34313/05_2025/8gwi_34313.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gwi_34313/05_2025/8gwi_34313.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gwi_34313/05_2025/8gwi_34313.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gwi_34313/05_2025/8gwi_34313.map" model { file = "/net/cci-nas-00/data/ceres_data/8gwi_34313/05_2025/8gwi_34313.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gwi_34313/05_2025/8gwi_34313.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2} 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, 'ASN:plan1': 1, 'GLN: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: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP: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: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP: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: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP: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: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP: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: 19.00, per 1000 atoms: 0.87 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: 5.60 Conformation dependent library (CDL) restraints added in 3.9 seconds 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: 7.09 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: 7.50 Time building geometry restraints manager: 6.59 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 593 or resid 701 throug \ h 703)) selection = (chain 'F' and (resid 1 through 473 or resid 475 through 593 or resid 701 throug \ h 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: 13.180 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 65.800 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5008 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 : 13.54 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (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 TRP 0.037 0.002 TRP G 53 HIS 0.007 0.001 HIS A 928 PHE 0.017 0.001 PHE F 437 TYR 0.022 0.001 TYR F 299 ARG 0.006 0.001 ARG F 303 Details of bonding type rmsd hydrogen bonds : bond 0.18370 ( 842) hydrogen bonds : angle 6.41261 ( 2324) metal coordination : bond 0.01942 ( 32) metal coordination : angle 5.22093 ( 27) covalent geometry : bond 0.00855 (22527) covalent geometry : angle 0.93982 (30879) *********************** 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 592 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 476 time to evaluate : 2.163 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: A 58 GLU cc_start: 0.5122 (tt0) cc_final: 0.4615 (tm-30) REVERT: A 73 LYS cc_start: 0.5142 (OUTLIER) cc_final: 0.4814 (pttp) REVERT: A 76 THR cc_start: 0.2705 (OUTLIER) cc_final: 0.1344 (m) REVERT: A 248 THR cc_start: 0.5941 (p) cc_final: 0.5736 (t) REVERT: A 548 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7936 (tt) REVERT: A 731 LEU cc_start: 0.4636 (OUTLIER) cc_final: 0.4251 (mt) REVERT: A 750 ARG cc_start: 0.6290 (mtp85) cc_final: 0.5789 (ttp-110) REVERT: A 857 GLU cc_start: 0.6351 (pm20) cc_final: 0.5877 (tp30) REVERT: B 58 LYS cc_start: 0.7337 (tppp) cc_final: 0.7127 (tppt) REVERT: B 148 THR cc_start: 0.5665 (p) cc_final: 0.5425 (t) REVERT: D 57 ARG cc_start: 0.5446 (mmt-90) cc_final: 0.5208 (ttp80) REVERT: D 60 GLU cc_start: 0.5644 (tm-30) cc_final: 0.5201 (mm-30) REVERT: D 182 TRP cc_start: 0.5387 (m100) cc_final: 0.4428 (m100) REVERT: F 14 LEU cc_start: 0.5261 (mt) cc_final: 0.4069 (tp) REVERT: F 133 PHE cc_start: 0.3553 (t80) cc_final: 0.3321 (t80) REVERT: F 194 GLN cc_start: 0.3459 (tm-30) cc_final: 0.3070 (tp-100) REVERT: F 396 TYR cc_start: 0.7297 (m-80) cc_final: 0.6932 (m-10) REVERT: F 419 PRO cc_start: 0.6605 (Cg_exo) cc_final: 0.6270 (Cg_endo) REVERT: F 430 LYS cc_start: 0.0919 (mtmm) cc_final: 0.0426 (mmtp) REVERT: F 576 MET cc_start: 0.2990 (mmt) cc_final: 0.2121 (mtp) REVERT: E 48 TYR cc_start: 0.5937 (m-10) cc_final: 0.5510 (m-10) REVERT: E 64 TYR cc_start: 0.6720 (m-80) cc_final: 0.6482 (m-80) REVERT: E 156 GLU cc_start: 0.2354 (pp20) cc_final: 0.1886 (mm-30) REVERT: E 175 PRO cc_start: 0.3467 (Cg_exo) cc_final: 0.2995 (Cg_endo) REVERT: E 180 TYR cc_start: 0.3908 (m-80) cc_final: 0.3699 (m-80) REVERT: E 183 THR cc_start: 0.6263 (OUTLIER) cc_final: 0.5962 (p) REVERT: E 263 SER cc_start: 0.5471 (m) cc_final: 0.5080 (p) REVERT: E 436 MET cc_start: 0.2753 (ttm) cc_final: 0.2447 (ttt) REVERT: E 460 LYS cc_start: 0.0426 (pttp) cc_final: 0.0054 (pttm) REVERT: E 572 ILE cc_start: 0.2184 (mp) cc_final: 0.1960 (mp) REVERT: E 579 ARG cc_start: 0.2913 (mmp80) cc_final: 0.2138 (mmm160) REVERT: G 33 ASN cc_start: 0.1922 (OUTLIER) cc_final: 0.1186 (t0) REVERT: G 36 LYS cc_start: 0.5719 (mppt) cc_final: 0.5078 (mppt) outliers start: 116 outliers final: 19 residues processed: 578 average time/residue: 0.3370 time to fit residues: 294.9728 Evaluate side-chains 287 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 262 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 102 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 225 optimal weight: 20.0000 chunk 202 optimal weight: 5.9990 chunk 112 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 136 optimal weight: 9.9990 chunk 108 optimal weight: 0.7980 chunk 209 optimal weight: 0.0040 chunk 80 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 155 optimal weight: 20.0000 chunk 242 optimal weight: 7.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS A 168 ASN A 752 HIS A 790 ASN B 100 ASN C 18 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS F 354 GLN F 516 ASN E 51 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 562 ASN G 27 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.229051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.196123 restraints weight = 57677.442| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 2.99 r_work: 0.3737 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3703 r_free = 0.3703 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3703 r_free = 0.3703 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 22559 Z= 0.228 Angle : 0.833 15.516 30906 Z= 0.427 Chirality : 0.047 0.323 3581 Planarity : 0.006 0.089 3748 Dihedral : 12.694 137.777 3769 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.62 % Favored : 91.11 % Rotamer: Outliers : 5.18 % Allowed : 30.03 % Favored : 64.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.15), residues: 2650 helix: 0.03 (0.17), residues: 965 sheet: -1.50 (0.32), residues: 253 loop : -2.45 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 182 HIS 0.016 0.002 HIS A 75 PHE 0.036 0.002 PHE B 15 TYR 0.025 0.002 TYR G 89 ARG 0.029 0.001 ARG F 490 Details of bonding type rmsd hydrogen bonds : bond 0.05460 ( 842) hydrogen bonds : angle 5.26558 ( 2324) metal coordination : bond 0.02257 ( 32) metal coordination : angle 5.32116 ( 27) covalent geometry : bond 0.00461 (22527) covalent geometry : angle 0.81867 (30879) *********************** 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 426 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 309 time to evaluate : 2.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 TYR cc_start: 0.7895 (p90) cc_final: 0.7656 (p90) REVERT: A 601 MET cc_start: 0.9086 (ttm) cc_final: 0.8877 (ttm) REVERT: A 648 LEU cc_start: 0.5841 (OUTLIER) cc_final: 0.5615 (tp) REVERT: B 61 LYS cc_start: 0.8428 (tmmt) cc_final: 0.8143 (tppt) REVERT: B 143 ASP cc_start: 0.5089 (p0) cc_final: 0.4810 (t0) REVERT: C 44 ASP cc_start: 0.7716 (p0) cc_final: 0.7477 (p0) REVERT: D 31 SER cc_start: 0.6895 (p) cc_final: 0.6486 (t) REVERT: D 58 LYS cc_start: 0.5607 (OUTLIER) cc_final: 0.5384 (tmtt) REVERT: D 60 GLU cc_start: 0.6424 (tm-30) cc_final: 0.6143 (mm-30) REVERT: F 297 LEU cc_start: 0.5063 (pp) cc_final: 0.4835 (tp) REVERT: F 531 GLN cc_start: -0.0701 (OUTLIER) cc_final: -0.1200 (mt0) REVERT: F 576 MET cc_start: 0.1886 (mmt) cc_final: 0.1160 (mtp) REVERT: E 183 THR cc_start: 0.5959 (m) cc_final: 0.5501 (p) REVERT: E 233 MET cc_start: 0.3111 (OUTLIER) cc_final: 0.1923 (mtt) REVERT: E 437 PHE cc_start: 0.5843 (OUTLIER) cc_final: 0.5327 (p90) REVERT: E 460 LYS cc_start: 0.0284 (pttp) cc_final: -0.0185 (pttm) REVERT: E 490 ARG cc_start: 0.2845 (ttp-170) cc_final: 0.2564 (ttp80) REVERT: G 12 MET cc_start: 0.2637 (pmm) cc_final: 0.2410 (pmm) REVERT: G 94 LEU cc_start: 0.5160 (tt) cc_final: 0.4884 (tp) outliers start: 117 outliers final: 38 residues processed: 408 average time/residue: 0.3362 time to fit residues: 210.4053 Evaluate side-chains 267 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 224 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain G residue 73 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 104 optimal weight: 0.3980 chunk 14 optimal weight: 0.0870 chunk 196 optimal weight: 20.0000 