Starting phenix.real_space_refine on Thu May 22 04:10:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gwf_34311/05_2025/8gwf_34311.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gwf_34311/05_2025/8gwf_34311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gwf_34311/05_2025/8gwf_34311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gwf_34311/05_2025/8gwf_34311.map" model { file = "/net/cci-nas-00/data/ceres_data/8gwf_34311/05_2025/8gwf_34311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gwf_34311/05_2025/8gwf_34311.cif" } resolution = 3.39 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= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 55 5.49 5 S 158 5.16 5 C 13735 2.51 5 N 3694 2.21 5 O 4305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 21955 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 7492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 931, 7492 Classifications: {'peptide': 931} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 900} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1396 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 600 Classifications: {'peptide': 78} Link IDs: {'TRANS': 77} Chain: "D" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1422 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 545 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 16, 'rna3p_pyr': 8} Link IDs: {'rna3p': 24} Chain: "J" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 565 Classifications: {'RNA': 27} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 25} Chain: "F" Number of atoms: 4513 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4598 Chain: "E" Number of atoms: 4513 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4598 Chain: "G" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 868 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' ZN': 2, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2465 SG CYS A 301 75.578 55.650 121.844 1.00 86.97 S ATOM 2506 SG CYS A 306 75.567 57.180 125.354 1.00 84.94 S ATOM 2538 SG CYS A 310 76.856 53.605 124.773 1.00 84.77 S ATOM 3946 SG CYS A 487 78.264 69.779 106.107 1.00 95.87 S ATOM 5199 SG CYS A 645 77.470 71.834 109.252 1.00 97.77 S ATOM 5205 SG CYS A 646 76.146 68.218 108.904 1.00 89.00 S ATOM 12129 SG CYS F 16 102.478 65.216 50.524 1.00183.45 S ATOM 12144 SG CYS F 19 103.212 62.542 47.852 1.00198.14 S ATOM 12047 SG CYS F 5 114.925 66.378 50.337 1.00183.01 S ATOM 12068 SG CYS F 8 115.808 69.235 47.969 1.00185.13 S ATOM 12206 SG CYS F 26 114.614 70.148 51.170 1.00172.26 S ATOM 12223 SG CYS F 29 112.090 68.304 48.775 1.00175.19 S ATOM 12388 SG CYS F 50 93.154 76.836 65.675 1.00158.72 S ATOM 12418 SG CYS F 55 89.756 76.042 64.216 1.00164.97 S ATOM 12551 SG CYS F 72 91.926 78.390 62.448 1.00168.17 S ATOM 16642 SG CYS E 16 61.349 74.627 65.591 1.00165.58 S ATOM 16657 SG CYS E 19 58.755 72.126 64.275 1.00179.24 S ATOM 16560 SG CYS E 5 70.232 70.535 57.925 1.00188.71 S ATOM 16581 SG CYS E 8 70.961 72.499 54.838 1.00197.10 S ATOM 16719 SG CYS E 26 72.392 73.907 58.159 1.00186.39 S ATOM 16736 SG CYS E 29 68.780 74.086 57.029 1.00167.57 S ATOM 16901 SG CYS E 50 66.240 87.403 79.620 1.00176.08 S ATOM 16931 SG CYS E 55 63.011 88.887 81.055 1.00192.48 S ATOM 17064 SG CYS E 72 65.078 90.922 78.545 1.00187.74 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AMET F 474 " occ=0.42 ... (14 atoms not shown) pdb=" CE BMET F 474 " occ=0.58 residue: pdb=" N AMET E 474 " occ=0.11 ... (14 atoms not shown) pdb=" CE BMET E 474 " occ=0.89 Time building chain proxies: 17.09, per 1000 atoms: 0.78 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: 6.64 Conformation dependent library (CDL) restraints added in 4.7 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: 8.74 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: 10.18 Time building geometry restraints manager: 8.01 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: 5.450 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: 0.970 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 72.810 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:4.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 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 412 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 296 time to evaluate : 2.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.7063 (tptt) cc_final: 0.6792 (tptp) REVERT: A 114 ILE cc_start: 0.5885 (mt) cc_final: 0.5594 (mt) REVERT: A 115 SER cc_start: 0.7645 (OUTLIER) cc_final: 0.7119 (m) REVERT: A 161 ASP cc_start: 0.7922 (m-30) cc_final: 0.7523 (m-30) REVERT: A 258 ASP cc_start: 0.8608 (m-30) cc_final: 0.8172 (t0) REVERT: A 366 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7602 (pp) REVERT: A 499 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.8526 (m-30) REVERT: A 607 SER cc_start: 0.8933 (OUTLIER) cc_final: 0.8723 (t) REVERT: A 665 GLU cc_start: 0.8760 (pm20) cc_final: 0.8497 (pm20) REVERT: B 135 TYR cc_start: 0.8245 (t80) cc_final: 0.8039 (t80) REVERT: C 15 SER cc_start: 0.8832 (t) cc_final: 0.8084 (m) REVERT: F 9 ASN cc_start: 0.7774 (t0) cc_final: 0.7491 (m-40) REVERT: F 68 MET cc_start: 0.7886 (mtm) cc_final: 0.6658 (mmt) REVERT: F 453 SER cc_start: 0.1031 (OUTLIER) cc_final: 0.0655 (t) REVERT: F 544 VAL cc_start: 0.0757 (OUTLIER) cc_final: 0.0246 (t) REVERT: F 576 MET cc_start: -0.0071 (mmt) cc_final: -0.2126 (mtt) REVERT: E 233 MET cc_start: 0.7716 (mpm) cc_final: 0.6808 (tpp) REVERT: E 315 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8439 (p0) REVERT: G 46 SER