Starting phenix.real_space_refine on Thu May 22 04:03:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gwg_34312/05_2025/8gwg_34312.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gwg_34312/05_2025/8gwg_34312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gwg_34312/05_2025/8gwg_34312.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gwg_34312/05_2025/8gwg_34312.map" model { file = "/net/cci-nas-00/data/ceres_data/8gwg_34312/05_2025/8gwg_34312.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gwg_34312/05_2025/8gwg_34312.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 55 5.49 5 S 158 5.16 5 C 13735 2.51 5 N 3694 2.21 5 O 4305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.06s 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: 17.24, per 1000 atoms: 0.79 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: 5.37 Conformation dependent library (CDL) restraints added in 3.4 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: 7.70 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: 7.73 Time building geometry restraints manager: 6.25 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: 10.050 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: 0.030 Extract box with map and model: 0.980 Check model and map are aligned: 0.160 Set scattering table: 0.230 Process input model: 62.980 Find NCS groups from input model: 0.550 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: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1795 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.055 22559 Z= 0.327 Angle : 0.952 34.266 30906 Z= 0.546 Chirality : 0.063 1.605 3581 Planarity : 0.006 0.140 3748 Dihedral : 18.826 166.450 8472 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.54 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 463 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 347 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: -0.2328 (OUTLIER) cc_final: -0.2780 (t) REVERT: A 520 SER cc_start: -0.0143 (OUTLIER) cc_final: -0.0412 (t) REVERT: A 629 MET cc_start: 0.0013 (mmm) cc_final: -0.0275 (pmm) REVERT: A 835 SER cc_start: 0.1783 (OUTLIER) cc_final: 0.1238 (m) REVERT: D 62 MET cc_start: 0.1578 (tmm) cc_final: 0.1267 (ppp) REVERT: D 179 ASN cc_start: 0.3873 (OUTLIER) cc_final: 0.2321 (m-40) REVERT: D 187 THR cc_start: 0.4711 (OUTLIER) cc_final: 0.3903 (p) REVERT: D 189 LEU cc_start: 0.6175 (mp) cc_final: 0.5881 (mt) REVERT: F 43 LEU cc_start: 0.7239 (mt) cc_final: 0.6989 (tt) REVERT: F 247 VAL cc_start: 0.4141 (t) cc_final: 0.2619 (t) REVERT: F 248 ARG cc_start: 0.5941 (tmm160) cc_final: 0.5060 (ptt-90) REVERT: F 274 MET cc_start: 0.2108 (ppp) cc_final: 0.1751 (pmm) REVERT: F 305 VAL cc_start: 0.7848 (t) cc_final: 0.7422 (t) REVERT: F 453 SER cc_start: -0.2824 (OUTLIER) cc_final: -0.3137 (m) REVERT: F 539 SER cc_start: 0.3734 (m) cc_final: 0.3234 (p) REVERT: F 561 PHE cc_start: 0.2848 (p90) cc_final: 0.2497 (m-10) REVERT: E 315 ASP cc_start: 0.6714 (OUTLIER) cc_final: 0.6448 (p0) REVERT: E 430 LYS cc_start: 0.5031 (tmtm) cc_final: 0.4704 (mmtt) outliers start: 116 outliers final: 22 residues processed: 448 average time/residue: 0.3300 time to fit residues: 229.0347 Evaluate side-chains 224 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain F residue 453 SER Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 84 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 225 optimal weight: 7.9990 chunk 202 optimal weight: 8.9990 chunk 112 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 136 optimal weight: 9.9990 chunk 108 optimal weight: 0.7980 chunk 209 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 242 optimal weight: 6.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 ASN A 113 HIS A 184 GLN A 198 ASN A 209 ASN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN A 492 GLN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN A 816 HIS ** A 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN B 100 ASN ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN D 176 ASN F 46 ASN F 164 HIS ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 492 GLN F 516 ASN ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 516 ASN G 1 ASN G 2 ASN G 11 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5344 r_free = 0.5344 target = 0.200272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5054 r_free = 0.5054 target = 0.170934 restraints weight = 109295.059| |-----------------------------------------------------------------------------| r_work (start): 0.5034 rms_B_bonded: 8.14 r_work: 0.4828 rms_B_bonded: 6.78 restraints_weight: 2.0000 r_work (final): 0.4828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4821 r_free = 0.4821 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4821 r_free = 0.4821 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4252 moved from start: 0.5537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.122 22559 Z= 0.351 Angle : 1.203 20.375 30906 Z= 0.607 Chirality : 0.060 0.335 3581 Planarity : 0.009 0.103 3748 Dihedral : 13.863 153.399 3779 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 25.82 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.25 % Favored : 89.45 % Rotamer: Outliers : 8.03 % Allowed : 29.32 % Favored : 62.