chunk 133 optimal weight: 0.9990 chunk 216 optimal weight: 0.9980 chunk 254 optimal weight: 50.0000 chunk 106 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 244 optimal weight: 0.2980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN B 158 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN E 51 ASN E 275 GLN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 562 ASN G 11 GLN G 33 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.224492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.199725 restraints weight = 77456.455| |-----------------------------------------------------------------------------| r_work (start): 0.4449 rms_B_bonded: 2.60 r_work: 0.4150 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4139 r_free = 0.4139 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4139 r_free = 0.4139 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22559 Z= 0.149 Angle : 0.699 13.731 30906 Z= 0.352 Chirality : 0.044 0.221 3581 Planarity : 0.005 0.098 3748 Dihedral : 12.335 139.216 3742 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.11 % Favored : 92.62 % Rotamer: Outliers : 3.60 % Allowed : 30.47 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.16), residues: 2650 helix: 0.28 (0.17), residues: 995 sheet: -1.03 (0.36), residues: 219 loop : -2.31 (0.15), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 182 HIS 0.005 0.001 HIS E 290 PHE 0.017 0.002 PHE E 373 TYR 0.028 0.002 TYR D 135 ARG 0.006 0.001 ARG E 390 Details of bonding type rmsd hydrogen bonds : bond 0.05080 ( 842) hydrogen bonds : angle 4.94013 ( 2324) metal coordination : bond 0.01395 ( 32) metal coordination : angle 4.18535 ( 27) covalent geometry : bond 0.00319 (22527) covalent geometry : angle 0.68869 (30879) *********************** 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 345 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 264 time to evaluate : 2.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.8287 (mmm) cc_final: 0.7996 (mmt) REVERT: A 731 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7711 (mp) REVERT: B 94 MET cc_start: 0.6201 (tmm) cc_final: 0.5640 (ttt) REVERT: D 58 LYS cc_start: 0.5262 (OUTLIER) cc_final: 0.4964 (tmtt) REVERT: D 182 TRP cc_start: 0.4345 (m100) cc_final: 0.4080 (m100) REVERT: F 378 MET cc_start: 0.0897 (mpp) cc_final: -0.1787 (mmt) REVERT: F 531 GLN cc_start: 0.0089 (OUTLIER) cc_final: -0.0661 (mt0) REVERT: F 554 HIS cc_start: -0.0910 (OUTLIER) cc_final: -0.1177 (m-70) REVERT: E 274 MET cc_start: 0.2255 (mmm) cc_final: 0.1878 (mmp) REVERT: E 460 LYS cc_start: 0.1094 (pttp) cc_final: 0.0342 (pttm) REVERT: E 579 ARG cc_start: 0.3907 (mmp80) cc_final: 0.3577 (mmp-170) outliers start: 81 outliers final: 43 residues processed: 332 average time/residue: 0.3115 time to fit residues: 162.6958 Evaluate side-chains 244 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 197 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 73 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 246 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 198 optimal weight: 0.9980 chunk 190 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 252 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 260 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS A 381 HIS ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN E 62 GLN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.215204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.182035 restraints weight = 64454.881| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 2.85 r_work: 0.3413 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.7482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 22559 Z= 0.190 Angle : 0.769 12.813 30906 Z= 0.389 Chirality : 0.046 0.274 3581 Planarity : 0.006 0.118 3748 Dihedral : 12.122 101.332 3741 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.55 % Favored : 91.23 % Rotamer: Outliers : 3.95 % Allowed : 30.64 % Favored : 65.