Starting phenix.real_space_refine on Thu Jun 19 10:14:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gwi_34313/06_2025/8gwi_34313.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gwi_34313/06_2025/8gwi_34313.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gwi_34313/06_2025/8gwi_34313.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gwi_34313/06_2025/8gwi_34313.map" model { file = "/net/cci-nas-00/data/ceres_data/8gwi_34313/06_2025/8gwi_34313.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gwi_34313/06_2025/8gwi_34313.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 55 5.49 5 S 158 5.16 5 C 13735 2.51 5 N 3694 2.21 5 O 4305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 18.25, per 1000 atoms: 0.83 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: 5.84 Conformation dependent library (CDL) restraints added in 4.1 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: 8.76 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: 9.45 Time building geometry restraints manager: 6.97 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: 849.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.910 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 70.090 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 925.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5008 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.055 22559 Z= 0.327 Angle : 0.952 34.266 30906 Z= 0.546 Chirality : 0.063 1.605 3581 Planarity : 0.006 0.140 3748 Dihedral : 18.826 166.450 8472 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.43 % Favored : 91.19 % Rotamer: Outliers : 5.14 % Allowed : 33.58 % Favored : 61.28 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.16), residues: 2650 helix: 0.34 (0.18), residues: 947 sheet: -1.60 (0.35), residues: 218 loop : -2.47 (0.15), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP G 53 HIS 0.007 0.001 HIS A 928 PHE 0.017 0.001 PHE F 437 TYR 0.022 0.001 TYR F 299 ARG 0.006 0.001 ARG F 303 Details of bonding type rmsd hydrogen bonds : bond 0.18370 ( 842) hydrogen bonds : angle 6.41261 ( 2324) metal coordination : bond 0.01942 ( 32) metal coordination : angle 5.22093 ( 27) covalent geometry : bond 0.00855 (22527) covalent geometry : angle 0.93982 (30879) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 476 time to evaluate : 2.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.5122 (tt0) cc_final: 0.4615 (tm-30) REVERT: A 73 LYS cc_start: 0.5142 (OUTLIER) cc_final: 0.4814 (pttp) REVERT: A 76 THR cc_start: 0.2705 (OUTLIER) cc_final: 0.1344 (m) REVERT: A 248 THR cc_start: 0.5941 (p) cc_final: 0.5736 (t) REVERT: A 548 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7936 (tt) REVERT: A 731 LEU cc_start: 0.4636 (OUTLIER) cc_final: 0.4251 (mt) REVERT: A 750 ARG cc_start: 0.6290 (mtp85) cc_final: 0.5789 (ttp-110) REVERT: A 857 GLU cc_start: 0.6351 (pm20) cc_final: 0.5877 (tp30) REVERT: B 58 LYS cc_start: 0.7337 (tppp) cc_final: 0.7127 (tppt) REVERT: B 148 THR cc_start: 0.5665 (p) cc_final: 0.5425 (t) REVERT: D 57 ARG cc_start: 0.5446 (mmt-90) cc_final: 0.5208 (ttp80) REVERT: D 60 GLU cc_start: 0.5644 (tm-30) cc_final: 0.5201 (mm-30) REVERT: D 182 TRP cc_start: 0.5387 (m100) cc_final: 0.4428 (m100) REVERT: F 14 LEU cc_start: 0.5261 (mt) cc_final: 0.4069 (tp) REVERT: F 133 PHE cc_start: 0.3553 (t80) cc_final: 0.3321 (t80) REVERT: F 194 GLN cc_start: 0.3459 (tm-30) cc_final: 0.3070 (tp-100) REVERT: F 396 TYR cc_start: 0.7297 (m-80) cc_final: 0.6932 (m-10) REVERT: F 419 PRO cc_start: 0.6605 (Cg_exo) cc_final: 0.6270 (Cg_endo) REVERT: F 430 LYS cc_start: 0.0919 (mtmm) cc_final: 0.0426 (mmtp) REVERT: F 576 MET cc_start: 0.2990 (mmt) cc_final: 0.2121 (mtp) REVERT: E 48 TYR cc_start: 0.5937 (m-10) cc_final: 0.5510 (m-10) REVERT: E 64 TYR cc_start: 0.6720 (m-80) cc_final: 0.6482 (m-80) REVERT: E 156 GLU cc_start: 0.2354 (pp20) cc_final: 0.1886 (mm-30) REVERT: E 175 PRO cc_start: 0.3467 (Cg_exo) cc_final: 0.2995 (Cg_endo) REVERT: E 180 TYR cc_start: 0.3908 (m-80) cc_final: 0.3699 (m-80) REVERT: E 183 THR cc_start: 0.6263 (OUTLIER) cc_final: 0.5962 (p) REVERT: E 263 SER cc_start: 0.5471 (m) cc_final: 0.5080 (p) REVERT: E 436 MET cc_start: 0.2753 (ttm) cc_final: 0.2447 (ttt) REVERT: E 460 LYS cc_start: 0.0426 (pttp) cc_final: 0.0054 (pttm) REVERT: E 572 ILE cc_start: 0.2184 (mp) cc_final: 0.1960 (mp) REVERT: E 579 ARG cc_start: 0.2913 (mmp80) cc_final: 0.2138 (mmm160) REVERT: G 33 ASN cc_start: 0.1922 (OUTLIER) cc_final: 0.1186 (t0) REVERT: G 36 LYS cc_start: 0.5719 (mppt) cc_final: 0.5078 (mppt) outliers start: 116 outliers final: 19 residues processed: 578 average time/residue: 0.3407 time to fit residues: 299.4114 Evaluate side-chains 287 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 262 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 102 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 225 optimal weight: 20.0000 chunk 202 optimal weight: 5.9990 chunk 112 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 136 optimal weight: 9.9990 chunk 108 optimal weight: 0.7980 chunk 209 optimal weight: 0.0040 chunk 80 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 155 optimal weight: 20.0000 chunk 242 optimal weight: 7.