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.20 % 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: -3.20 (0.15), residues: 2650 helix: -1.33 (0.15), residues: 955 sheet: -2.10 (0.34), residues: 203 loop : -2.77 (0.14), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.006 TRP A 216 HIS 0.025 0.004 HIS F 39 PHE 0.050 0.005 PHE A 287 TYR 0.048 0.004 TYR A 163 ARG 0.018 0.002 ARG A 118 Details of bonding type rmsd hydrogen bonds : bond 0.07455 ( 842) hydrogen bonds : angle 7.11974 ( 2324) metal coordination : bond 0.04645 ( 32) metal coordination : angle 7.08049 ( 27) covalent geometry : bond 0.00749 (22527) covalent geometry : angle 1.18561 (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 452 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 270 time to evaluate : 2.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.4497 (OUTLIER) cc_final: 0.4287 (mtt180) REVERT: A 116 ARG cc_start: 0.5725 (OUTLIER) cc_final: 0.3930 (mtm-85) REVERT: A 294 TYR cc_start: 0.4499 (OUTLIER) cc_final: 0.3119 (t80) REVERT: A 326 PHE cc_start: 0.5228 (m-80) cc_final: 0.5000 (m-80) REVERT: A 629 MET cc_start: 0.2719 (mmm) cc_final: 0.2033 (pmm) REVERT: A 782 PHE cc_start: 0.5003 (m-80) cc_final: 0.4422 (m-80) REVERT: A 855 MET cc_start: 0.3535 (mmt) cc_final: 0.3292 (mmt) REVERT: A 881 PHE cc_start: 0.4434 (t80) cc_final: 0.4217 (t80) REVERT: A 924 MET cc_start: 0.6502 (OUTLIER) cc_final: 0.6135 (mmt) REVERT: B 61 LYS cc_start: 0.6586 (OUTLIER) cc_final: 0.6361 (mmtt) REVERT: B 97 LYS cc_start: 0.2864 (OUTLIER) cc_final: 0.2600 (pttm) REVERT: B 174 MET cc_start: 0.6645 (tpp) cc_final: 0.6353 (tpp) REVERT: C 63 GLN cc_start: 0.5835 (mm110) cc_final: 0.5562 (mm-40) REVERT: D 90 MET cc_start: 0.4345 (mtp) cc_final: 0.4094 (mtp) REVERT: F 60 VAL cc_start: 0.6920 (p) cc_final: 0.6535 (t) REVERT: F 185 TYR cc_start: 0.8391 (p90) cc_final: 0.8107 (p90) REVERT: F 241 VAL cc_start: 0.3397 (OUTLIER) cc_final: 0.3125 (t) REVERT: F 539 SER cc_start: 0.4164 (m) cc_final: 0.3726 (p) REVERT: E 15 ARG cc_start: 0.7905 (mtm180) cc_final: 0.7567 (mpp80) REVERT: E 51 ASN cc_start: 0.7377 (m110) cc_final: 0.6874 (t0) REVERT: E 252 LEU cc_start: 0.2522 (OUTLIER) cc_final: 0.2249 (mt) REVERT: E 359 THR cc_start: -0.4073 (OUTLIER) cc_final: -0.4396 (m) REVERT: E 378 MET cc_start: 0.6430 (ppp) cc_final: 0.6218 (tmm) REVERT: E 430 LYS cc_start: 0.5012 (tmtm) cc_final: 0.4681 (mmtt) REVERT: E 575 ILE cc_start: -0.0661 (OUTLIER) cc_final: -0.1341 (tp) REVERT: G 2 ASN cc_start: 0.4931 (OUTLIER) cc_final: 0.4400 (m110) REVERT: G 35 THR cc_start: 0.1489 (OUTLIER) cc_final: 0.1083 (m) outliers start: 182 outliers final: 56 residues processed: 426 average time/residue: 0.3372 time to fit residues: 222.9803 Evaluate side-chains 264 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 196 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 694 PHE Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 730 CYS Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 36 HIS Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 436 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 575 ILE Chi-restraints excluded: chain G residue 2 ASN Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 92 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 104 optimal weight: 0.6980 chunk 14 optimal weight: 0.0170 chunk 196 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 216 optimal weight: 9.9990 chunk 254 optimal weight: 6.9990 chunk 106 optimal weight: 0.0010 chunk 252 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 244 optimal weight: 9.9990 overall best weight: 1.5226 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 184 GLN A 292 GLN ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 ASN ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 ASN B 69 GLN B 100 ASN B 118 ASN ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 GLN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 516 ASN ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN G 33 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5212 r_free = 0.5212 target = 0.194866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.159760 restraints weight = 154267.178| |-----------------------------------------------------------------------------| r_work (start): 0.4766 rms_B_bonded: 10.41 r_work: 0.4516 rms_B_bonded: 8.69 restraints_weight: 2.0000 r_work: 0.4657 rms_B_bonded: 5.49 restraints_weight: 4.0000 r_work (final): 0.4657 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4663 r_free = 0.4663 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4663 r_free = 0.4663 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4680 moved from start: 0.6761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 22559 Z= 0.192 Angle : 0.812 14.282 30906 Z= 0.410 Chirality : 0.047 0.219 3581 Planarity : 0.006 0.054 3748 Dihedral : 13.119 132.915 3743 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.94 % Favored : 91.79 % Rotamer: Outliers : 5.14 % Allowed : 30.95 % Favored : 63.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.67 (0.15), residues: 2650 helix: -0.81 (0.16), residues: 979 sheet: -1.68 (0.34), residues: 221 loop : -2.56 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 617 HIS 0.008 0.001 HIS A 725 PHE 0.036 0.003 PHE D 92 TYR 0.030 0.002 TYR A 455 ARG 0.017 0.001 ARG E 21 Details of bonding type rmsd hydrogen bonds : bond 0.05250 ( 842) hydrogen bonds : angle 5.94601 ( 2324) metal coordination : bond 0.02705 ( 32) metal coordination : angle 4.61234 ( 27) covalent geometry : bond 0.00426 (22527) covalent geometry : angle 0.80071 (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 340 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 226 time to evaluate : 2.