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.16), residues: 2650 helix: 0.16 (0.17), residues: 983 sheet: -1.08 (0.34), residues: 235 loop : -2.25 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 216 HIS 0.009 0.001 HIS C 36 PHE 0.024 0.002 PHE F 357 TYR 0.051 0.002 TYR F 306 ARG 0.016 0.001 ARG G 111 Details of bonding type rmsd hydrogen bonds : bond 0.05822 ( 842) hydrogen bonds : angle 4.89205 ( 2324) metal coordination : bond 0.02087 ( 32) metal coordination : angle 4.47655 ( 27) covalent geometry : bond 0.00432 (22527) covalent geometry : angle 0.75788 (30879) *********************** 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 346 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 257 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.6485 (OUTLIER) cc_final: 0.6158 (t0) REVERT: A 281 LYS cc_start: 0.8556 (ttmt) cc_final: 0.8110 (mmtt) REVERT: A 284 ASP cc_start: 0.8294 (t70) cc_final: 0.8058 (m-30) REVERT: A 477 ASP cc_start: 0.7696 (t70) cc_final: 0.7425 (t0) REVERT: B 73 GLN cc_start: 0.7840 (tp40) cc_final: 0.7192 (tt0) REVERT: B 77 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7493 (mt-10) REVERT: B 82 LYS cc_start: 0.8690 (tmmt) cc_final: 0.8350 (tttm) REVERT: B 94 MET cc_start: 0.6744 (tmm) cc_final: 0.6410 (ttp) REVERT: B 96 ARG cc_start: 0.5718 (ttp-110) cc_final: 0.5478 (mtm110) REVERT: B 136 ASN cc_start: 0.8449 (t0) cc_final: 0.8188 (t0) REVERT: B 165 LYS cc_start: 0.8342 (mttt) cc_final: 0.7830 (mmtt) REVERT: F 120 TYR cc_start: 0.4872 (OUTLIER) cc_final: 0.4576 (m-80) REVERT: F 233 MET cc_start: 0.4507 (pmm) cc_final: 0.4084 (ppp) REVERT: F 343 PHE cc_start: 0.2605 (t80) cc_final: 0.1719 (m-80) REVERT: F 531 GLN cc_start: 0.0066 (OUTLIER) cc_final: -0.0544 (mt0) REVERT: E 233 MET cc_start: 0.3964 (OUTLIER) cc_final: 0.2809 (mtp) REVERT: E 405 LEU cc_start: 0.2193 (OUTLIER) cc_final: 0.1967 (pt) REVERT: E 429 MET cc_start: 0.3449 (ptp) cc_final: 0.3075 (mmp) REVERT: E 579 ARG cc_start: 0.3238 (mmp80) cc_final: 0.2501 (mmp-170) outliers start: 89 outliers final: 46 residues processed: 331 average time/residue: 0.3392 time to fit residues: 173.5492 Evaluate side-chains 268 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 217 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 44 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 73 optimal weight: 0.2980 chunk 180 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 172 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 209 optimal weight: 10.0000 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 158 ASN ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 GLN A 497 ASN C 63 GLN D 43 ASN D 73 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 459 ASN ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.213117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.175697 restraints weight = 64827.468| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 3.02 r_work: 0.3421 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3394 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3394 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.7899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 22559 Z= 0.127 Angle : 0.643 13.758 30906 Z= 0.323 Chirality : 0.042 0.228 3581 Planarity : 0.004 0.062 3748 Dihedral : 11.854 73.798 3739 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.03 % Favored : 92.74 % Rotamer: Outliers : 3.07 % Allowed : 31.04 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.16), residues: 2650 helix: 0.37 (0.17), residues: 994 sheet: -1.24 (0.33), residues: 246 loop : -2.17 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 182 HIS 0.006 0.001 HIS C 36 PHE 0.020 0.001 PHE E 422 TYR 0.017 0.001 TYR F 31 ARG 0.009 0.001 ARG E 490 Details of bonding type rmsd hydrogen bonds : bond 0.04916 ( 842) hydrogen bonds : angle 4.63521 ( 2324) metal coordination : bond 0.01526 ( 32) metal coordination : angle 4.02985 ( 27) covalent geometry : bond 0.00277 (22527) covalent geometry : angle 0.63170 (30879) *********************** 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 295 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 226 time to evaluate : 2.