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS A 168 ASN A 752 HIS A 790 ASN B 100 ASN C 18 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS F 354 GLN F 516 ASN E 51 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 562 ASN G 27 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.229081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.195072 restraints weight = 57736.927| |-----------------------------------------------------------------------------| r_work (start): 0.4376 rms_B_bonded: 3.14 r_work: 0.3724 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 22559 Z= 0.227 Angle : 0.833 15.484 30906 Z= 0.427 Chirality : 0.047 0.322 3581 Planarity : 0.006 0.089 3748 Dihedral : 12.694 137.808 3769 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.66 % Favored : 91.07 % Rotamer: Outliers : 5.18 % Allowed : 29.98 % Favored : 64.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.15), residues: 2650 helix: 0.03 (0.17), residues: 965 sheet: -1.50 (0.32), residues: 253 loop : -2.45 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 182 HIS 0.016 0.002 HIS A 75 PHE 0.036 0.002 PHE B 15 TYR 0.025 0.002 TYR G 89 ARG 0.029 0.001 ARG F 490 Details of bonding type rmsd hydrogen bonds : bond 0.05459 ( 842) hydrogen bonds : angle 5.26516 ( 2324) metal coordination : bond 0.02256 ( 32) metal coordination : angle 5.32055 ( 27) covalent geometry : bond 0.00460 (22527) covalent geometry : angle 0.81809 (30879) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 309 time to evaluate : 2.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 TYR cc_start: 0.7894 (p90) cc_final: 0.7653 (p90) REVERT: A 601 MET cc_start: 0.9094 (ttm) cc_final: 0.8889 (ttm) REVERT: A 648 LEU cc_start: 0.5850 (OUTLIER) cc_final: 0.5623 (tp) REVERT: B 61 LYS cc_start: 0.8429 (tmmt) cc_final: 0.8133 (tppt) REVERT: B 143 ASP cc_start: 0.5094 (p0) cc_final: 0.4814 (t0) REVERT: C 44 ASP cc_start: 0.7724 (p0) cc_final: 0.7472 (p0) REVERT: D 31 SER cc_start: 0.6929 (p) cc_final: 0.6524 (t) REVERT: D 58 LYS cc_start: 0.5581 (OUTLIER) cc_final: 0.5365 (tmtt) REVERT: D 60 GLU cc_start: 0.6452 (tm-30) cc_final: 0.6144 (mm-30) REVERT: F 297 LEU cc_start: 0.5035 (pp) cc_final: 0.4814 (tp) REVERT: F 531 GLN cc_start: -0.0685 (OUTLIER) cc_final: -0.1195 (mt0) REVERT: F 576 MET cc_start: 0.1903 (mmt) cc_final: 0.1162 (mtp) REVERT: E 183 THR cc_start: 0.5953 (m) cc_final: 0.5487 (p) REVERT: E 233 MET cc_start: 0.3111 (OUTLIER) cc_final: 0.1923 (mtt) REVERT: E 437 PHE cc_start: 0.5835 (OUTLIER) cc_final: 0.5323 (p90) REVERT: E 460 LYS cc_start: 0.0299 (pttp) cc_final: -0.0171 (pttm) REVERT: E 490 ARG cc_start: 0.2847 (ttp-170) cc_final: 0.2563 (ttp80) REVERT: G 12 MET cc_start: 0.2636 (pmm) cc_final: 0.2407 (pmm) REVERT: G 94 LEU cc_start: 0.5197 (tt) cc_final: 0.4909 (tp) outliers start: 117 outliers final: 38 residues processed: 408 average time/residue: 0.3446 time to fit residues: 215.7606 Evaluate side-chains 268 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 225 time to evaluate : 2.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain G residue 73 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 104 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 chunk 196 optimal weight: 30.0000 chunk 133 optimal weight: 0.5980 chunk 216 optimal weight: 0.8980 chunk 254 optimal weight: 50.0000 chunk 106 optimal weight: 2.9990 chunk 252 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 244 optimal weight: 20.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 HIS A 543 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN E 51 ASN E 275 GLN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 562 ASN G 11 GLN G 33 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.222680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.197266 restraints weight = 76728.117| |-----------------------------------------------------------------------------| r_work (start): 0.4412 rms_B_bonded: 2.56 r_work: 0.4041 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work: 0.3956 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3948 r_free = 0.3948 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3948 r_free = 0.3948 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.5543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 22559 Z= 0.166 Angle : 0.732 14.755 30906 Z= 0.369 Chirality : 0.045 0.272 3581 Planarity : 0.005 0.123 3748 Dihedral : 12.330 137.522 