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.7136 (mtpp) REVERT: A 127 LEU cc_start: -0.0025 (OUTLIER) cc_final: -0.0269 (tt) REVERT: A 196 MET cc_start: -0.0758 (tpp) cc_final: -0.1625 (ptt) REVERT: A 308 LEU cc_start: 0.4398 (OUTLIER) cc_final: 0.3975 (mp) REVERT: A 408 GLN cc_start: 0.1582 (OUTLIER) cc_final: 0.0764 (mp10) REVERT: A 466 ILE cc_start: 0.4887 (OUTLIER) cc_final: 0.4216 (mp) REVERT: A 493 VAL cc_start: 0.7498 (p) cc_final: 0.7097 (p) REVERT: A 542 MET cc_start: 0.5322 (tpp) cc_final: 0.4611 (mpp) REVERT: A 629 MET cc_start: 0.3990 (mmm) cc_final: 0.3502 (pmm) REVERT: A 729 GLU cc_start: 0.6607 (mt-10) cc_final: 0.6380 (mt-10) REVERT: A 782 PHE cc_start: 0.5074 (m-80) cc_final: 0.4707 (m-80) REVERT: A 924 MET cc_start: 0.6862 (mpp) cc_final: 0.6636 (mtt) REVERT: B 78 ASP cc_start: 0.3901 (OUTLIER) cc_final: 0.3587 (m-30) REVERT: B 174 MET cc_start: 0.6733 (tpp) cc_final: 0.6443 (tpp) REVERT: F 57 VAL cc_start: -0.1313 (OUTLIER) cc_final: -0.1581 (m) REVERT: F 164 HIS cc_start: 0.4393 (OUTLIER) cc_final: 0.4189 (t-90) REVERT: F 373 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7422 (t80) REVERT: F 539 SER cc_start: 0.4516 (m) cc_final: 0.4182 (p) REVERT: E 15 ARG cc_start: 0.8018 (mtm180) cc_final: 0.7626 (mpp80) REVERT: E 68 MET cc_start: 0.8127 (mmt) cc_final: 0.7094 (pmm) REVERT: E 359 THR cc_start: -0.3801 (OUTLIER) cc_final: -0.4200 (m) REVERT: G 23 CYS cc_start: 0.0745 (OUTLIER) cc_final: -0.0122 (m) REVERT: G 35 THR cc_start: 0.2013 (OUTLIER) cc_final: 0.1645 (m) outliers start: 114 outliers final: 51 residues processed: 318 average time/residue: 0.3231 time to fit residues: 161.6944 Evaluate side-chains 250 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 187 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 781 ASN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 36 HIS Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 164 HIS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 373 PHE Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 382 TYR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain G residue 91 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 246 optimal weight: 2.9990 chunk 41 optimal weight: 0.0980 chunk 198 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 117 optimal weight: 0.0060 chunk 124 optimal weight: 0.8980 chunk 252 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 260 optimal weight: 0.8980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN A 599 HIS ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN A 724 GLN A 734 ASN B 100 ASN ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 GLN ** E 518 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 = 0.5215 r_free = 0.5215 target = 0.195448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4866 r_free = 0.4866 target = 0.162979 restraints weight = 133605.151| |-----------------------------------------------------------------------------| r_work (start): 0.4771 rms_B_bonded: 9.18 r_work: 0.4528 rms_B_bonded: 7.75 restraints_weight: 2.0000 r_work: 0.4658 rms_B_bonded: 5.27 restraints_weight: 4.0000 r_work (final): 0.4658 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4662 r_free = 0.4662 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4662 r_free = 0.4662 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4712 moved from start: 0.7332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 22559 Z= 0.138 Angle : 0.713 11.437 30906 Z= 0.358 Chirality : 0.043 0.188 3581 Planarity : 0.005 0.053 3748 Dihedral : 12.779 131.107 3741 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.98 % Favored : 91.79 % Rotamer: Outliers : 4.13 % Allowed : 30.73 % Favored : 65.14 % 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: -2.25 (0.15), residues: 2650 helix: -0.32 (0.16), residues: 956 sheet: -1.26 (0.36), residues: 199 loop : -2.43 (0.15), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 916 HIS 0.005 0.001 HIS A 725 PHE 0.020 0.002 PHE A 753 TYR 0.024 0.002 TYR G 87 ARG 0.007 0.001 ARG A 640 Details of bonding type rmsd hydrogen bonds : bond 0.04603 ( 842) hydrogen bonds : angle 5.50913 ( 2324) metal coordination : bond 0.01950 ( 32) metal coordination : angle 4.15612 ( 27) covalent geometry : bond 0.00285 (22527) covalent geometry : angle 0.70313 (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 301 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 210 time to evaluate : 2.