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 LYS cc_start: 0.8723 (ttmt) cc_final: 0.8170 (mmtt) REVERT: A 284 ASP cc_start: 0.8726 (t70) cc_final: 0.8499 (m-30) REVERT: A 477 ASP cc_start: 0.7925 (t70) cc_final: 0.7673 (t0) REVERT: B 73 GLN cc_start: 0.7946 (tp40) cc_final: 0.7476 (tt0) REVERT: B 82 LYS cc_start: 0.8690 (tmmt) cc_final: 0.8371 (tttm) REVERT: B 94 MET cc_start: 0.7037 (tmm) cc_final: 0.6809 (ttp) REVERT: D 65 GLN cc_start: 0.7608 (tm-30) cc_final: 0.7011 (mm-40) REVERT: F 120 TYR cc_start: 0.4720 (OUTLIER) cc_final: 0.4273 (m-80) REVERT: F 343 PHE cc_start: 0.2149 (t80) cc_final: 0.1468 (m-80) REVERT: F 497 ARG cc_start: 0.2888 (mmp80) cc_final: 0.1756 (mmt180) REVERT: F 531 GLN cc_start: 0.0238 (OUTLIER) cc_final: -0.0474 (mt0) REVERT: E 233 MET cc_start: 0.4001 (OUTLIER) cc_final: 0.2815 (mtp) REVERT: E 579 ARG cc_start: 0.3695 (mmp80) cc_final: 0.2946 (mmp-170) REVERT: G 86 LYS cc_start: 0.0090 (mmtm) cc_final: -0.0143 (mmtp) outliers start: 69 outliers final: 36 residues processed: 276 average time/residue: 0.3495 time to fit residues: 152.5456 Evaluate side-chains 243 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 204 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 77 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 124 optimal weight: 1.9990 chunk 205 optimal weight: 10.0000 chunk 217 optimal weight: 10.0000 chunk 244 optimal weight: 20.0000 chunk 185 optimal weight: 9.9990 chunk 250 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 239 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN D 73 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.209290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.167995 restraints weight = 52014.645| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 3.24 r_work: 0.3588 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.8585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 22559 Z= 0.157 Angle : 0.673 13.486 30906 Z= 0.339 Chirality : 0.043 0.263 3581 Planarity : 0.005 0.057 3748 Dihedral : 11.660 73.788 3738 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.72 % Favored : 92.06 % Rotamer: Outliers : 2.90 % Allowed : 30.51 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.16), residues: 2650 helix: 0.43 (0.17), residues: 992 sheet: -1.22 (0.33), residues: 248 loop : -2.15 (0.15), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.009 0.001 HIS C 36 PHE 0.031 0.002 PHE F 145 TYR 0.019 0.002 TYR F 31 ARG 0.008 0.001 ARG E 490 Details of bonding type rmsd hydrogen bonds : bond 0.05368 ( 842) hydrogen bonds : angle 4.54663 ( 2324) metal coordination : bond 0.02195 ( 32) metal coordination : angle 4.23021 ( 27) covalent geometry : bond 0.00353 (22527) covalent geometry : angle 0.66171 (30879) *********************** 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 286 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 221 time to evaluate : 2.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 ASP cc_start: 0.7462 (t0) cc_final: 0.6979 (p0) REVERT: A 284 ASP cc_start: 0.8802 (t70) cc_final: 0.8585 (m-30) REVERT: A 477 ASP cc_start: 0.8066 (t70) cc_final: 0.7841 (t0) REVERT: B 73 GLN cc_start: 0.8087 (tp40) cc_final: 0.7729 (tt0) REVERT: B 80 ARG cc_start: 0.8079 (ttt180) cc_final: 0.7874 (ttt-90) REVERT: B 96 ARG cc_start: 0.6163 (ttp-110) cc_final: 0.5921 (mtm110) REVERT: D 70 MET cc_start: 0.8420 (ttp) cc_final: 0.8167 (ttp) REVERT: F 120 TYR cc_start: 0.4379 (OUTLIER) cc_final: 0.3722 (m-80) REVERT: F 343 PHE cc_start: 0.1390 (t80) cc_final: 0.0957 (m-80) REVERT: F 497 ARG cc_start: 0.2558 (mmp80) cc_final: 0.1522 (mmt180) REVERT: F 531 GLN cc_start: 0.0663 (OUTLIER) cc_final: -0.0127 (mt0) REVERT: E 233 MET cc_start: 0.4021 (OUTLIER) cc_final: 0.2880 (mtt) REVERT: E 579 ARG cc_start: 0.4107 (mmp80) cc_final: 0.3365 (mmp-170) outliers start: 65 outliers final: 42 residues processed: 269 average time/residue: 0.3270 time to fit residues: 136.7619 Evaluate side-chains 242 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 197 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 398 TYR Chi-restraints excluded: chain F residue 421 TYR Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 73 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 192 optimal weight: 0.4980 chunk 245 optimal weight: 10.0000 chunk 222 optimal weight: 0.1980 chunk 239 optimal weight: 1.9990 chunk 206 optimal weight: 0.4980 chunk 177 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 165 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 GLN D 73 GLN ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.208706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.168661 restraints weight = 59114.368| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 3.15 r_work: 0.3277 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.9054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.274 22559 Z= 0.152 Angle : 0.649 14.415 30906 Z= 0.326 Chirality : 0.043 0.238 3581 Planarity : 0.004 0.053 3748 Dihedral : 11.642 73.770 3738 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.88 % Favored : 92.93 % Rotamer: Outliers : 2.94 % Allowed : 30.33 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.16), residues: 2650 helix: 0.54 (0.17), residues: 992 sheet: -1.15 (0.35), residues: 233 loop : -2.10 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.020 0.001 HIS F 75 PHE 0.025 0.002 PHE F 472 TYR 0.029 0.001 TYR B 71 ARG 0.006 0.001 ARG E 490 Details of bonding type rmsd hydrogen bonds : bond 0.05093 ( 842) hydrogen bonds : angle 4.54050 ( 2324) metal coordination : bond 0.05030 ( 32) metal coordination : angle 4.86591 ( 27) covalent geometry : bond 0.00338 (22527) covalent geometry : angle 0.63312 (30879) *********************** 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 273 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 207 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 ASP cc_start: 0.8050 (t0) cc_final: 0.7759 (t0) REVERT: A 284 ASP cc_start: 0.8867 (t70) cc_final: 0.8623 (m-30) REVERT: A 477 ASP cc_start: 0.8014 (t70) cc_final: 0.7761 (t0) REVERT: A 857 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7438 (tp30) REVERT: B 67 MET cc_start: 0.8298 (tpt) cc_final: 0.8010 (tpt) REVERT: B 73 GLN cc_start: 0.8031 (tp40) cc_final: 0.7746 (tt0) REVERT: B 80 ARG cc_start: 0.8049 (ttt180) cc_final: 0.7745 (ttt-90) REVERT: B 153 LEU cc_start: 0.8646 (mp) cc_final: 0.8430 (mt) REVERT: F 270 GLN cc_start: 0.5736 (tp-100) cc_final: 0.4875 (mm110) REVERT: F 343 PHE cc_start: 0.2145 (t80) cc_final: 0.1498 (m-80) REVERT: F 497 ARG cc_start: 0.2961 (mmp80) cc_final: 0.1837 (mmt180) REVERT: F 531 GLN cc_start: 0.0511 (OUTLIER) cc_final: -0.0142 (mt0) REVERT: F 545 ILE cc_start: 0.3349 (mm) cc_final: 0.3102 (mt) REVERT: E 233 MET cc_start: 0.4538 (OUTLIER) cc_final: 0.3310 (mtt) REVERT: E 576 MET cc_start: 0.3865 (ppp) cc_final: 0.2693 (pmm) REVERT: E 579 ARG cc_start: 0.3701 (mmp80) cc_final: 0.2900 (mmp-170) REVERT: G 86 LYS cc_start: 0.1280 (mmtm) cc_final: 0.0798 (mmtp) outliers start: 66 outliers final: 45 residues processed: 255 average time/residue: 0.3304 time to fit residues: 133.3334 Evaluate side-chains 242 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 194 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 421 TYR Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 45 optimal weight: 0.6980 chunk 150 optimal weight: 0.0570 chunk 51 optimal weight: 0.0570 chunk 141 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 173 optimal weight: 0.6980 chunk 16 optimal weight: 0.0870 chunk 62 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 HIS ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 519 ASN ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.210434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.168813 restraints weight = 76808.293| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 8.35 r_work: 0.3095 rms_B_bonded: 5.63 restraints_weight: 2.0000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.9185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.323 22559 Z= 0.117 Angle : 0.618 13.396 30906 Z= 0.309 Chirality : 0.041 0.220 3581 Planarity : 0.004 0.049 3748 Dihedral : 11.559 73.703 3738 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.22 % Favored : 92.59 % Rotamer: Outliers : 1.84 % Allowed : 31.69 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.16), residues: 2650 helix: 0.73 (0.17), residues: 992 sheet: -1.27 (0.33), residues: 242 loop : -1.97 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 182 HIS 0.008 0.001 HIS E 290 PHE 0.022 0.001 PHE F 472 TYR 0.017 0.001 TYR F 31 ARG 0.006 0.000 ARG D 111 Details of bonding type rmsd hydrogen bonds : bond 0.04498 ( 842) hydrogen bonds : angle 4.36097 ( 2324) metal coordination : bond 0.05862 ( 32) metal coordination : angle 4.60982 ( 27) covalent geometry : bond 0.00231 (22527) covalent geometry : angle 0.60346 (30879) *********************** 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 259 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 ASP cc_start: 0.8256 (t0) cc_final: 0.7860 (t0) REVERT: A 284 ASP cc_start: 0.8855 (t70) cc_final: 0.8515 (m-30) REVERT: A 477 ASP cc_start: 0.8126 (t70) cc_final: 0.7783 (t0) REVERT: A 768 SER cc_start: 0.8872 (t) cc_final: 0.8347 (p) REVERT: B 67 MET cc_start: 0.8297 (tpt) cc_final: 0.7905 (tpt) REVERT: B 80 ARG