3742 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.22 % Favored : 92.51 % Rotamer: Outliers : 3.82 % Allowed : 30.11 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.16), residues: 2650 helix: 0.24 (0.17), residues: 995 sheet: -1.01 (0.36), residues: 219 loop : -2.34 (0.15), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 182 HIS 0.006 0.001 HIS E 290 PHE 0.017 0.002 PHE G 75 TYR 0.030 0.002 TYR D 135 ARG 0.007 0.001 ARG F 390 Details of bonding type rmsd hydrogen bonds : bond 0.05421 ( 842) hydrogen bonds : angle 4.98507 ( 2324) metal coordination : bond 0.01394 ( 32) metal coordination : angle 4.33927 ( 27) covalent geometry : bond 0.00359 (22527) covalent geometry : angle 0.72077 (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 358 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 272 time to evaluate : 2.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 ASP cc_start: 0.7889 (t70) cc_final: 0.7654 (m-30) REVERT: A 731 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8069 (mp) REVERT: A 750 ARG cc_start: 0.8017 (ttt-90) cc_final: 0.7757 (ttm110) REVERT: B 94 MET cc_start: 0.6213 (tmm) cc_final: 0.5652 (ttt) REVERT: D 43 ASN cc_start: 0.7478 (t0) cc_final: 0.7237 (t0) REVERT: D 58 LYS cc_start: 0.5673 (OUTLIER) cc_final: 0.5331 (tmtt) REVERT: D 182 TRP cc_start: 0.4720 (m100) cc_final: 0.4416 (m100) REVERT: F 192 LYS cc_start: 0.1056 (OUTLIER) cc_final: 0.0851 (ptpt) REVERT: F 378 MET cc_start: 0.1018 (mpp) cc_final: -0.1560 (mmt) REVERT: F 531 GLN cc_start: 0.0086 (OUTLIER) cc_final: -0.0704 (mt0) REVERT: F 554 HIS cc_start: -0.0965 (OUTLIER) cc_final: -0.1216 (m-70) REVERT: E 183 THR cc_start: 0.4361 (m) cc_final: 0.4087 (p) REVERT: E 274 MET cc_start: 0.2244 (mmm) cc_final: 0.1890 (mmp) REVERT: E 460 LYS cc_start: 0.1054 (pttp) cc_final: 0.0237 (pttm) REVERT: E 579 ARG cc_start: 0.3765 (mmp80) cc_final: 0.3372 (mmp-170) outliers start: 86 outliers final: 41 residues processed: 345 average time/residue: 0.3365 time to fit residues: 181.5751 Evaluate side-chains 257 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 211 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 73 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 246 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 198 optimal weight: 0.7980 chunk 190 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 252 optimal weight: 20.0000 chunk 63 optimal weight: 0.6980 chunk 260 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 309 HIS A 404 ASN ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 ASN ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.214538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.166855 restraints weight = 67110.860| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 4.31 r_work: 0.3256 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.6574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22559 Z= 0.158 Angle : 0.678 12.998 30906 Z= 0.342 Chirality : 0.043 0.215 3581 Planarity : 0.005 0.095 3748 Dihedral : 12.204 138.198 3741 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.90 % Favored : 91.87 % Rotamer: Outliers : 3.25 % Allowed : 31.43 % Favored : 65.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.16), residues: 2650 helix: 0.32 (0.17), residues: 991 sheet: -1.06 (0.34), residues: 240 loop : -2.24 (0.15), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 182 HIS 0.007 0.001 HIS C 36 PHE 0.034 0.002 PHE E 422 TYR 0.037 0.002 TYR E 421 ARG 0.010 0.001 ARG F 248 Details of bonding type rmsd hydrogen bonds : bond 0.05061 ( 842) hydrogen bonds : angle 4.71238 ( 2324) metal coordination : bond 0.01632 ( 32) metal coordination : angle 4.00013 ( 27) covalent geometry : bond 0.00344 (22527) covalent geometry : angle 0.66810 (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 313 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 240 time to evaluate : 2.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 ASP cc_start: 0.8533 (t70) cc_final: 0.8202 (m-30) REVERT: A 750 ARG cc_start: 0.8750 (ttt-90) cc_final: 0.8262 (ttp-110) REVERT: B 73 GLN cc_start: 0.7634 (tp40) cc_final: 0.6653 (tt0) REVERT: B 77 GLU cc_start: 0.7259 (mm-30) cc_final: 0.6882 (mt-10) REVERT: B 79 LYS cc_start: 0.8150 (ttpt) cc_final: 0.7920 (ttpt) REVERT: B 165 LYS cc_start: 0.8187 (mmpt) cc_final: 0.7927 (mmpt) REVERT: D 182 TRP cc_start: 0.5836 (OUTLIER) cc_final: 0.5015 (m100) REVERT: F 343 PHE cc_start: 0.2438 (t80) cc_final: 0.1959 (m-80) REVERT: F 396 TYR cc_start: 0.7345 (m-10) cc_final: 0.7083 (m-10) REVERT: F 531 GLN cc_start: 0.0040 (OUTLIER) cc_final: -0.0379 (mt0) REVERT: F 554 HIS cc_start: -0.0673 (OUTLIER) cc_final: -0.1246 (m-70) REVERT: F 576 MET cc_start: 0.2400 (mtm) cc_final: 0.2135 (mtp) REVERT: E 183 THR cc_start: 0.6128 (m) cc_final: 0.5712 (p) REVERT: E 233 MET