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LYS cc_start: 0.6005 (mmtm) cc_final: 0.4874 (mtmt) REVERT: A 103 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.7281 (mtpp) REVERT: A 196 MET cc_start: -0.0676 (tpp) cc_final: -0.1096 (ptt) REVERT: A 201 ILE cc_start: 0.4431 (mt) cc_final: 0.4170 (mm) REVERT: A 308 LEU cc_start: 0.4903 (OUTLIER) cc_final: 0.4655 (mp) REVERT: A 484 ASP cc_start: 0.4803 (p0) cc_final: 0.4498 (p0) REVERT: A 629 MET cc_start: 0.4637 (mmm) cc_final: 0.4272 (pmm) REVERT: A 781 ASN cc_start: 0.6080 (OUTLIER) cc_final: 0.5136 (m-40) REVERT: A 782 PHE cc_start: 0.5182 (m-80) cc_final: 0.4959 (m-80) REVERT: B 38 LEU cc_start: 0.1900 (OUTLIER) cc_final: 0.1563 (mp) REVERT: B 174 MET cc_start: 0.6540 (tpp) cc_final: 0.6237 (tpp) REVERT: F 57 VAL cc_start: -0.2038 (OUTLIER) cc_final: -0.2273 (m) REVERT: F 164 HIS cc_start: 0.4428 (OUTLIER) cc_final: 0.4224 (t-90) REVERT: F 274 MET cc_start: 0.2224 (ppp) cc_final: 0.2008 (ppp) REVERT: F 539 SER cc_start: 0.4405 (m) cc_final: 0.4076 (p) REVERT: E 15 ARG cc_start: 0.7927 (mtm180) cc_final: 0.7569 (mpp80) REVERT: E 68 MET cc_start: 0.8024 (mmt) cc_final: 0.7080 (pmm) REVERT: E 359 THR cc_start: -0.4236 (OUTLIER) cc_final: -0.4616 (m) REVERT: G 23 CYS cc_start: 0.0363 (OUTLIER) cc_final: -0.0063 (m) REVERT: G 35 THR cc_start: 0.2029 (OUTLIER) cc_final: 0.1699 (m) outliers start: 91 outliers final: 55 residues processed: 283 average time/residue: 0.3267 time to fit residues: 146.7156 Evaluate side-chains 253 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 189 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 781 ASN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 884 TYR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 164 HIS Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 373 PHE Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 382 TYR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain G residue 92 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 44 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 35 optimal weight: 0.0470 chunk 28 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 180 optimal weight: 30.0000 chunk 76 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 172 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 209 optimal weight: 8.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN B 118 ASN ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN E 116 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5194 r_free = 0.5194 target = 0.192817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.156157 restraints weight = 130557.408| |-----------------------------------------------------------------------------| r_work (start): 0.4732 rms_B_bonded: 10.16 r_work: 0.4519 rms_B_bonded: 7.34 restraints_weight: 2.0000 r_work (final): 0.4519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4530 r_free = 0.4530 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4530 r_free = 0.4530 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5107 moved from start: 0.8277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 22559 Z= 0.156 Angle : 0.729 13.752 30906 Z= 0.365 Chirality : 0.044 0.332 3581 Planarity : 0.005 0.090 3748 Dihedral : 12.677 121.983 3741 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.87 % Favored : 91.91 % Rotamer: Outliers : 4.30 % Allowed : 30.77 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.13 (0.16), residues: 2650 helix: -0.26 (0.16), residues: 961 sheet: -1.40 (0.35), residues: 217 loop : -2.30 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 916 HIS 0.009 0.001 HIS A 113 PHE 0.021 0.002 PHE A 753 TYR 0.037 0.002 TYR D 71 ARG 0.009 0.001 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.04587 ( 842) hydrogen bonds : angle 5.56072 ( 2324) metal coordination : bond 0.01744 ( 32) metal coordination : angle 4.14304 ( 27) covalent geometry : bond 0.00330 (22527) covalent geometry : angle 0.71899 (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 301 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 206 time to evaluate : 2.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.7383 (tmmt) cc_final: 0.6895 (tppt) REVERT: A 196 MET cc_start: -0.0634 (tpp) cc_final: -0.0937 (ptt) REVERT: A 201 ILE cc_start: 0.4749 (mt) cc_final: 0.4402 (mm) REVERT: A 308 LEU cc_start: 0.5756 (OUTLIER) cc_final: 0.5418 (mp) REVERT: A 422 PHE cc_start: 0.7778 (OUTLIER) cc_final: 0.7563 (t80) REVERT: A 466 ILE cc_start: 0.5757 (OUTLIER) cc_final: 0.5123 (mp) REVERT: A 484 ASP cc_start: 0.5587 (p0) cc_final: 0.5316 (p0) REVERT: A 805 LEU cc_start: 0.3117 (OUTLIER) cc_final: 0.2809 (tp) REVERT: A 858 ARG cc_start: 0.7265 (mtp-110) cc_final: 0.6828 (ttt-90) REVERT: B 174 MET cc_start: 0.6690 (tpp) cc_final: 0.6488 (tpp) REVERT: C 35 LEU cc_start: 0.4491 (OUTLIER) cc_final: 0.4276 (tp) REVERT: F 57 VAL cc_start: -0.1653 (OUTLIER) cc_final: -0.1882 (m) REVERT: F 539 SER cc_start: 0.4501 (m) cc_final: 0.4241 (p) REVERT: E 68 MET cc_start: 0.8168 (mmt) cc_final: 0.7221 (pmm) REVERT: E 116 ASN cc_start: 0.0529 (OUTLIER) cc_final: 0.0294 (p0) REVERT: E 359 THR cc_start: -0.4443 (OUTLIER) cc_final: -0.4747 (m) REVERT: E 378 MET cc_start: 0.6785 (ppp) cc_final: 0.6411 (ppp) REVERT: G 12 MET cc_start: 0.7177 (mpp) cc_final: 0.6624 (mmp) REVERT: G 23 CYS cc_start: 0.1398 (OUTLIER) cc_final: 0.0509 (m) REVERT: G 35 THR cc_start: 0.1915 (OUTLIER) cc_final: 0.1564 (m) REVERT: G 52 LYS cc_start: 0.6497 (OUTLIER) cc_final: 0.6060 (tmtt) outliers start: 95 outliers final: 57 residues processed: 293 average time/residue: 0.3189 time to fit residues: 146.4223 Evaluate side-chains 247 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 179 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 884 TYR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 373 PHE Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 116 ASN Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 382 TYR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 