cc_start: 0.8081 (ttt180) cc_final: 0.7808 (ttt-90) REVERT: B 87 MET cc_start: 0.8153 (ttm) cc_final: 0.7935 (mtm) REVERT: F 270 GLN cc_start: 0.5358 (tp-100) cc_final: 0.4927 (mm110) REVERT: F 343 PHE cc_start: 0.2575 (t80) cc_final: 0.2139 (m-80) REVERT: F 497 ARG cc_start: 0.2896 (mmp80) cc_final: 0.2130 (mmt180) REVERT: F 531 GLN cc_start: 0.0548 (OUTLIER) cc_final: 0.0155 (mt0) REVERT: F 545 ILE cc_start: 0.2749 (mm) cc_final: 0.2502 (mt) REVERT: E 233 MET cc_start: 0.4391 (OUTLIER) cc_final: 0.3378 (mtt) REVERT: E 576 MET cc_start: 0.3238 (ppp) cc_final: 0.2292 (pmm) REVERT: E 579 ARG cc_start: 0.3270 (mmp80) cc_final: 0.2653 (mmp-170) outliers start: 41 outliers final: 32 residues processed: 249 average time/residue: 0.3169 time to fit residues: 123.3237 Evaluate side-chains 229 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 145 PHE Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 73 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 50 optimal weight: 0.8980 chunk 249 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 237 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 262 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 ASN D 73 GLN ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 537 GLN ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.206733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.168518 restraints weight = 59854.157| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 2.81 r_work: 0.3265 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.9552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.323 22559 Z= 0.176 Angle : 0.677 14.877 30906 Z= 0.340 Chirality : 0.044 0.277 3581 Planarity : 0.005 0.153 3748 Dihedral : 11.626 73.885 3738 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.38 % Favored : 92.44 % Rotamer: Outliers : 2.15 % Allowed : 31.56 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.16), residues: 2650 helix: 0.60 (0.17), residues: 991 sheet: -1.12 (0.33), residues: 247 loop : -2.00 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 268 HIS 0.010 0.001 HIS C 36 PHE 0.020 0.002 PHE A 741 TYR 0.020 0.002 TYR F 31 ARG 0.008 0.001 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.05536 ( 842) hydrogen bonds : angle 4.48002 ( 2324) metal coordination : bond 0.05903 ( 32) metal coordination : angle 5.10574 ( 27) covalent geometry : bond 0.00400 (22527) covalent geometry : angle 0.66051 (30879) *********************** 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 245 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 197 time to evaluate : 2.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 ASP cc_start: 0.8101 (t0) cc_final: 0.7818 (t0) REVERT: A 477 ASP cc_start: 0.8098 (t70) cc_final: 0.7710 (t0) REVERT: A 857 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7497 (tp30) REVERT: B 67 MET cc_start: 0.8325 (tpt) cc_final: 0.7998 (tpt) REVERT: B 171 GLU cc_start: 0.7471 (pt0) cc_final: 0.7266 (pt0) REVERT: F 270 GLN cc_start: 0.5756 (tp-100) cc_final: 0.4932 (mm110) REVERT: F 343 PHE cc_start: 0.2107 (t80) cc_final: 0.1528 (m-80) REVERT: F 497 ARG cc_start: 0.2930 (mmp80) cc_final: 0.1829 (mmt180) REVERT: F 531 GLN cc_start: 0.0490 (OUTLIER) cc_final: -0.0159 (mt0) REVERT: F 545 ILE cc_start: 0.3412 (mm) cc_final: 0.3167 (mt) REVERT: E 147 LEU cc_start: 0.6432 (OUTLIER) cc_final: 0.6206 (tt) REVERT: E 233 MET cc_start: 0.4788 (OUTLIER) cc_final: 0.3699 (mtt) REVERT: E 576 MET cc_start: 0.4139 (OUTLIER) cc_final: 0.3100 (pmm) REVERT: E 579 ARG cc_start: 0.3578 (mmp80) cc_final: 0.2938 (mmp-170) outliers start: 48 outliers final: 36 residues processed: 233 average time/residue: 0.3398 time to fit residues: 124.4661 Evaluate side-chains 226 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 185 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 145 PHE Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 576 MET Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 73 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 181 optimal weight: 0.6980 chunk 161 optimal weight: 0.8980 chunk 53 optimal weight: 0.0870 chunk 187 optimal weight: 7.9990 chunk 84 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 225 optimal weight: 6.9990 chunk 192 optimal weight: 0.0770 chunk 175 optimal weight: 10.0000 chunk 64 optimal weight: 0.4980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 790 ASN