cc_start: 0.6456 (OUTLIER) cc_final: 0.5763 (t) outliers start: 116 outliers final: 27 residues processed: 398 average time/residue: 0.3598 time to fit residues: 216.2279 Evaluate side-chains 195 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 318 CYS Chi-restraints excluded: chain F residue 453 SER Chi-restraints excluded: chain F residue 544 VAL Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain G residue 2 ASN Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 27 ASN Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 84 LYS 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: 0.0970 chunk 202 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 136 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 209 optimal weight: 10.0000 chunk 80 optimal weight: 0.0070 chunk 127 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 242 optimal weight: 30.0000 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS B 73 GLN C 34 GLN D 176 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 492 GLN ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 554 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.138587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.093899 restraints weight = 119144.080| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 6.30 r_work: 0.3580 rms_B_bonded: 5.84 restraints_weight: 2.0000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 22559 Z= 0.150 Angle : 0.731 16.937 30906 Z= 0.368 Chirality : 0.044 0.253 3581 Planarity : 0.005 0.059 3748 Dihedral : 12.971 150.987 3781 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.28 % Favored : 91.45 % Rotamer: Outliers : 4.52 % Allowed : 30.42 % Favored : 65.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.16), residues: 2650 helix: 0.30 (0.17), residues: 965 sheet: -1.22 (0.35), residues: 217 loop : -2.34 (0.15), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 182 HIS 0.007 0.001 HIS E 554 PHE 0.030 0.002 PHE E 422 TYR 0.020 0.002 TYR F 299 ARG 0.006 0.001 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.05110 ( 842) hydrogen bonds : angle 5.26640 ( 2324) metal coordination : bond 0.01766 ( 32) metal coordination : angle 5.28922 ( 27) covalent geometry : bond 0.00331 (22527) covalent geometry : angle 0.71418 (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 281 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 179 time to evaluate : 2.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.7611 (tptt) cc_final: 0.7308 (tptp) REVERT: A 114 ILE cc_start: 0.7252 (mt) cc_final: 0.6882 (mt) REVERT: A 258 ASP cc_start: 0.8830 (m-30) cc_final: 0.8393 (t0) REVERT: A 499 ASP cc_start: 0.9132 (OUTLIER) cc_final: 0.8928 (m-30) REVERT: A 924 MET cc_start: 0.8702 (mmm) cc_final: 0.8112 (mtt) REVERT: B 62 MET cc_start: 0.8490 (ttt) cc_final: 0.8088 (tpp) REVERT: B 174 MET cc_start: 0.9232 (tpp) cc_final: 0.8939 (tpp) REVERT: C 38 ASP cc_start: 0.8683 (t0) cc_final: 0.8459 (t0) REVERT: C 67 ASP cc_start: 0.8244 (t0) cc_final: 0.7938 (t0) REVERT: D 60 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7947 (pp20) REVERT: D 70 MET cc_start: 0.8695 (ttp) cc_final: 0.8448 (ttp) REVERT: D 75 ARG cc_start: 0.7633 (tpp80) cc_final: 0.7408 (tpt-90) REVERT: F 9 ASN cc_start: 0.8246 (t0) cc_final: 0.7890 (m110) REVERT: F 68 MET cc_start: 0.8069 (mtm) cc_final: 0.6745 (mmt) REVERT: F 233 MET cc_start: 0.8424 (mpp) cc_final: 0.7338 (tmm) REVERT: F 460 LYS cc_start: -0.2436 (OUTLIER) cc_final: -0.2813 (tmmt) REVERT: F 531 GLN cc_start: 0.2557 (OUTLIER) cc_final: 0.1838 (mm-40) REVERT: F 576 MET cc_start: 0.1670 (mmt) cc_final: 0.0939 (mtt) REVERT: E 274 MET cc_start: 0.8230 (mmm) cc_final: 0.7541 (mmp) REVERT: G 12 MET cc_start: 0.8272 (pmm) cc_final: 0.8029 (pmm) REVERT: G 31 TYR cc_start: 0.7924 (m-10) cc_final: 0.7543 (m-80) REVERT: G 35 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8118 (m) outliers start: 102 outliers final: 35 residues processed: 271 average time/residue: 0.3564 time to fit residues: 147.7501 Evaluate side-chains 177 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 138 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 318 CYS Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 436 MET Chi-restraints excluded: chain F residue 460 LYS Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 426 CYS Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 77 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 104 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 196 optimal weight: 50.0000 chunk 133 optimal weight: 0.7980 chunk 216 optimal weight: 6.9990 chunk 254 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 252 optimal weight: 50.0000 chunk 94 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 244 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 9 ASN A 447 ASN A 725 HIS ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.124834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.076240 restraints weight = 153523.086| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 8.05 r_work: 0.3141 rms_B_bonded: 6.03 restraints_weight: 2.0000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22559 Z= 0.167 Angle : 0.684 14.387 30906 Z= 0.344 Chirality : 0.043 0.215 3581 Planarity : 0.005 0.052 3748 Dihedral : 12.555 138.648 3751 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.87 % Favored : 91.87 % Rotamer: Outliers : 4.17 % Allowed : 29.68 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.16), residues: 2650 helix: 0.42 (0.17), residues: 964 sheet: -1.05 (0.35), residues: 226 loop : -2.24 (0.15), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 182 HIS 0.004 0.001 HIS F 39 PHE 0.023 0.002 PHE F 373 TYR 0.019 0.002 TYR F 299 ARG 0.010 0.001 ARG A 555 Details of bonding type rmsd hydrogen bonds : bond 0.04874 ( 842) hydrogen bonds : angle 5.03419 ( 2324) metal coordination : bond 0.01531 ( 32) metal coordination : angle 4.74745 ( 27) covalent geometry : bond 0.00369 (22527) covalent geometry : angle 0.66929 (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 243 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 149 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.7516 (tptt) cc_final: 0.7244 (tptp) REVERT: A 61 GLU cc_start: 0.9261 (OUTLIER) cc_final: 0.8826 (pm20) REVERT: A 105 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8575 (ptp-110) REVERT: A 138 ASN cc_start: 0.9092 (OUTLIER) cc_final: 0.8413 (p0) REVERT: A 258 ASP cc_start: 0.9047 (m-30) cc_final: 0.8594 (t0) REVERT: A 499 ASP cc_start: 0.9261 (OUTLIER) cc_final: 0.9025 (m-30) REVERT: A 527 LEU cc_start: 0.9103 (tp) cc_final: 0.8883 (tt) REVERT: A 553 ARG cc_start: 0.8580 (ptm-80) cc_final: 0.8367 (ptm-80) REVERT: A 665 GLU cc_start: 0.8834 (pm20) cc_final: 0.8583 (pm20) REVERT: A 924 MET cc_start: 0.8747 (mmm) cc_final: 0.8419 (mtp) REVERT: B 57 ARG cc_start: 0.7124 (mpt180) cc_final: 0.6629 (mpt180) REVERT: B 157 GLN cc_start: 0.8612 (mm-40) cc_final: 0.8387 (mm110) REVERT: C 38 ASP cc_start: 0.9040 (t0) cc_final: 0.8707 (t0) REVERT: F 9 ASN cc_start: 0.8407 (t0) cc_final: 0.7995 (m-40) REVERT: F 68 MET cc_start: 0.8125 (mtm) cc_final: 0.6739 (mmt) REVERT: F 289 SER cc_start: 0.5262 (OUTLIER) cc_final: 0.4970 (p) REVERT: F 429 MET cc_start: -0.5515 (ttp) cc_final: -0.5756 (ttp) REVERT: F 460 LYS cc_start: -0.2462 (OUTLIER) cc_final: -0.3093 (tttm) REVERT: F 490 ARG cc_start: -0.0150 (OUTLIER) cc_final: -0.0782 (mtm-85) REVERT: F 531 GLN cc_start: 0.2284 (OUTLIER) cc_final: 0.1518 (mm-40) REVERT: F 576 MET cc_start: 0.1501 (mmt) cc_final: 0.0378 (mtt) REVERT: E 233 MET cc_start: 0.7240 (mmp) cc_final: 0.7034 (mmm) REVERT: E 274 MET cc_start: 0.8484 (mmm) cc_final: 0.8076 (mmp) REVERT: E 429 MET cc_start: 0.4465 (ptm) cc_final: 0.4108 (ppp) REVERT: E 576 MET cc_start: -0.3341 (tmm) cc_final: -0.3566 (ttp) outliers start: 94 outliers final: 49 residues processed: 230 average time/residue: 0.3463 time to fit residues: 121.6130 Evaluate side-chains 194 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 137 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASN Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 318 CYS Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 460 LYS Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 490 ARG Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 77 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 246 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 198 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 117 optimal weight: 0.0980 chunk 124 optimal weight: 5.9990 chunk 252 optimal weight: 0.0020 chunk 63 optimal weight: 0.9980 chunk 260 optimal weight: 8.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN A 898 HIS C 34 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.127358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.077183 restraints weight = 130068.415| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 7.77 r_work: 0.3132 rms_B_bonded: 6.39 restraints_weight: 2.0000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22559 Z= 0.114 Angle : 0.628 14.139 30906 Z= 0.315 Chirality : 0.042 0.216 3581 Planarity : 0.004 0.053 3748 Dihedral : 12.378 129.330 3748 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.53 % Favored : 92.21 % Rotamer: Outliers : 3.07 % Allowed : 30.20 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.16), residues: 2650 helix: 0.46 (0.17), residues: 979 sheet: -0.85 (0.35), residues: 229 loop : -2.14 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 182 HIS 0.016 0.001 HIS A 898 PHE 0.018 0.001 PHE E 422 TYR 0.021 0.001 TYR D 135 ARG 0.005 0.000 ARG D 75 Details of bonding type rmsd hydrogen bonds : bond 0.04420 ( 842) hydrogen bonds : angle 4.82273 ( 2324) metal coordination : bond 0.01211 ( 32) metal coordination : angle 4.43512 ( 27) covalent geometry : bond 0.00242 (22527) covalent geometry : angle 0.61399 (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 216 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 147 time to evaluate : 2.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.7461 (tptt) cc_final: 0.7171 (tptp) REVERT: A 61 GLU cc_start: 0.9252 (OUTLIER) cc_final: 0.8789 (pm20) REVERT: A 63 ASP cc_start: 0.9117 (OUTLIER) cc_final: 0.8596 (t0) REVERT: A 138 ASN cc_start: 0.9056 (OUTLIER) cc_final: 0.8376 (p0) REVERT: A 167 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7938 (pp20) REVERT: A 258 ASP cc_start: 0.9047 (m-30) cc_final: 0.8602 (t0) REVERT: A 499 ASP cc_start: 0.9245 (OUTLIER) cc_final: 0.9041 (m-30) REVERT: A 527 LEU cc_start: 0.9014 (tp) cc_final: 0.8765 (tt) REVERT: A 543 ASN cc_start: 0.7957 (m-40) cc_final: 0.7543 (m-40) REVERT: A 553 ARG cc_start: 0.8514 (ptm-80) cc_final: 0.8213 (ptm-80) REVERT: A 618 ASP cc_start: 0.8479 (t0) cc_final: 0.8215 (t0) REVERT: C 19 GLN cc_start: 0.8268 (mp10) cc_final: 0.7502 (mp10) REVERT: C 38 ASP cc_start: 0.9056 (t0) cc_final: 0.8656 (t0) REVERT: D 60 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7928 (pp20) REVERT: D 62 MET cc_start: 0.7824 (tmm) cc_final: 0.7600 (tmm) REVERT: D 71 TYR cc_start: 0.7548 (OUTLIER) cc_final: 0.7264 (t80) REVERT: F 9 ASN cc_start: 0.8454 (t0) cc_final: 0.8012 (m110) REVERT: F 68 MET cc_start: 0.8045 (mtm) cc_final: 0.6743 (mmt) REVERT: F 289 SER cc_start: 0.4877 (OUTLIER) cc_final: 0.4601 (p) REVERT: F 460 LYS cc_start: -0.1286 (OUTLIER) cc_final: -0.2217 (tttm) REVERT: F 531 GLN cc_start: 0.3207 (OUTLIER) cc_final: 0.2564 (mm-40) REVERT: F 576 MET cc_start: 0.1752 (mmt) cc_final: 0.1050 (mtt) REVERT: E 25 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.6462 (mm) REVERT: E 274 MET cc_start: 0.8564 (mmm) cc_final: 0.8204 (mmp) REVERT: E 429 MET cc_start: 0.4763 (ptm) cc_final: 0.4555 (ppp) REVERT: G 31 TYR cc_start: 0.7993 (m-10) cc_final: 0.7597 (m-80) outliers start: 69 outliers final: 41 residues processed: 209 average time/residue: 0.3518 time to fit residues: 114.5295 Evaluate side-chains 180 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 129 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 248 ARG Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 318 CYS Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 460 LYS Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 77 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 44 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 180 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 16 optimal weight: 0.0370 chunk 172 optimal weight: 40.0000 chunk 8 optimal weight: 4.9990 chunk 209 optimal weight: 7.9990 overall best weight: 1.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 447 ASN ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 GLN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.123010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.073510 restraints weight = 133108.262| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 7.43 r_work: 0.3075 rms_B_bonded: 5.52 restraints_weight: 2.0000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22559 Z= 0.172 Angle : 0.662 14.945 30906 Z= 0.334 Chirality : 0.043 0.255 3581 Planarity : 0.005 0.054 3748 Dihedral : 12.323 121.053 3748 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.94 % Favored : 91.79 % Rotamer: Outliers : 4.30 % Allowed : 29.81 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.16), residues: 2650 helix: 0.43 (0.17), residues: 973 sheet: -1.08 (0.34), residues: 229 loop : -2.08 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 916 HIS 0.004 0.001 HIS F 39 PHE 0.020 0.002 PHE A 741 TYR 0.015 0.002 TYR A 788 ARG 0.004 0.001 ARG F 22 Details of bonding type rmsd hydrogen bonds : bond 0.04873 ( 842) hydrogen bonds : angle 4.83239 ( 2324) metal coordination : bond 0.01292 ( 32) metal coordination : angle 4.53453 ( 27) covalent geometry : bond 0.00386 (22527) covalent geometry : angle 0.64869 (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 230 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 133 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.7736 (tptt) cc_final: 0.7480 (tptp) REVERT: A 63 ASP cc_start: 0.9145 (OUTLIER) cc_final: 0.8621 (t0) REVERT: A 138 ASN cc_start: 0.9132 (OUTLIER) cc_final: 0.8455 (p0) REVERT: A 161 ASP cc_start: 0.8445 (m-30) cc_final: 0.8099 (m-30) REVERT: A 167 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7813 (pp20) REVERT: A 258 ASP cc_start: 0.9200 (m-30) cc_final: 0.8775 (t0) REVERT: A 527 LEU cc_start: 0.9051 (tp) cc_final: 0.8833 (tt) REVERT: A 553 ARG cc_start: 0.8574 (ptm-80) cc_final: 0.8292 (ptm-80) REVERT: A 665 GLU cc_start: 0.8764 (pm20) cc_final: 0.8493 (pm20) REVERT: A 798 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8797 (mtmm) REVERT: A 924 MET cc_start: 0.8752 (mmm) cc_final: 0.8324 (mtt) REVERT: B 77 GLU cc_start: 0.8514 (tp30) cc_final: 0.8126 (tp30) REVERT: B 155 GLU cc_start: 0.8027 (pp20) cc_final: 0.7479 (pp20) REVERT: C 19 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7765 (mp10) REVERT: C 38 ASP cc_start: 0.9257 (t0) cc_final: 0.8857 (t0) REVERT: D 48 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8152 (tm-30) REVERT: D 62 MET cc_start: 0.8151 (tmm) cc_final: 0.7922 (tmm) REVERT: F 9 ASN cc_start: 0.8362 (t0) cc_final: 0.7940 (m110) REVERT: F 68 MET cc_start: 0.8203 (mtm) cc_final: 0.6927 (mmt) REVERT: F 289 SER cc_start: 0.5216 (OUTLIER) cc_final: 0.4888 (p) REVERT: F 460 LYS cc_start: -0.2776 (OUTLIER) cc_final: -0.3315 (tttm) REVERT: F 576 MET cc_start: 0.1512 (mmt) cc_final: 0.0029 (mtt) REVERT: E 21 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8537 (mmm160) REVERT: E 25 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6728 (mm) REVERT: E 274 MET cc_start: 0.8493 (mmm) cc_final: 0.7997 (mmp) REVERT: E 429 MET cc_start: 0.4785 (ptm) cc_final: 0.4461 (ppp) REVERT: E 436 MET cc_start: 0.6873 (mmm) cc_final: 0.6607 (mmm) REVERT: E 475 PHE cc_start: 0.4491 (OUTLIER) cc_final: 0.4097 (p90) outliers start: 97 outliers final: 55 residues processed: 220 average time/residue: 0.3323 time to fit residues: 113.6416 Evaluate side-chains 193 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 128 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 12 TYR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 29 CYS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 248 ARG Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 318 CYS Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 460 LYS Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 475 PHE Chi-restraints excluded: chain E residue 545 ILE Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 109 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 124 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 