86 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 124 optimal weight: 0.8980 chunk 205 optimal weight: 4.9990 chunk 217 optimal weight: 20.0000 chunk 244 optimal weight: 0.8980 chunk 185 optimal weight: 9.9990 chunk 250 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 239 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 309 HIS ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN B 69 GLN B 100 ASN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5170 r_free = 0.5170 target = 0.188202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.148648 restraints weight = 102408.421| |-----------------------------------------------------------------------------| r_work (start): 0.4625 rms_B_bonded: 8.89 r_work: 0.4447 rms_B_bonded: 6.78 restraints_weight: 2.0000 r_work (final): 0.4447 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4453 r_free = 0.4453 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4453 r_free = 0.4453 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5734 moved from start: 1.0285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.124 22559 Z= 0.218 Angle : 0.858 15.891 30906 Z= 0.432 Chirality : 0.049 0.260 3581 Planarity : 0.006 0.098 3748 Dihedral : 12.939 123.045 3741 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.43 % Favored : 91.30 % Rotamer: Outliers : 5.14 % Allowed : 30.29 % Favored : 64.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.35 (0.15), residues: 2650 helix: -0.58 (0.16), residues: 951 sheet: -1.47 (0.40), residues: 179 loop : -2.31 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 268 HIS 0.012 0.002 HIS A 725 PHE 0.032 0.003 PHE A 741 TYR 0.037 0.003 TYR A 149 ARG 0.009 0.001 ARG B 190 Details of bonding type rmsd hydrogen bonds : bond 0.05481 ( 842) hydrogen bonds : angle 6.05185 ( 2324) metal coordination : bond 0.01342 ( 32) metal coordination : angle 4.82353 ( 27) covalent geometry : bond 0.00476 (22527) covalent geometry : angle 0.84619 (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 326 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 212 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: -0.0273 (tpp) cc_final: -0.0886 (ptt) REVERT: A 619 TYR cc_start: 0.7066 (m-80) cc_final: 0.6282 (m-80) REVERT: A 663 LEU cc_start: 0.7656 (tp) cc_final: 0.7377 (tp) REVERT: A 668 MET cc_start: 0.6025 (OUTLIER) cc_final: 0.3671 (tpt) REVERT: A 781 ASN cc_start: 0.7211 (m-40) cc_final: 0.6844 (m110) REVERT: A 782 PHE cc_start: 0.6004 (m-80) cc_final: 0.5596 (m-80) REVERT: A 794 MET cc_start: -0.2327 (ttm) cc_final: -0.3196 (tpt) REVERT: A 884 TYR cc_start: 0.8960 (OUTLIER) cc_final: 0.8205 (m-80) REVERT: B 174 MET cc_start: 0.7054 (tpp) cc_final: 0.6670 (tpp) REVERT: D 128 LEU cc_start: 0.1425 (OUTLIER) cc_final: 0.0513 (tp) REVERT: F 57 VAL cc_start: -0.1422 (OUTLIER) cc_final: -0.1681 (m) REVERT: F 274 MET cc_start: 0.2302 (ppp) cc_final: 0.1793 (pmm) REVERT: F 440 THR cc_start: 0.5777 (m) cc_final: 0.4332 (p) REVERT: F 442 ARG cc_start: 0.0388 (mmt180) cc_final: -0.0676 (ptt180) REVERT: E 359 THR cc_start: -0.4880 (OUTLIER) cc_final: -0.5138 (m) REVERT: E 378 MET cc_start: 0.6711 (ppp) cc_final: 0.6353 (ppp) REVERT: E 475 PHE cc_start: 0.4711 (OUTLIER) cc_final: 0.4442 (p90) REVERT: G 23 CYS cc_start: 0.1472 (OUTLIER) cc_final: 0.0540 (m) REVERT: G 35 THR cc_start: 0.2589 (OUTLIER) cc_final: 0.2231 (m) REVERT: G 52 LYS cc_start: 0.6428 (OUTLIER) cc_final: 0.6036 (tmtt) REVERT: G 86 LYS cc_start: 0.5448 (OUTLIER) cc_final: 0.4922 (mttt) outliers start: 114 outliers final: 68 residues processed: 306 average time/residue: 0.3129 time to fit residues: 152.4044 Evaluate side-chains 259 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 181 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 884 TYR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 373 PHE Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 382 TYR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 475 PHE Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain E residue 531 GLN Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 86 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 192 optimal weight: 8.9990 chunk 245 optimal weight: 9.9990 chunk 222 optimal weight: 0.0470 chunk 239 optimal weight: 0.7980 chunk 206 optimal weight: 9.9990 chunk 177 optimal weight: 7.9990 chunk 100 optimal weight: 0.7980 chunk 93 optimal weight: 0.3980 chunk 103 optimal weight: 0.3980 chunk 165 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN B 69 GLN ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5168 r_free = 0.5168 target = 0.189708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.150230 restraints weight = 119315.536| |-----------------------------------------------------------------------------| r_work (start): 0.4647 rms_B_bonded: 10.36 r_work: 0.4479 rms_B_bonded: 6.62 restraints_weight: 2.0000 r_work (final): 0.4479 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4489 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4489 r_free = 0.4489 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4489 r_free = 0.4489 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4489 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5598 moved from start: 1.0479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22559 Z= 0.129 Angle : 0.712 14.556 30906 Z= 0.352 Chirality : 0.043 0.189 3581 Planarity : 0.005 0.077 3748 Dihedral : 12.684 124.799 3740 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.38 % Favored : 92.44 % Rotamer: Outliers : 3.73 % Allowed : 32.22 % Favored : 64.