cc_start: 0.3444 (OUTLIER) cc_final: 0.2296 (mtt) REVERT: E 373 PHE cc_start: 0.6564 (t80) cc_final: 0.5980 (t80) REVERT: E 460 LYS cc_start: 0.0415 (pttp) cc_final: -0.0285 (pttm) REVERT: E 579 ARG cc_start: 0.2888 (mmp80) cc_final: 0.2355 (mmp-170) outliers start: 73 outliers final: 45 residues processed: 294 average time/residue: 0.3455 time to fit residues: 158.9549 Evaluate side-chains 259 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 210 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 576 MET Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 44 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 35 optimal weight: 0.2980 chunk 28 optimal weight: 0.8980 chunk 73 optimal weight: 0.0030 chunk 180 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 209 optimal weight: 6.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN B 19 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.213702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.166800 restraints weight = 66507.803| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 4.31 r_work: 0.3233 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.7156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22559 Z= 0.124 Angle : 0.634 13.565 30906 Z= 0.319 Chirality : 0.041 0.228 3581 Planarity : 0.004 0.054 3748 Dihedral : 12.084 130.610 3741 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.19 % Favored : 92.59 % Rotamer: Outliers : 3.42 % Allowed : 30.77 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.16), residues: 2650 helix: 0.47 (0.17), residues: 997 sheet: -1.23 (0.34), residues: 233 loop : -2.15 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 182 HIS 0.006 0.001 HIS C 36 PHE 0.022 0.001 PHE E 422 TYR 0.017 0.001 TYR E 421 ARG 0.005 0.000 ARG D 111 Details of bonding type rmsd hydrogen bonds : bond 0.04702 ( 842) hydrogen bonds : angle 4.55311 ( 2324) metal coordination : bond 0.01331 ( 32) metal coordination : angle 3.73012 ( 27) covalent geometry : bond 0.00266 (22527) covalent geometry : angle 0.62418 (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 320 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 243 time to evaluate : 2.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.7485 (ttp-170) cc_final: 0.7027 (tpt170) REVERT: A 258 ASP cc_start: 0.8263 (t0) cc_final: 0.8042 (t0) REVERT: A 284 ASP cc_start: 0.8695 (t70) cc_final: 0.8286 (m-30) REVERT: A 477 ASP cc_start: 0.7880 (t70) cc_final: 0.7558 (t0) REVERT: A 750 ARG cc_start: 0.8844 (ttt-90) cc_final: 0.8348 (ttp-110) REVERT: B 52 ASP cc_start: 0.6452 (m-30) cc_final: 0.6079 (m-30) REVERT: B 73 GLN cc_start: 0.7686 (tp40) cc_final: 0.6841 (tt0) REVERT: B 77 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7187 (mt-10) REVERT: C 75 MET cc_start: 0.5206 (tpt) cc_final: 0.4972 (tpt) REVERT: F 192 LYS cc_start: 0.0872 (OUTLIER) cc_final: 0.0360 (ptpt) REVERT: F 233 MET cc_start: 0.4684 (OUTLIER) cc_final: 0.4460 (ppp) REVERT: F 343 PHE cc_start: 0.2690 (t80) cc_final: 0.2177 (m-80) REVERT: F 396 TYR cc_start: 0.7289 (m-10) cc_final: 0.7084 (m-10) REVERT: F 497 ARG cc_start: 0.3012 (mmp80) cc_final: 0.2047 (mmt180) REVERT: F 508 LYS cc_start: 0.3601 (OUTLIER) cc_final: 0.3283 (pttt) REVERT: F 531 GLN cc_start: 0.0042 (OUTLIER) cc_final: -0.0378 (mt0) REVERT: F 554 HIS cc_start: -0.0718 (OUTLIER) cc_final: -0.1214 (m-70) REVERT: F 576 MET cc_start: 0.2504 (mtm) cc_final: 0.2240 (mtp) REVERT: E 183 THR cc_start: 0.6138 (m) cc_final: 0.5672 (p) REVERT: E 233 MET cc_start: 0.3790 (OUTLIER) cc_final: 0.2761 (mtp) REVERT: E 533 VAL cc_start: -0.0335 (OUTLIER) cc_final: -0.0710 (t) REVERT: E 579 ARG cc_start: 0.3249 (mmp80) cc_final: 0.2584 (mmp-170) REVERT: G 48 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8085 (tt) REVERT: G 86 LYS cc_start: 0.1133 (OUTLIER) cc_final: 0.0540 (mptt) outliers start: 77 outliers final: 40 residues processed: 299 average time/residue: 0.3456 time to fit residues: 160.6431 Evaluate side-chains 258 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 209 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 508 LYS Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 73 CYS 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: 0.0000 chunk 217 optimal weight: 20.0000 chunk 244 optimal weight: 9.9990 chunk 185 optimal weight: 0.7980 chunk 250 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 239 optimal weight: 4.9990 chunk 159 optimal weight: 0.0870 chunk 92 optimal weight: 0.3980 overall best weight: 0.