217 optimal weight: 20.0000 chunk 244 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 250 optimal weight: 30.0000 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 239 optimal weight: 0.7980 chunk 159 optimal weight: 9.9990 chunk 92 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN B 118 ASN D 73 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.123596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.073542 restraints weight = 106634.134| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 6.78 r_work: 0.3147 rms_B_bonded: 5.08 restraints_weight: 2.0000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4404 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= 0.139 Angle : 0.634 19.038 30906 Z= 0.315 Chirality : 0.042 0.219 3581 Planarity : 0.004 0.062 3748 Dihedral : 12.221 102.956 3746 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.53 % Favored : 92.21 % Rotamer: Outliers : 4.30 % Allowed : 29.85 % Favored : 65.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.16), residues: 2650 helix: 0.51 (0.17), residues: 976 sheet: -0.90 (0.35), residues: 221 loop : -2.02 (0.16), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 182 HIS 0.003 0.001 HIS A 613 PHE 0.016 0.001 PHE F 373 TYR 0.014 0.001 TYR A 237 ARG 0.003 0.000 ARG D 75 Details of bonding type rmsd hydrogen bonds : bond 0.04467 ( 842) hydrogen bonds : angle 4.70334 ( 2324) metal coordination : bond 0.01035 ( 32) metal coordination : angle 4.18986 ( 27) covalent geometry : bond 0.00312 (22527) covalent geometry : angle 0.62205 (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 230 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 133 time to evaluate : 2.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.7831 (tptt) cc_final: 0.7581 (tptp) REVERT: A 63 ASP cc_start: 0.9218 (OUTLIER) cc_final: 0.8563 (t70) REVERT: A 138 ASN cc_start: 0.9128 (OUTLIER) cc_final: 0.8412 (p0) REVERT: A 161 ASP cc_start: 0.8424 (m-30) cc_final: 0.8146 (m-30) REVERT: A 167 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7942 (pp20) REVERT: A 258 ASP cc_start: 0.9126 (m-30) cc_final: 0.8773 (t0) REVERT: A 527 LEU cc_start: 0.9086 (tp) cc_final: 0.8841 (tt) REVERT: A 553 ARG cc_start: 0.8554 (ptm-80) cc_final: 0.8238 (ptm-80) REVERT: A 668 MET cc_start: 0.9084 (ttp) cc_final: 0.8604 (ttt) REVERT: A 924 MET cc_start: 0.8812 (mmm) cc_final: 0.8276 (mtt) REVERT: B 155 GLU cc_start: 0.8007 (pp20) cc_final: 0.7474 (pp20) REVERT: C 19 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7716 (mp10) REVERT: C 38 ASP cc_start: 0.9164 (t0) cc_final: 0.8769 (t0) REVERT: D 48 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8146 (tm-30) REVERT: D 60 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8092 (pp20) REVERT: D 62 MET cc_start: 0.8190 (tmm) cc_final: 0.7968 (tmm) REVERT: F 9 ASN cc_start: 0.8454 (t0) cc_final: 0.7989 (m-40) REVERT: F 68 MET cc_start: 0.8121 (mtm) cc_final: 0.6930 (mmt) REVERT: F 460 LYS cc_start: -0.2908 (OUTLIER) cc_final: -0.3362 (tttm) REVERT: F 576 MET cc_start: 0.1446 (mmt) cc_final: -0.0162 (mtt) REVERT: E 21 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8478 (mmm160) REVERT: E 25 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6832 (mm) REVERT: E 274 MET cc_start: 0.8604 (mmm) cc_final: 0.8190 (mmp) REVERT: E 436 MET cc_start: 0.6876 (mmm) cc_final: 0.6586 (mmm) REVERT: G 64 THR cc_start: 0.7725 (OUTLIER) cc_final: 0.7305 (m) outliers start: 97 outliers final: 60 residues processed: 219 average time/residue: 0.3457 time to fit residues: 117.8803 Evaluate side-chains 195 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 127 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 12 TYR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 29 CYS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 248 ARG Chi-restraints excluded: chain F residue 318 CYS Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 460 LYS Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 426 CYS Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 77 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 192 optimal weight: 30.0000 chunk 245 optimal weight: 7.9990 chunk 222 optimal weight: 30.0000 chunk 239 optimal weight: 8.9990 chunk 206 optimal weight: 0.0770 chunk 177 optimal weight: 10.0000 chunk 100 optimal weight: 0.1980 chunk 93 optimal weight: 0.1980 chunk 103 optimal weight: 6.9990 chunk 165 optimal weight: 30.0000 chunk 97 optimal weight: 0.7980 overall best weight: 1.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 GLN ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 GLN ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 537 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.120825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.070968 restraints weight = 119471.828| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 6.45 r_work: 0.3078 rms_B_bonded: 5.00 restraints_weight: 2.0000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 22559 Z= 0.156 Angle : 0.641 15.330 30906 Z= 0.320 Chirality : 0.042 0.230 3581 Planarity : 0.004 0.054 3748 Dihedral : 12.016 74.992 3746 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.64 % Favored : 92.17 % Rotamer: Outliers : 3.86 % Allowed : 29.89 % Favored : 66.