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.98 (0.16), residues: 2650 helix: -0.20 (0.16), residues: 946 sheet: -1.26 (0.40), residues: 180 loop : -2.14 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 268 HIS 0.013 0.001 HIS F 33 PHE 0.016 0.001 PHE A 753 TYR 0.019 0.001 TYR A 217 ARG 0.007 0.001 ARG E 15 Details of bonding type rmsd hydrogen bonds : bond 0.04479 ( 842) hydrogen bonds : angle 5.52126 ( 2324) metal coordination : bond 0.01537 ( 32) metal coordination : angle 4.87727 ( 27) covalent geometry : bond 0.00273 (22527) covalent geometry : angle 0.69792 (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 288 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 206 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: -0.2066 (OUTLIER) cc_final: -0.2637 (t) REVERT: A 91 LYS cc_start: 0.7565 (tmmt) cc_final: 0.7002 (tppt) REVERT: A 103 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7580 (mtpp) REVERT: A 129 TYR cc_start: 0.1664 (t80) cc_final: 0.1359 (t80) REVERT: A 196 MET cc_start: -0.0227 (tpp) cc_final: -0.0505 (ptt) REVERT: A 304 ASP cc_start: 0.6636 (p0) cc_final: 0.6366 (p0) REVERT: A 484 ASP cc_start: 0.6630 (p0) cc_final: 0.6386 (p0) REVERT: A 619 TYR cc_start: 0.7059 (m-80) cc_final: 0.4812 (m-80) REVERT: A 668 MET cc_start: 0.6333 (OUTLIER) cc_final: 0.3953 (tpt) REVERT: A 782 PHE cc_start: 0.6288 (m-80) cc_final: 0.5891 (m-80) REVERT: A 884 TYR cc_start: 0.8873 (OUTLIER) cc_final: 0.8244 (m-80) REVERT: B 174 MET cc_start: 0.6909 (tpp) cc_final: 0.6463 (tpp) REVERT: C 63 GLN cc_start: 0.5737 (mm110) cc_final: 0.5473 (mm-40) REVERT: F 57 VAL cc_start: -0.0499 (OUTLIER) cc_final: -0.0832 (m) REVERT: E 359 THR cc_start: -0.4751 (OUTLIER) cc_final: -0.5015 (m) REVERT: G 23 CYS cc_start: 0.2744 (OUTLIER) cc_final: 0.2407 (m) REVERT: G 31 TYR cc_start: 0.7189 (m-10) cc_final: 0.6780 (m-80) REVERT: G 35 THR cc_start: 0.2547 (OUTLIER) cc_final: 0.2226 (m) REVERT: G 52 LYS cc_start: 0.6098 (OUTLIER) cc_final: 0.5692 (tptp) REVERT: G 69 LEU cc_start: 0.3798 (tp) cc_final: 0.2771 (tp) REVERT: G 86 LYS cc_start: 0.6074 (OUTLIER) cc_final: 0.5522 (mppt) outliers start: 82 outliers final: 53 residues processed: 276 average time/residue: 0.3108 time to fit residues: 137.0353 Evaluate side-chains 240 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 177 time to evaluate : 2.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 884 TYR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 373 PHE Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 382 TYR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 86 LYS 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: 8.9990 chunk 51 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 173 optimal weight: 0.9990 chunk 16 optimal weight: 0.0970 chunk 62 optimal weight: 0.0000 chunk 88 optimal weight: 3.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN A 381 HIS A 414 ASN A 459 ASN A 695 ASN A 816 HIS E 9 ASN ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5155 r_free = 0.5155 target = 0.191575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.160488 restraints weight = 164377.487| |-----------------------------------------------------------------------------| r_work (start): 0.4640 rms_B_bonded: 9.19 r_work: 0.4332 rms_B_bonded: 7.60 restraints_weight: 2.0000 r_work (final): 0.4332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4366 r_free = 0.4366 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4366 r_free = 0.4366 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5720 moved from start: 1.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22559 Z= 0.134 Angle : 0.723 13.528 30906 Z= 0.356 Chirality : 0.043 0.226 3581 Planarity : 0.005 0.075 3748 Dihedral : 12.576 125.731 3740 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.60 % Favored : 92.17 % Rotamer: Outliers : 3.42 % Allowed : 32.88 % Favored : 63.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.86 (0.16), residues: 2650 helix: -0.12 (0.17), residues: 951 sheet: -1.27 (0.40), residues: 191 loop : -2.05 (0.15), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 182 HIS 0.010 0.001 HIS F 33 PHE 0.018 0.002 PHE A 753 TYR 0.033 0.002 TYR A 289 ARG 0.006 0.001 ARG A 116 Details of bonding type rmsd hydrogen bonds : bond 0.04515 ( 842) hydrogen bonds : angle 5.52434 ( 2324) metal coordination : bond 0.01331 ( 32) metal coordination : angle 4.55394 ( 27) covalent geometry : bond 0.00293 (22527) covalent geometry : angle 0.71023 (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 265 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 190 time to evaluate : 2.