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 381 HIS A 497 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 459 ASN ** E 548 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 = 0.4596 r_free = 0.4596 target = 0.213217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.149672 restraints weight = 53697.999| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 4.29 r_work: 0.3213 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.7646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22559 Z= 0.117 Angle : 0.618 12.226 30906 Z= 0.310 Chirality : 0.041 0.210 3581 Planarity : 0.004 0.059 3748 Dihedral : 11.865 107.540 3738 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.60 % Favored : 92.17 % Rotamer: Outliers : 3.07 % Allowed : 30.68 % Favored : 66.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.16), residues: 2650 helix: 0.66 (0.17), residues: 988 sheet: -1.46 (0.32), residues: 254 loop : -2.04 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 182 HIS 0.005 0.001 HIS C 36 PHE 0.021 0.001 PHE D 15 TYR 0.034 0.001 TYR E 421 ARG 0.005 0.000 ARG D 111 Details of bonding type rmsd hydrogen bonds : bond 0.04507 ( 842) hydrogen bonds : angle 4.39553 ( 2324) metal coordination : bond 0.01525 ( 32) metal coordination : angle 3.46609 ( 27) covalent geometry : bond 0.00246 (22527) covalent geometry : angle 0.60983 (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 285 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 216 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.7446 (ttp-170) cc_final: 0.6806 (tpt170) REVERT: A 221 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.7623 (t0) REVERT: A 242 MET cc_start: 0.8801 (mmm) cc_final: 0.8122 (mtt) REVERT: A 258 ASP cc_start: 0.8353 (t0) cc_final: 0.7896 (t0) REVERT: A 284 ASP cc_start: 0.8696 (t70) cc_final: 0.8185 (m-30) REVERT: A 370 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7920 (mm-30) REVERT: A 477 ASP cc_start: 0.7688 (t70) cc_final: 0.7340 (t0) REVERT: A 499 ASP cc_start: 0.8070 (m-30) cc_final: 0.7751 (m-30) REVERT: A 730 CYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8850 (m) REVERT: A 750 ARG cc_start: 0.8876 (ttt-90) cc_final: 0.8213 (ttp-110) REVERT: B 52 ASP cc_start: 0.6588 (m-30) cc_final: 0.6163 (m-30) REVERT: B 73 GLN cc_start: 0.7346 (tp40) cc_final: 0.6554 (tt0) REVERT: B 77 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6920 (mt-10) REVERT: B 82 LYS cc_start: 0.8344 (tmmt) cc_final: 0.8082 (tttm) REVERT: B 94 MET cc_start: 0.6020 (tmm) cc_final: 0.5720 (ttp) REVERT: C 75 MET cc_start: 0.4907 (tpt) cc_final: 0.4585 (tpt) REVERT: D 65 GLN cc_start: 0.7001 (tm-30) cc_final: 0.6475 (tt0) REVERT: F 192 LYS cc_start: 0.0650 (OUTLIER) cc_final: 0.0258 (ptmt) REVERT: F 497 ARG cc_start: 0.3035 (mmp80) cc_final: 0.2350 (mmt180) REVERT: F 531 GLN cc_start: 0.0277 (OUTLIER) cc_final: 0.0003 (mt0) REVERT: F 545 ILE cc_start: 0.2255 (mm) cc_final: 0.2038 (mt) REVERT: F 554 HIS cc_start: -0.0458 (OUTLIER) cc_final: -0.0985 (m-70) REVERT: F 576 MET cc_start: 0.1729 (mtm) cc_final: 0.1505 (mtp) REVERT: E 183 THR cc_start: 0.6150 (m) cc_final: 0.5845 (p) REVERT: E 233 MET cc_start: 0.3630 (OUTLIER) cc_final: 0.2649 (mtt) REVERT: E 579 ARG cc_start: 0.3339 (mmp80) cc_final: 0.2687 (mmp-170) REVERT: G 48 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8154 (tt) outliers start: 69 outliers final: 39 residues processed: 266 average time/residue: 0.3198 time to fit residues: 133.9956 Evaluate side-chains 248 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 202 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 730 CYS Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 192 optimal weight: 50.0000 chunk 245 optimal weight: 5.9990 chunk 222 optimal weight: 0.7980 chunk 239 optimal weight: 5.9990 chunk 206 optimal weight: 0.0970 chunk 177 optimal weight: 7.9990 chunk 100 optimal weight: 0.0770 chunk 93 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 165 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 HIS A 725 HIS A 822 GLN A 911 ASN B 88 GLN B 157 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.205451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.161795 restraints weight = 59864.273| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 3.33 r_work: 0.3129 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.8856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 22559 Z= 0.231 Angle : 0.771 14.007 30906 Z= 0.393 Chirality : 0.047 0.328 3581 Planarity : 0.005 0.056 3748 Dihedral : 11.830 73.845 3737 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.47 % Favored : 91.34 % Rotamer: Outliers : 3.16 % Allowed : 30.42 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.16), residues: 2650 helix: 0.16 (0.17), residues: 986 sheet: -1.09 (0.35), residues: 221 loop : -2.22 (0.15), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 509 HIS 0.015 0.002 HIS C 36 PHE 0.024 0.002 PHE E 422 TYR 0.031 0.002 TYR E 421 ARG 0.010 0.001 ARG D 111 Details of bonding type rmsd hydrogen bonds : bond 0.06696 ( 842) hydrogen bonds : angle 4.76798 ( 2324) metal coordination : bond 0.01817 ( 32) metal coordination : angle 5.19123 ( 27) covalent geometry : bond 0.00536 (22527) covalent geometry : angle 0.75618 (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 292 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 221 time to evaluate : 2.