B 109 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.208939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.169600 restraints weight = 54039.033| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 3.09 r_work: 0.3280 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.9655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.237 22559 Z= 0.118 Angle : 0.631 15.209 30906 Z= 0.315 Chirality : 0.041 0.219 3581 Planarity : 0.005 0.124 3748 Dihedral : 11.533 73.728 3738 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.34 % Favored : 92.51 % Rotamer: Outliers : 2.02 % Allowed : 31.83 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.16), residues: 2650 helix: 0.79 (0.17), residues: 987 sheet: -1.14 (0.34), residues: 252 loop : -1.92 (0.16), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 182 HIS 0.005 0.001 HIS C 36 PHE 0.021 0.001 PHE D 15 TYR 0.019 0.001 TYR F 31 ARG 0.015 0.000 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.04630 ( 842) hydrogen bonds : angle 4.35755 ( 2324) metal coordination : bond 0.04282 ( 32) metal coordination : angle 4.97204 ( 27) covalent geometry : bond 0.00245 (22527) covalent geometry : angle 0.61408 (30879) ********************** 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 247 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 202 time to evaluate : 2.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 ASP cc_start: 0.7981 (t0) cc_final: 0.7720 (t0) REVERT: A 477 ASP cc_start: 0.8038 (t70) cc_final: 0.7792 (t0) REVERT: A 768 SER cc_start: 0.8674 (t) cc_final: 0.8120 (p) REVERT: B 67 MET cc_start: 0.8271 (tpt) cc_final: 0.7930 (tpt) REVERT: F 270 GLN cc_start: 0.5684 (tp-100) cc_final: 0.4921 (mm110) REVERT: F 343 PHE cc_start: 0.2306 (t80) cc_final: 0.1632 (m-80) REVERT: F 497 ARG cc_start: 0.2910 (mmp80) cc_final: 0.1837 (mmt180) REVERT: F 531 GLN cc_start: 0.0472 (OUTLIER) cc_final: -0.0170 (mt0) REVERT: F 545 ILE cc_start: 0.3337 (mm) cc_final: 0.3102 (mt) REVERT: E 147 LEU cc_start: 0.6460 (OUTLIER) cc_final: 0.6237 (tt) REVERT: E 233 MET cc_start: 0.4742 (OUTLIER) cc_final: 0.3831 (mtp) REVERT: E 576 MET cc_start: 0.3923 (OUTLIER) cc_final: 0.2990 (pmm) REVERT: E 579 ARG cc_start: 0.3495 (mmp80) cc_final: 0.2887 (mmp-170) outliers start: 45 outliers final: 36 residues processed: 235 average time/residue: 0.3444 time to fit residues: 125.7560 Evaluate side-chains 232 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 145 PHE Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 398 TYR Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 576 MET Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 73 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 243 optimal weight: 20.0000 chunk 263 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 266 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 73 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 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 = 0.4540 r_free = 0.4540 target = 0.208875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.168744 restraints weight = 58803.583| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 3.15 r_work: 0.3291 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3274 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3274 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.9669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.378 22559 Z= 0.185 Angle : 0.796 59.193 30906 Z= 0.435 Chirality : 0.043 0.401 3581 Planarity : 0.006 0.237 3748 Dihedral : 11.536 73.784 3738 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.15 % Favored : 92.70 % Rotamer: Outliers : 2.19 % Allowed : 31.78 % Favored : 66.02 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.16), residues: 2650 helix: 0.78 (0.17), residues: 988 sheet: -1.14 (0.34), residues: 252 loop : -1.91 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 182 HIS 0.006 0.001 HIS C 36 PHE 0.020 0.001 PHE D 15 TYR 0.019 0.001 TYR F 31 ARG 0.058 0.001 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.04693 ( 842) hydrogen bonds : angle 4.35780 ( 2324) metal coordination : bond 0.07865 ( 32) metal coordination : angle 4.24598 ( 27) covalent geometry : bond 0.00349 (22527) covalent geometry : angle 0.78647 (30879) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13053.34 seconds wall clock time: 226 minutes 46.17 seconds (13606.17 seconds total)