Starting phenix.real_space_refine on Sat Jul 4 17:16:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gwf_34311/07_2026/8gwf_34311.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gwf_34311/07_2026/8gwf_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 { model { file = "/net/cci-nas-00/data/ceres_data/8gwf_34311/07_2026/8gwf_34311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gwf_34311/07_2026/8gwf_34311.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gwf_34311/07_2026/8gwf_34311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gwf_34311/07_2026/8gwf_34311.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8gwf_34311/07_2026/8gwf_34311.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gwf_34311/07_2026/8gwf_34311.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21955 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 7492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 931, 7492 Classifications: {'peptide': 931} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 900} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1396 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 600 Classifications: {'peptide': 78} Link IDs: {'TRANS': 77} Chain: "D" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1422 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 545 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 16, 'rna3p_pyr': 8} Link IDs: {'rna3p': 24} Chain: "J" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 565 Classifications: {'RNA': 27} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 25} Chain: "F" Number of atoms: 4513 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4598 Chain: "E" Number of atoms: 4513 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4598 Chain: "G" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 868 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' ZN': 2, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2465 SG CYS A 301 75.578 55.650 121.844 1.00 86.97 S ATOM 2506 SG CYS A 306 75.567 57.180 125.354 1.00 84.94 S ATOM 2538 SG CYS A 310 76.856 53.605 124.773 1.00 84.77 S ATOM 3946 SG CYS A 487 78.264 69.779 106.107 1.00 95.87 S ATOM 5199 SG CYS A 645 77.470 71.834 109.252 1.00 97.77 S ATOM 5205 SG CYS A 646 76.146 68.218 108.904 1.00 89.00 S ATOM 12129 SG CYS F 16 102.478 65.216 50.524 1.00183.45 S ATOM 12144 SG CYS F 19 103.212 62.542 47.852 1.00198.14 S ATOM 12047 SG CYS F 5 114.925 66.378 50.337 1.00183.01 S ATOM 12068 SG CYS F 8 115.808 69.235 47.969 1.00185.13 S ATOM 12206 SG CYS F 26 114.614 70.148 51.170 1.00172.26 S ATOM 12223 SG CYS F 29 112.090 68.304 48.775 1.00175.19 S ATOM 12388 SG CYS F 50 93.154 76.836 65.675 1.00158.72 S ATOM 12418 SG CYS F 55 89.756 76.042 64.216 1.00164.97 S ATOM 12551 SG CYS F 72 91.926 78.390 62.448 1.00168.17 S ATOM 16642 SG CYS E 16 61.349 74.627 65.591 1.00165.58 S ATOM 16657 SG CYS E 19 58.755 72.126 64.275 1.00179.24 S ATOM 16560 SG CYS E 5 70.232 70.535 57.925 1.00188.71 S ATOM 16581 SG CYS E 8 70.961 72.499 54.838 1.00197.10 S ATOM 16719 SG CYS E 26 72.392 73.907 58.159 1.00186.39 S ATOM 16736 SG CYS E 29 68.780 74.086 57.029 1.00167.57 S ATOM 16901 SG CYS E 50 66.240 87.403 79.620 1.00176.08 S ATOM 16931 SG CYS E 55 63.011 88.887 81.055 1.00192.48 S ATOM 17064 SG CYS E 72 65.078 90.922 78.545 1.00187.74 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AMET F 474 " occ=0.42 ... (14 atoms not shown) pdb=" CE BMET F 474 " occ=0.58 residue: pdb=" N AMET E 474 " occ=0.11 ... (14 atoms not shown) pdb=" CE BMET E 474 " occ=0.89 Time building chain proxies: 6.03, per 1000 atoms: 0.27 Number of scatterers: 21955 At special positions: 0 Unit cell: (154.98, 136.94, 186.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 158 16.00 P 55 15.00 O 4305 8.00 N 3694 7.00 C 13735 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 1.3 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: 2.75 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 removed outlier: 3.974A pdb=" N ASN A 9 " --> pdb=" O GLN A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 91 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.649A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.622A pdb=" N TYR A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.815A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A 159 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.630A pdb=" N ASN A 209 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 206 through 210' Processing helix chain 'A' and resid 234 through 242 removed outlier: 3.528A pdb=" N TYR A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.865A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.569A pdb=" N HIS A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 removed outlier: 3.558A pdb=" N ARG A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 280 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.616A pdb=" N CYS A 301 " --> pdb=" O CYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.645A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.554A pdb=" N SER A 325 " --> pdb=" O PRO A 322 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 322 through 326' Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.506A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 425 Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 4.154A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.622A pdb=" N TRP A 509 " --> pdb=" O PHE A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.867A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 removed outlier: 3.610A pdb=" N THR A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 580 removed outlier: 4.033A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 removed outlier: 3.589A pdb=" N SER A 607 " --> pdb=" O LYS