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8405 (ttp-170) cc_final: 0.8039 (ttm-80) REVERT: A 258 ASP cc_start: 0.8441 (t0) cc_final: 0.8053 (t0) REVERT: A 284 ASP cc_start: 0.8809 (t70) cc_final: 0.8569 (m-30) REVERT: A 344 THR cc_start: 0.9372 (p) cc_final: 0.9160 (t) REVERT: A 477 ASP cc_start: 0.8282 (t70) cc_final: 0.7865 (t0) REVERT: B 73 GLN cc_start: 0.7977 (tp40) cc_final: 0.7394 (tt0) REVERT: B 94 MET cc_start: 0.6981 (tmm) cc_final: 0.6464 (ttp) REVERT: B 96 ARG cc_start: 0.6140 (ttp-110) cc_final: 0.5890 (mtm110) REVERT: C 75 MET cc_start: 0.5089 (tpt) cc_final: 0.4815 (tpt) REVERT: D 65 GLN cc_start: 0.7234 (tm-30) cc_final: 0.6449 (mm110) REVERT: D 70 MET cc_start: 0.8729 (ttm) cc_final: 0.8498 (ttp) REVERT: F 192 LYS cc_start: 0.0622 (OUTLIER) cc_final: 0.0148 (ptmt) REVERT: F 224 TYR cc_start: 0.6031 (m-80) cc_final: 0.5790 (m-80) REVERT: F 233 MET cc_start: 0.5006 (ppp) cc_final: 0.4736 (ppp) REVERT: F 378 MET cc_start: 0.1914 (mpp) cc_final: 0.1259 (mpp) REVERT: F 497 ARG cc_start: 0.2936 (mmp80) cc_final: 0.1943 (mmt180) REVERT: F 531 GLN cc_start: 0.0220 (OUTLIER) cc_final: -0.0230 (mt0) REVERT: F 576 MET cc_start: 0.2527 (mtm) cc_final: 0.2273 (mtp) REVERT: E 183 THR cc_start: 0.5971 (m) cc_final: 0.5465 (p) REVERT: E 233 MET cc_start: 0.4434 (OUTLIER) cc_final: 0.3218 (mtt) REVERT: E 576 MET cc_start: 0.3482 (ppp) cc_final: 0.2315 (pmm) REVERT: E 579 ARG cc_start: 0.3334 (mmp80) cc_final: 0.2614 (mmp-170) REVERT: G 48 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8198 (tt) outliers start: 71 outliers final: 50 residues processed: 275 average time/residue: 0.3382 time to fit residues: 145.9591 Evaluate side-chains 252 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 198 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 730 CYS Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 398 TYR Chi-restraints excluded: chain F residue 421 TYR Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 45 optimal weight: 0.6980 chunk 150 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 137 optimal weight: 9.9990 chunk 140 optimal weight: 0.9980 chunk 173 optimal weight: 20.0000 chunk 16 optimal weight: 0.0060 chunk 62 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 HIS ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 459 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 ASN ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.207410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.152551 restraints weight = 77629.901| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 6.07 r_work: 0.3007 rms_B_bonded: 5.51 restraints_weight: 2.0000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.9069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.298 22559 Z= 0.134 Angle : 0.646 13.965 30906 Z= 0.325 Chirality : 0.042 0.223 3581 Planarity : 0.004 0.051 3748 Dihedral : 11.605 73.744 3737 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.22 % Favored : 92.59 % Rotamer: Outliers : 2.94 % Allowed : 31.12 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.16), residues: 2650 helix: 0.52 (0.17), residues: 992 sheet: -1.38 (0.33), residues: 251 loop : -2.00 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 182 HIS 0.007 0.001 HIS E 290 PHE 0.024 0.001 PHE E 422 TYR 0.029 0.001 TYR B 71 ARG 0.005 0.000 ARG D 111 Details of bonding type rmsd hydrogen bonds : bond 0.04960 ( 842) hydrogen bonds : angle 4.45722 ( 2324) metal coordination : bond 0.05389 ( 32) metal coordination : angle 4.77340 ( 27) covalent geometry : bond 0.00286 (22527) covalent geometry : angle 0.63055 (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 291 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 225 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8341 (ttp-170) cc_final: 0.7498 (tpt170) REVERT: A 221 ASP cc_start: 0.8444 (t0) cc_final: 0.7642 (p0) REVERT: A 258 ASP cc_start: 0.8378 (t0) cc_final: 0.7872 (t0) REVERT: A 284 ASP cc_start: 0.8894 (t70) cc_final: 0.8524 (m-30) REVERT: A 477 ASP cc_start: 0.8112 (t70) cc_final: 0.7728 (t0) REVERT: B 67 MET cc_start: 0.8073 (tpt) cc_final: 0.7642 (tpt) REVERT: B 80 ARG cc_start: 0.7853 (ttt180) cc_final: 0.7580 (ttt-90) REVERT: C 75 MET cc_start: 0.5030 (tpt) cc_final: 0.4647 (tpt) REVERT: D 65 GLN cc_start: 0.7143 (tm-30) cc_final: 0.6167 (mm110) REVERT: D 70 MET cc_start: 0.8566 (ttm) cc_final: 0.8321 (ttp) REVERT: D 165 LYS cc_start: 0.6967 (mtmm) cc_final: 0.6766 (ptpt) REVERT: F 192 LYS cc_start: 0.0355 (OUTLIER) cc_final: -0.0002 (ptmt) REVERT: F 233 MET cc_start: 0.5449 (ppp) cc_final: 0.5181 (ppp) REVERT: F 497 ARG cc_start: 0.2952 (mmp80) cc_final: 0.2245 (mmt180) REVERT: F 531 GLN cc_start: 0.0304 (OUTLIER) cc_final: 0.0015 (mt0) REVERT: E 183 THR cc_start: 0.6065 (m) cc_final: 0.5719 (p) REVERT: E 233 MET cc_start: 0.4295 (OUTLIER) cc_final: 0.3306 (mtt) REVERT: E 290 HIS cc_start: 0.3487 (m-70) cc_final: 0.3218 (m170) REVERT: E 579 ARG cc_start: 0.3301 (mmp80) cc_final: 0.2683 (mmp-170) REVERT: G 48 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8228 (tt) REVERT: G 86 LYS cc_start: 0.1329 (OUTLIER) cc_final: 0.0591 (mptt) outliers start: 66 outliers final: 45 residues processed: 274 average time/residue: 0.3440 time to fit residues: 148.0686 Evaluate side-chains 243 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 193 time to evaluate : 2.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 730 CYS Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 398 TYR Chi-restraints excluded: chain F residue 421 TYR Chi-restraints excluded: chain F residue 459 ASN Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 79 THR 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: 0.9980 chunk 249 optimal weight: 8.9990 chunk 118 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 237 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 262 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 HIS B 109 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 537 GLN ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.204169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.138367 restraints weight = 60699.313| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 4.89 r_work: 0.3017 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.9415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.341 22559 Z= 0.185 Angle : 0.688 15.605 30906 Z= 0.349 Chirality : 0.044 0.273 3581 Planarity : 0.005 0.053 3748 Dihedral : 11.647 73.785 3737 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.56 % Favored : 92.25 % Rotamer: Outliers : 2.59 % Allowed : 31.34 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.16), residues: 2650 helix: 0.51 (0.17), residues: 980 sheet: -1.19 (0.34), residues: 233 loop : -2.07 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.011 0.001 HIS C 36 PHE 0.020 0.002 PHE A 741 TYR 0.052 0.002 TYR E 421 ARG 0.007 0.001 ARG D 111 Details of bonding type rmsd hydrogen bonds : bond 0.05643 ( 842) hydrogen bonds : angle 4.50006 ( 2324) metal coordination : bond 0.06131 ( 32) metal coordination : angle 4.95985 ( 27) covalent geometry : bond 0.00426 (22527) covalent geometry : angle 0.67223 (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 254 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 196 time to evaluate : 2.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8379 (ttp-170) cc_final: 0.7682 (ttm-80) REVERT: A 221 ASP cc_start: 0.8533 (t0) cc_final: 0.8318 (t0) REVERT: A 258 ASP cc_start: 0.8372 (t0) cc_final: 0.7899 (t0) REVERT: A 284 ASP cc_start: 0.8809 (t70) cc_final: 0.8445 (m-30) REVERT: A 477 ASP cc_start: 0.8245 (t70) cc_final: 0.7824 (t0) REVERT: B 67 MET cc_start: 0.7920 (tpt) cc_final: 0.7443 (tpt) REVERT: C 75 MET cc_start: 0.5142 (tpt) cc_final: 0.4773 (tpt) REVERT: D 65 GLN cc_start: 0.7151 (tm-30) cc_final: 0.6250 (mm110) REVERT: D 70 MET cc_start: 0.8612 (ttm) cc_final: 0.8394 (ttp) REVERT: F 192 LYS cc_start: 0.0332 (OUTLIER) cc_final: -0.0012 (ptmt) REVERT: F 497 ARG cc_start: 0.2918 (mmp80) cc_final: 0.2241 (mmt180) REVERT: F 531 GLN cc_start: 0.0324 (OUTLIER) cc_final: 0.0032 (mt0) REVERT: E 183 THR cc_start: 0.6120 (m) cc_final: 0.5768 (p) REVERT: E 233 MET cc_start: 0.4600 (OUTLIER) cc_final: 0.3609 (mtt) REVERT: E 290 HIS cc_start: 0.3496 (m-70) cc_final: 0.3260 (m170) REVERT: E 579 ARG cc_start: 0.3328 (mmp80) cc_final: 0.2765 (mmp-170) outliers start: 58 outliers final: 45 residues processed: 244 average time/residue: 0.3566 time to fit residues: 135.1796 Evaluate side-chains 239 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 191 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 730 CYS Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 398 TYR Chi-restraints excluded: chain F residue 421 TYR Chi-restraints excluded: chain F residue 459 ASN Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 181 optimal weight: 10.0000 chunk 161 optimal weight: 0.0370 chunk 53 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 225 optimal weight: 9.9990 chunk 192 optimal weight: 0.0020 chunk 175 optimal weight: 0.0570 chunk 64 optimal weight: 0.4980 overall best weight: 0.