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: -0.1933 (OUTLIER) cc_final: -0.2526 (t) REVERT: A 91 LYS cc_start: 0.7689 (tmmt) cc_final: 0.7127 (tppt) REVERT: A 196 MET cc_start: -0.0145 (tpp) cc_final: -0.0519 (ptp) REVERT: A 380 MET cc_start: 0.3321 (ptp) cc_final: 0.2526 (pmm) REVERT: A 484 ASP cc_start: 0.6941 (p0) cc_final: 0.6648 (p0) REVERT: A 633 MET cc_start: 0.6253 (mmt) cc_final: 0.5859 (ttt) REVERT: A 666 MET cc_start: 0.5350 (ppp) cc_final: 0.4679 (ptp) REVERT: A 668 MET cc_start: 0.6544 (OUTLIER) cc_final: 0.4411 (tpt) REVERT: A 807 LYS cc_start: 0.6673 (OUTLIER) cc_final: 0.6132 (tptm) REVERT: A 884 TYR cc_start: 0.8856 (OUTLIER) cc_final: 0.8091 (m-80) REVERT: B 174 MET cc_start: 0.7018 (tpp) cc_final: 0.6566 (tpp) REVERT: F 57 VAL cc_start: -0.1216 (OUTLIER) cc_final: -0.1472 (m) REVERT: F 156 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.5791 (pm20) REVERT: G 23 CYS cc_start: 0.1591 (OUTLIER) cc_final: 0.1080 (m) REVERT: G 31 TYR cc_start: 0.7286 (m-10) cc_final: 0.6833 (m-80) REVERT: G 35 THR cc_start: 0.2341 (OUTLIER) cc_final: 0.1973 (m) REVERT: G 52 LYS cc_start: 0.6396 (OUTLIER) cc_final: 0.5906 (tptp) REVERT: G 86 LYS cc_start: 0.6087 (OUTLIER) cc_final: 0.5420 (mppt) outliers start: 75 outliers final: 51 residues processed: 255 average time/residue: 0.3363 time to fit residues: 135.0095 Evaluate side-chains 230 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 169 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 884 TYR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 382 TYR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain E residue 576 MET Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 86 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 50 optimal weight: 0.4980 chunk 249 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 16 optimal weight: 0.2980 chunk 101 optimal weight: 0.5980 chunk 11 optimal weight: 0.2980 chunk 237 optimal weight: 0.2980 chunk 56 optimal weight: 0.0770 chunk 262 optimal weight: 10.0000 chunk 102 optimal weight: 0.6980 overall best weight: 0.2938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 309 HIS ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 ASN B 69 GLN ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN E 354 GLN ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5137 r_free = 0.5137 target = 0.188142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.151494 restraints weight = 123747.134| |-----------------------------------------------------------------------------| r_work (start): 0.4639 rms_B_bonded: 9.46 r_work: 0.4373 rms_B_bonded: 7.59 restraints_weight: 2.0000 r_work: 0.4510 rms_B_bonded: 5.10 restraints_weight: 4.0000 r_work (final): 0.4510 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4537 r_free = 0.4537 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4537 r_free = 0.4537 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5582 moved from start: 1.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22559 Z= 0.123 Angle : 0.711 13.671 30906 Z= 0.347 Chirality : 0.043 0.195 3581 Planarity : 0.005 0.071 3748 Dihedral : 12.428 120.616 3740 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.19 % Favored : 92.55 % Rotamer: Outliers : 2.90 % Allowed : 33.63 % Favored : 63.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.16), residues: 2650 helix: -0.01 (0.17), residues: 940 sheet: -0.90 (0.43), residues: 161 loop : -1.96 (0.15), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 182 HIS 0.011 0.001 HIS F 33 PHE 0.018 0.001 PHE E 262 TYR 0.020 0.001 TYR A 80 ARG 0.006 0.001 ARG A 116 Details of bonding type rmsd hydrogen bonds : bond 0.04367 ( 842) hydrogen bonds : angle 5.33711 ( 2324) metal coordination : bond 0.01394 ( 32) metal coordination : angle 4.78150 ( 27) covalent geometry : bond 0.00258 (22527) covalent geometry : angle 0.69661 (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: 63 poor density : 182 time to evaluate : 2.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: -0.1992 (OUTLIER) cc_final: -0.2438 (t) REVERT: A 91 LYS cc_start: 0.7415 (tmmt) cc_final: 0.6901 (tppt) REVERT: A 124 MET cc_start: -0.0765 (mtp) cc_final: -0.3170 (ttm) REVERT: A 211 ASP cc_start: 0.5350 (p0) cc_final: 0.4611 (p0) REVERT: A 668 MET cc_start: 0.6213 (OUTLIER) cc_final: 0.4547 (tpt) REVERT: A 726 ARG cc_start: 0.7496 (mmm160) cc_final: 0.6537 (mmp80) REVERT: A 807 LYS cc_start: 0.6823 (OUTLIER) cc_final: 0.6283 (tptm) REVERT: A 884 TYR cc_start: 0.8955 (OUTLIER) cc_final: 0.8173 (m-80) REVERT: B 174 MET cc_start: 0.6623 (tpp) cc_final: 0.6154 (tpp) REVERT: F 57 VAL cc_start: -0.1394 (OUTLIER) cc_final: -0.1639 (m) REVERT: F 156 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6073 (pm20) REVERT: F 442 ARG cc_start: 0.0299 (mmt180) cc_final: -0.0753 (ptt180) REVERT: E 12 THR cc_start: -0.5366 (OUTLIER) cc_final: -0.5850 (p) REVERT: G 23 CYS cc_start: 0.1263 (OUTLIER) cc_final: 0.0779 (m) REVERT: G 31 TYR cc_start: 0.7368 (m-10) cc_final: 0.6892 (m-80) REVERT: G 35 THR cc_start: 0.2103 (OUTLIER) cc_final: 0.1731 (m) REVERT: G 52 LYS cc_start: 0.6390 (OUTLIER) cc_final: 0.5867 (tptp) REVERT: G 86 LYS cc_start: 0.6160 (OUTLIER) cc_final: 0.5496 (mppt) outliers start: 63 outliers final: 49 residues processed: 233 average time/residue: 0.3224 time to fit residues: 119.2608 Evaluate side-chains 227 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 167 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 884 TYR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 382 TYR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 86 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 181 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 187 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 225 optimal weight: 5.9990 chunk 192 optimal weight: 20.0000 chunk 175 optimal weight: 30.0000 chunk 64 optimal weight: 4.