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.16), residues: 2650 helix: 0.47 (0.17), residues: 980 sheet: -1.25 (0.34), residues: 235 loop : -1.98 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 182 HIS 0.003 0.001 HIS A 810 PHE 0.019 0.001 PHE A 753 TYR 0.023 0.001 TYR F 457 ARG 0.004 0.000 ARG G 74 Details of bonding type rmsd hydrogen bonds : bond 0.04528 ( 842) hydrogen bonds : angle 4.65992 ( 2324) metal coordination : bond 0.01079 ( 32) metal coordination : angle 4.26370 ( 27) covalent geometry : bond 0.00349 (22527) covalent geometry : angle 0.62908 (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 220 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 133 time to evaluate : 2.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.9137 (tp40) cc_final: 0.8928 (tp40) REVERT: A 50 LYS cc_start: 0.7765 (tptt) cc_final: 0.7504 (tptp) REVERT: A 63 ASP cc_start: 0.9191 (OUTLIER) cc_final: 0.8887 (t70) REVERT: A 138 ASN cc_start: 0.9140 (OUTLIER) cc_final: 0.8428 (p0) REVERT: A 161 ASP cc_start: 0.8548 (m-30) cc_final: 0.8289 (m-30) REVERT: A 167 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8056 (pp20) REVERT: A 258 ASP cc_start: 0.9176 (m-30) cc_final: 0.8807 (t0) REVERT: A 527 LEU cc_start: 0.9069 (tp) cc_final: 0.8809 (tt) REVERT: A 553 ARG cc_start: 0.8545 (ptm-80) cc_final: 0.8194 (ptm-80) REVERT: A 668 MET cc_start: 0.9029 (ttp) cc_final: 0.8525 (ttt) REVERT: A 798 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8811 (mtmm) REVERT: A 924 MET cc_start: 0.8747 (mmm) cc_final: 0.8259 (mtt) REVERT: B 77 GLU cc_start: 0.8497 (tp30) cc_final: 0.8014 (tp30) REVERT: B 129 MET cc_start: 0.9035 (mtm) cc_final: 0.8831 (mtt) REVERT: B 155 GLU cc_start: 0.7962 (pp20) cc_final: 0.7376 (pp20) REVERT: C 19 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8097 (mt0) REVERT: C 38 ASP cc_start: 0.9253 (t0) cc_final: 0.8855 (t0) REVERT: D 48 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8158 (tm-30) REVERT: D 129 MET cc_start: 0.8079 (mpp) cc_final: 0.7499 (mtp) REVERT: F 9 ASN cc_start: 0.8413 (t0) cc_final: 0.7993 (m-40) REVERT: F 68 MET cc_start: 0.8242 (mtm) cc_final: 0.7102 (mmt) REVERT: F 460 LYS cc_start: -0.2958 (OUTLIER) cc_final: -0.3501 (tttm) REVERT: F 576 MET cc_start: 0.1169 (mmt) cc_final: -0.0333 (mtt) REVERT: E 25 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.7016 (mm) REVERT: E 274 MET cc_start: 0.8558 (mmm) cc_final: 0.8057 (mmp) REVERT: E 436 MET cc_start: 0.6948 (mmm) cc_final: 0.6677 (mmm) REVERT: E 475 PHE cc_start: 0.4403 (OUTLIER) cc_final: 0.4099 (p90) outliers start: 87 outliers final: 60 residues processed: 210 average time/residue: 0.3419 time to fit residues: 112.1492 Evaluate side-chains 197 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 129 time to evaluate : 2.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 12 TYR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 29 CYS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 248 ARG Chi-restraints excluded: chain F residue 318 CYS Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 429 MET Chi-restraints excluded: chain F residue 460 LYS Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 475 PHE Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 77 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 45 optimal weight: 2.9990 chunk 150 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 141 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 chunk 173 optimal weight: 20.0000 chunk 16 optimal weight: 0.1980 chunk 62 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 447 ASN ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 HIS ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 2 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.121024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.070677 restraints weight = 150671.979| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 7.52 r_work: 0.3046 rms_B_bonded: 5.73 restraints_weight: 2.0000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22559 Z= 0.176 Angle : 0.657 15.832 30906 Z= 0.328 Chirality : 0.043 0.233 3581 Planarity : 0.004 0.068 3748 Dihedral : 11.935 75.726 3746 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.72 % Favored : 92.10 % Rotamer: Outliers : 3.78 % Allowed : 30.20 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.16), residues: 2650 helix: 0.40 (0.17), residues: 986 sheet: -1.18 (0.34), residues: 230 loop : -1.98 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 916 HIS 0.004 0.001 HIS A 898 PHE 0.017 0.002 PHE A 753 TYR 0.021 0.002 TYR G 89 ARG 0.006 0.000 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.04633 ( 842) hydrogen bonds : angle 4.65778 ( 2324) metal coordination : bond 0.01086 ( 32) metal coordination : angle 4.39367 ( 27) covalent geometry : bond 0.00401 (22527) covalent geometry : angle 0.64449 (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 217 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 132 time to evaluate : 2.506 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: A 50 LYS cc_start: 0.7830 (tptt) cc_final: 0.7615 (tptp) REVERT: A 63 ASP cc_start: 0.9232 (OUTLIER) cc_final: 0.8851 (t70) REVERT: A 138 ASN cc_start: 0.9120 (OUTLIER) cc_final: 0.8416 (p0) REVERT: A 258 ASP cc_start: 0.9184 (m-30) cc_final: 0.8824 (t0) REVERT: A 365 ARG cc_start: 0.7282 (tpp-160) cc_final: 0.7063 (tpp-160) REVERT: A 380 MET cc_start: 0.7738 (tpp) cc_final: 0.7519 (tpp) REVERT: A 527 LEU cc_start: 0.9091 (tp) cc_final: 0.8819 (tt) REVERT: A 553 ARG cc_start: 0.8619 (ptm-80) cc_final: 0.8281 (ptm-80) REVERT: A 668 MET cc_start: 0.9128 (ttp) cc_final: 0.8664 (ttt) REVERT: A 798 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8803 (mtmm) REVERT: A 924 MET cc_start: 0.8824 (mmm) cc_final: 0.8379 (mtt) REVERT: B 52 ASP cc_start: 0.8195 (m-30) cc_final: 0.7877 (t0) REVERT: B 77 GLU cc_start: 0.8509 (tp30) cc_final: 0.8018 (tp30) REVERT: B 155 GLU cc_start: 0.7978 (pp20) cc_final: 0.7392 (pp20) REVERT: C 19 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8144 (mt0) REVERT: C 38 ASP cc_start: 0.9266 (t0) cc_final: 0.8885 (t0) REVERT: D 60 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8131 (pp20) REVERT: D 129 MET cc_start: 0.8143 (mpp) cc_final: 0.7727 (mtt) REVERT: F 9 ASN cc_start: 0.8624 (t0) cc_final: 0.8142 (m-40) REVERT: F 68 MET cc_start: 0.8240 (mtm) cc_final: 0.7095 (mmt) REVERT: F 378 MET cc_start: 0.5308 (OUTLIER) cc_final: 0.5046 (mmt) REVERT: F 576 MET cc_start: 0.1269 (mmt) cc_final: -0.0075 (mtt) REVERT: E 25 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6995 (mm) REVERT: E 274 MET cc_start: 0.8595 (mmm) cc_final: 0.8090 (mmp) REVERT: E 436 MET cc_start: 0.7084 (mmm) cc_final: 0.6828 (mmm) REVERT: G 29 LEU cc_start: 0.4979 (OUTLIER) cc_final: 0.4321 (tp) outliers start: 85 outliers final: 59 residues processed: 205 average time/residue: 0.3438 time to fit residues: 109.7855 Evaluate side-chains 190 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 124 time to evaluate : 2.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 12 TYR Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 29 CYS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 248 ARG Chi-restraints excluded: chain F residue 318 CYS Chi-restraints excluded: chain F residue 378 MET Chi-restraints excluded: chain F residue 429 MET Chi-restraints excluded: chain F residue 460 LYS Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 77 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 50 optimal weight: 1.9990 chunk 249 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 36 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 237 optimal weight: 30.0000 chunk 56 optimal weight: 0.1980 chunk 262 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 GLN ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.121795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.071025 restraints weight = 122688.422| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 7.02 r_work: 0.3089 rms_B_bonded: 5.03 restraints_weight: 2.0000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.5311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22559 Z= 0.131 Angle : 0.623 15.013 30906 Z= 0.310 Chirality : 0.042 0.218 3581 Planarity : 0.004 0.067 3748 Dihedral : 11.861 73.603 3746 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.15 % Favored : 92.66 % Rotamer: Outliers : 3.20 % Allowed : 30.60 % Favored : 66.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.16), residues: 2650 helix: 0.56 (0.17), residues: 977 sheet: -1.12 (0.34), residues: 231 loop : -1.90 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 182 HIS 0.003 0.001 HIS A 113 PHE 0.018 0.001 PHE F 422 TYR 0.015 0.001 TYR F 457 ARG 0.009 0.000 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.04330 ( 842) hydrogen bonds : angle 4.53547 ( 2324) metal coordination : bond 0.00971 ( 32) metal coordination : angle 4.14574 ( 27) covalent geometry : bond 0.00293 (22527) covalent geometry : angle 0.61148 (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 200 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 128 time to evaluate : 2.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.7759 (tptt) cc_final: 0.7550 (tptp) REVERT: A 63 ASP cc_start: 0.9212 (OUTLIER) cc_final: 0.8956 (t70) REVERT: A 138 ASN cc_start: 0.9110 (OUTLIER) cc_final: 0.8392 (p0) REVERT: A 161 ASP cc_start: 0.8202 (m-30) cc_final: 0.7797 (t0) REVERT: A 258 ASP cc_start: 0.9154 (m-30) cc_final: 0.8800 (t0) REVERT: A 380 MET cc_start: 0.7572 (tpp) cc_final: 0.7370 (tpp) REVERT: A 527 LEU cc_start: 0.9064 (tp) cc_final: 0.8792 (tt) REVERT: A 553 ARG cc_start: 0.8577 (ptm-80) cc_final: 0.8214 (ptm-80) REVERT: A 668 MET cc_start: 0.9065 (ttp) cc_final: 0.8572 (ttt) REVERT: A 798 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8772 (mtmm) REVERT: A 902 MET cc_start: 0.8417 (pmm) cc_final: 0.8191 (pmm) REVERT: A 924 MET cc_start: 0.8781 (mmm) cc_final: 0.8260 (mtt) REVERT: B 77 GLU cc_start: 0.8473 (tp30) cc_final: 0.8005 (tp30) REVERT: B 155 GLU cc_start: 0.7856 (pp20) cc_final: 0.7269 (pp20) REVERT: C 19 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8045 (mt0) REVERT: C 38 ASP cc_start: 0.9210 (t0) cc_final: 0.8791 (t0) REVERT: D 60 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8170 (pp20) REVERT: D 129 MET cc_start: 0.8051 (mpp) cc_final: 0.7679 (mtt) REVERT: F 9 ASN cc_start: 0.8611 (t0) cc_final: 0.8144 (m-40) REVERT: F 68 MET cc_start: 0.8248 (mtm) cc_final: 0.7072 (mmt) REVERT: F 378 MET cc_start: 0.5186 (OUTLIER) cc_final: 0.4956 (mmt) REVERT: F 460 LYS cc_start: -0.2378 (OUTLIER) cc_final: -0.2720 (ttpp) REVERT: F 576 MET cc_start: 0.1431 (mmt) cc_final: 0.0223 (mtt) REVERT: E 274 MET cc_start: 0.8654 (mmm) cc_final: 0.8274 (mmp) REVERT: G 29 LEU cc_start: 0.4371 (OUTLIER) cc_final: 0.4042 (tp) outliers start: 72 outliers final: 59 residues processed: 188 average time/residue: 0.3433 time to fit residues: 100.8194 Evaluate side-chains 192 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 126 time to evaluate : 2.