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 HIS B 109 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 459 ASN ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.208532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.144715 restraints weight = 54977.922| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 4.21 r_work: 0.3112 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.9532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.267 22559 Z= 0.119 Angle : 0.629 13.774 30906 Z= 0.314 Chirality : 0.041 0.193 3581 Planarity : 0.004 0.049 3748 Dihedral : 11.485 73.692 3735 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.19 % Favored : 92.62 % Rotamer: Outliers : 1.93 % Allowed : 32.40 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.16), residues: 2650 helix: 0.80 (0.17), residues: 979 sheet: -1.18 (0.34), residues: 246 loop : -1.94 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 182 HIS 0.007 0.001 HIS F 75 PHE 0.022 0.001 PHE F 145 TYR 0.019 0.001 TYR F 31 ARG 0.007 0.000 ARG D 111 Details of bonding type rmsd hydrogen bonds : bond 0.04453 ( 842) hydrogen bonds : angle 4.35686 ( 2324) metal coordination : bond 0.04811 ( 32) metal coordination : angle 4.46097 ( 27) covalent geometry : bond 0.00241 (22527) covalent geometry : angle 0.61540 (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 252 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 209 time to evaluate : 4.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8134 (ttp-170) cc_final: 0.7537 (ttm-80) REVERT: A 221 ASP cc_start: 0.8340 (t0) cc_final: 0.7493 (p0) REVERT: A 258 ASP cc_start: 0.8281 (t0) cc_final: 0.7805 (t0) REVERT: A 284 ASP cc_start: 0.8729 (t70) cc_final: 0.8327 (m-30) REVERT: A 477 ASP cc_start: 0.7846 (t70) cc_final: 0.7507 (t0) REVERT: A 768 SER cc_start: 0.8609 (t) cc_final: 0.7955 (p) REVERT: B 67 MET cc_start: 0.7889 (tpt) cc_final: 0.7512 (tpt) REVERT: B 171 GLU cc_start: 0.7364 (pt0) cc_final: 0.6894 (pt0) REVERT: C 75 MET cc_start: 0.5108 (tpt) cc_final: 0.4744 (tpt) REVERT: D 65 GLN cc_start: 0.7205 (tm-30) cc_final: 0.6341 (mm110) REVERT: D 70 MET cc_start: 0.8532 (ttm) cc_final: 0.8295 (ttp) REVERT: F 192 LYS cc_start: 0.0321 (OUTLIER) cc_final: -0.0046 (ptmt) REVERT: F 233 MET cc_start: 0.5614 (ppp) cc_final: 0.5097 (ppp) REVERT: F 270 GLN cc_start: 0.5122 (tp-100) cc_final: 0.4880 (mm110) REVERT: F 349 ASN cc_start: 0.5676 (m-40) cc_final: 0.5314 (p0) REVERT: F 421 TYR cc_start: 0.7519 (OUTLIER) cc_final: 0.7299 (m-10) REVERT: F 497 ARG cc_start: 0.2972 (mmp80) cc_final: 0.2311 (mmt180) REVERT: F 531 GLN cc_start: 0.0619 (OUTLIER) cc_final: 0.0318 (mt0) REVERT: E 183 THR cc_start: 0.6048 (m) cc_final: 0.5701 (p) REVERT: E 233 MET cc_start: 0.4415 (OUTLIER) cc_final: 0.3564 (mtt) REVERT: E 290 HIS cc_start: 0.3521 (m-70) cc_final: 0.3290 (m170) REVERT: E 579 ARG cc_start: 0.3308 (mmp80) cc_final: 0.2751 (mmp-170) REVERT: G 86 LYS cc_start: 0.1590 (OUTLIER) cc_final: 0.0903 (mptt) outliers start: 43 outliers final: 35 residues processed: 242 average time/residue: 0.4247 time to fit residues: 161.9615 Evaluate side-chains 235 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 2.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 730 CYS Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 421 TYR Chi-restraints excluded: chain F residue 459 ASN Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 79 THR 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: 30.0000 chunk 263 optimal weight: 5.9990 chunk 117 optimal weight: 0.0770 chunk 97 optimal weight: 9.9990 chunk 171 optimal weight: 20.0000 chunk 74 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 266 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN A 822 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.206847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.141725 restraints weight = 57298.434| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 4.39 r_work: 0.3073 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.9598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.275 22559 Z= 0.143 Angle : 0.644 13.941 30906 Z= 0.324 Chirality : 0.043 0.230 3581 Planarity : 0.004 0.053 3748 Dihedral : 11.483 73.722 3735 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.56 % Favored : 92.28 % Rotamer: Outliers : 2.15 % Allowed : 32.13 % Favored : 65.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.16), residues: 2650 helix: 0.79 (0.17), residues: 973 sheet: -1.40 (0.32), residues: 251 loop : -1.90 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 182 HIS 0.007 0.001 HIS C 36 PHE 0.030 0.001 PHE F 145 TYR 0.022 0.001 TYR F 31 ARG 0.007 0.000 ARG D 111 Details of bonding type rmsd hydrogen bonds : bond 0.04763 ( 842) hydrogen bonds : angle 4.35151 ( 2324) metal coordination : bond 0.05022 ( 32) metal coordination : angle 4.25834 ( 27) covalent geometry : bond 0.00317 (22527) covalent geometry : angle 0.63181 (30879) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18140.72 seconds wall clock time: 317 minutes 11.73 seconds (19031.73 seconds total)