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 HIS B 73 GLN F 51 ASN F 388 ASN F 537 GLN E 88 GLN ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5035 r_free = 0.5035 target = 0.178450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.140000 restraints weight = 106424.069| |-----------------------------------------------------------------------------| r_work (start): 0.4512 rms_B_bonded: 8.25 r_work: 0.4219 rms_B_bonded: 7.17 restraints_weight: 2.0000 r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4223 r_free = 0.4223 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4223 r_free = 0.4223 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 moved from start: 1.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.172 22559 Z= 0.288 Angle : 1.032 21.444 30906 Z= 0.521 Chirality : 0.055 0.603 3581 Planarity : 0.008 0.131 3748 Dihedral : 13.187 124.426 3740 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 24.37 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.33 % Favored : 89.37 % Rotamer: Outliers : 3.29 % Allowed : 33.23 % Favored : 63.48 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.59 (0.15), residues: 2650 helix: -1.01 (0.16), residues: 952 sheet: -1.58 (0.39), residues: 180 loop : -2.29 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.004 TRP A 509 HIS 0.016 0.003 HIS A 133 PHE 0.041 0.003 PHE A 102 TYR 0.056 0.003 TYR A 149 ARG 0.013 0.001 ARG A 569 Details of bonding type rmsd hydrogen bonds : bond 0.06597 ( 842) hydrogen bonds : angle 6.61717 ( 2324) metal coordination : bond 0.02037 ( 32) metal coordination : angle 6.92446 ( 27) covalent geometry : bond 0.00651 (22527) covalent geometry : angle 1.01164 (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 281 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 209 time to evaluate : 2.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.4767 (OUTLIER) cc_final: 0.4486 (t80) REVERT: A 81 GLN cc_start: 0.7853 (mt0) cc_final: 0.7643 (tm-30) REVERT: A 166 VAL cc_start: 0.7312 (t) cc_final: 0.6830 (p) REVERT: A 346 TYR cc_start: 0.6146 (t80) cc_final: 0.5820 (t80) REVERT: A 542 MET cc_start: 0.7565 (tpp) cc_final: 0.7291 (tmm) REVERT: A 666 MET cc_start: 0.7403 (ppp) cc_final: 0.7093 (ttm) REVERT: A 668 MET cc_start: 0.6910 (OUTLIER) cc_final: 0.5243 (ttt) REVERT: A 807 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7295 (tptm) REVERT: B 174 MET cc_start: 0.6727 (tpp) cc_final: 0.6306 (tpp) REVERT: D 62 MET cc_start: 0.7007 (ppp) cc_final: 0.6466 (ppp) REVERT: G 11 GLN cc_start: 0.6391 (mm-40) cc_final: 0.6105 (mm-40) REVERT: G 23 CYS cc_start: 0.2055 (OUTLIER) cc_final: 0.0824 (m) REVERT: G 31 TYR cc_start: 0.7414 (m-10) cc_final: 0.6924 (m-80) REVERT: G 52 LYS cc_start: 0.6530 (OUTLIER) cc_final: 0.6035 (tptp) REVERT: G 66 TYR cc_start: 0.5115 (m-10) cc_final: 0.4422 (p90) REVERT: G 86 LYS cc_start: 0.6751 (OUTLIER) cc_final: 0.6067 (mppt) REVERT: G 87 TYR cc_start: 0.8074 (t80) cc_final: 0.7714 (t80) outliers start: 72 outliers final: 49 residues processed: 269 average time/residue: 0.3364 time to fit residues: 145.0297 Evaluate side-chains 228 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 173 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 382 TYR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 86 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 243 optimal weight: 7.9990 chunk 263 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 chunk 97 optimal weight: 0.3980 chunk 171 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 6 optimal weight: 0.1980 chunk 266 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 GLN F 388 ASN F 537 GLN E 88 GLN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5094 r_free = 0.5094 target = 0.183611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.150509 restraints weight = 110611.610| |-----------------------------------------------------------------------------| r_work (start): 0.4631 rms_B_bonded: 6.80 r_work: 0.4338 rms_B_bonded: 6.18 restraints_weight: 2.0000 r_work (final): 0.4338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4340 r_free = 0.4340 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4340 r_free = 0.4340 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6063 moved from start: 1.3201 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= 0.143 Angle : 0.790 17.758 30906 Z= 0.392 Chirality : 0.045 0.325 3581 Planarity : 0.005 0.074 3748 Dihedral : 12.795 132.609 3740 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.06 % Favored : 91.79 % Rotamer: Outliers : 2.63 % Allowed : 34.77 % Favored : 62.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.08 (0.16), residues: 2650 helix: -0.38 (0.16), residues: 949 sheet: -1.42 (0.39), residues: 186 loop : -2.12 (0.15), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 509 HIS 0.019 0.001 HIS A 613 PHE 0.020 0.002 PHE A 694 TYR 0.020 0.002 TYR A 80 ARG 0.007 0.001 ARG A 116 Details of bonding type rmsd hydrogen bonds : bond 0.04799 ( 842) hydrogen bonds : angle 5.72826 ( 2324) metal coordination : bond 0.01546 ( 32) metal coordination : angle 5.13041 ( 27) covalent geometry : bond 0.00312 (22527) covalent geometry : angle 0.77598 (30879) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25936.93 seconds wall clock time: 445 minutes 16.64 seconds (26716.64 seconds total)