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 12 TYR Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 29 CYS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 248 ARG Chi-restraints excluded: chain F residue 318 CYS Chi-restraints excluded: chain F residue 378 MET Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 429 MET Chi-restraints excluded: chain F residue 460 LYS Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 181 optimal weight: 3.9990 chunk 161 optimal weight: 30.0000 chunk 53 optimal weight: 1.9990 chunk 187 optimal weight: 30.0000 chunk 84 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 225 optimal weight: 7.9990 chunk 192 optimal weight: 0.9990 chunk 175 optimal weight: 30.0000 chunk 64 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN A 898 HIS ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.121551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.071808 restraints weight = 110466.712| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 5.83 r_work: 0.3108 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.211 22559 Z= 0.214 Angle : 0.766 59.141 30906 Z= 0.417 Chirality : 0.044 0.520 3581 Planarity : 0.005 0.096 3748 Dihedral : 11.861 73.597 3746 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.38 % Favored : 92.44 % Rotamer: Outliers : 3.38 % Allowed : 30.42 % Favored : 66.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.16), residues: 2650 helix: 0.51 (0.17), residues: 981 sheet: -1.11 (0.34), residues: 231 loop : -1.89 (0.16), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 182 HIS 0.009 0.001 HIS A 898 PHE 0.018 0.001 PHE F 422 TYR 0.018 0.002 TYR E 421 ARG 0.009 0.000 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.04395 ( 842) hydrogen bonds : angle 4.54101 ( 2324) metal coordination : bond 0.01045 ( 32) metal coordination : angle 4.14389 ( 27) covalent geometry : bond 0.00480 (22527) covalent geometry : angle 0.75613 (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 203 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 127 time to evaluate : 2.374 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: A 50 LYS cc_start: 0.7719 (tptt) cc_final: 0.7499 (tptp) REVERT: A 63 ASP cc_start: 0.9205 (OUTLIER) cc_final: 0.8948 (t70) REVERT: A 138 ASN cc_start: 0.9106 (OUTLIER) cc_final: 0.8383 (p0) REVERT: A 161 ASP cc_start: 0.8194 (m-30) cc_final: 0.7787 (t0) REVERT: A 258 ASP cc_start: 0.9170 (m-30) cc_final: 0.8813 (t0) REVERT: A 527 LEU cc_start: 0.9069 (tp) cc_final: 0.8798 (tt) REVERT: A 553 ARG cc_start: 0.8555 (ptm-80) cc_final: 0.8193 (ptm-80) REVERT: A 668 MET cc_start: 0.9051 (ttp) cc_final: 0.8552 (ttt) REVERT: A 798 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8766 (mtmm) REVERT: A 902 MET cc_start: 0.8433 (pmm) cc_final: 0.8230 (pmm) REVERT: A 924 MET cc_start: 0.8772 (mmm) cc_final: 0.8282 (mtt) REVERT: B 52 ASP cc_start: 0.8182 (m-30) cc_final: 0.7922 (t0) REVERT: B 77 GLU cc_start: 0.8459 (tp30) cc_final: 0.7976 (tp30) REVERT: B 155 GLU cc_start: 0.7835 (pp20) cc_final: 0.7242 (pp20) REVERT: C 19 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8046 (mt0) REVERT: C 38 ASP cc_start: 0.9240 (t0) cc_final: 0.8838 (t0) REVERT: D 60 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8164 (pp20) REVERT: D 129 MET cc_start: 0.8008 (mpp) cc_final: 0.7690 (mtt) REVERT: F 9 ASN cc_start: 0.8525 (t0) cc_final: 0.8083 (m-40) REVERT: F 68 MET cc_start: 0.8247 (mtm) cc_final: 0.7081 (mmt) REVERT: F 378 MET cc_start: 0.5234 (OUTLIER) cc_final: 0.4969 (mmt) REVERT: F 576 MET cc_start: 0.1162 (mmt) cc_final: -0.0449 (mtt) REVERT: E 274 MET cc_start: 0.8556 (mmm) cc_final: 0.8039 (mmp) REVERT: G 29 LEU cc_start: 0.4576 (OUTLIER) cc_final: 0.4102 (tp) outliers start: 76 outliers final: 60 residues processed: 191 average time/residue: 0.3386 time to fit residues: 101.7710 Evaluate side-chains 190 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 124 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 12 TYR Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 29 CYS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 248 ARG Chi-restraints excluded: chain F residue 318 CYS Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 378 MET Chi-restraints excluded: chain F residue 420 GLU Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 429 MET Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 243 optimal weight: 5.9990 chunk 263 optimal weight: 7.9990 chunk 117 optimal weight: 0.0050 chunk 97 optimal weight: 2.9990 chunk 171 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 266 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.121452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.070609 restraints weight = 120032.690| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 6.89 r_work: 0.3084 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.211 22559 Z= 0.214 Angle : 0.766 59.140 30906 Z= 0.417 Chirality : 0.044 0.520 3581 Planarity : 0.005 0.096 3748 Dihedral : 11.861 73.597 3746 Min Nonbonded Distance : 1.423 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.38 % Favored : 92.44 % Rotamer: Outliers : 2.94 % Allowed : 30.77 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.16), residues: 2650 helix: 0.51 (0.17), residues: 981 sheet: -1.11 (0.34), residues: 231 loop : -1.89 (0.16), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 182 HIS 0.009 0.001 HIS A 898 PHE 0.018 0.001 PHE F 422 TYR 0.018 0.002 TYR E 421 ARG 0.009 0.000 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.04395 ( 842) hydrogen bonds : angle 4.54101 ( 2324) metal coordination : bond 0.01045 ( 32) metal coordination : angle 4.14389 ( 27) covalent geometry : bond 0.00480 (22527) covalent geometry : angle 0.75613 (30879) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21612.76 seconds wall clock time: 371 minutes 35.42 seconds (22295.42 seconds total)