A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 removed outlier: 3.572A pdb=" N ARG A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 647 through 663 removed outlier: 3.586A pdb=" N ARG A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.525A pdb=" N ALA A 690 " --> pdb=" O THR A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 733 removed outlier: 3.504A pdb=" N ARG A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.792A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 851 through 855 Processing helix chain 'A' and resid 856 through 866 Processing helix chain 'A' and resid 867 through 872 removed outlier: 3.581A pdb=" N LYS A 871 " --> pdb=" O PRO A 868 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS A 872 " --> pdb=" O LEU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 903 removed outlier: 4.388A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N MET A 902 " --> pdb=" O HIS A 898 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR A 903 " --> pdb=" O MET A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 917 removed outlier: 3.678A pdb=" N GLU A 917 " --> pdb=" O ARG A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 923 removed outlier: 3.608A pdb=" N ALA A 923 " --> pdb=" O GLU A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 11 through 28 Processing helix chain 'B' and resid 31 through 96 removed outlier: 3.645A pdb=" N LEU B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP B 52 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 109 removed outlier: 3.763A pdb=" N ASN B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.619A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 25 through 41 removed outlier: 3.665A pdb=" N LEU C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 61 removed outlier: 3.681A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 73 Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 31 through 80 removed outlier: 3.885A pdb=" N LEU D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA D 45 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP D 52 " --> pdb=" O GLU D 48 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA D 54 " --> pdb=" O ASP D 50 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 99 removed outlier: 3.842A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 134 through 142 removed outlier: 3.570A pdb=" N TYR D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'F' and resid 26 through 36 Processing helix chain 'F' and resid 104 through 110 Processing helix chain 'F' and resid 116 through 125 removed outlier: 4.231A pdb=" N TYR F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 147 Processing helix chain 'F' and resid 265 through 275 Processing helix chain 'F' and resid 290 through 299 Processing helix chain 'F' and resid 310 through 325 removed outlier: 3.684A pdb=" N ALA F 316 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU F 317 " --> pdb=" O ALA F 313 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N LYS F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU F 322 " --> pdb=" O CYS F 318 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N LYS F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 328 No H-bonds generated for 'chain 'F' and resid 326 through 328' Processing helix chain 'F' and resid 381 through 391 removed outlier: 3.632A pdb=" N LEU F 391 " --> pdb=" O VAL F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 433 removed outlier: 3.999A pdb=" N LYS F 430 " --> pdb=" O CYS F 426 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR F 431 " --> pdb=" O ARG F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 456 removed outlier: 3.616A pdb=" N VAL F 449 " --> pdb=" O PRO F 445 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR F 451 " --> pdb=" O GLU F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 501 Processing helix chain 'F' and resid 503 through 507 removed outlier: 3.912A pdb=" N TRP F 506 " --> pdb=" O ASN F 503 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG F 507 " --> pdb=" O PRO F 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 503 through 507' Processing helix chain 'F' and resid 516 through 523 Processing helix chain 'E' and resid 26 through 36 Processing helix chain 'E' and resid 103 through 112 Processing helix chain 'E' and resid 116 through 124 removed outlier: 4.094A pdb=" N TYR E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 148 Processing helix chain 'E' and resid 264 through 273 Processing helix chain 'E' and resid 290 through 299 removed outlier: 3.748A pdb=" N LEU E 297 " --> pdb=" O ILE E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 325 removed outlier: 4.509A pdb=" N LYS E 320 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ALA E 321 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU E 322 " --> pdb=" O CYS E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 391 Processing helix chain 'E' and resid 418 through 422 Processing helix chain 'E' and resid 423 through 432 removed outlier: 3.864A pdb=" N LYS E 430 " --> pdb=" O CYS E 426 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE E 432 " --> pdb=" O LEU E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 456 removed outlier: 4.497A pdb=" N VAL E 449 " --> pdb=" O PRO E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 494 Processing helix chain 'E' and resid 494 through 500 Processing helix chain 'E' and resid 505 through 509 removed outlier: 4.422A pdb=" N LYS E 508 " --> pdb=" O ALA E 505 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA E 509 " --> pdb=" O TRP E 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 505 through 509' Processing helix chain 'E' and resid 515 through 526 Processing helix chain 'E' and resid 560 through 565 removed outlier: 4.014A pdb=" N ALA E 564 " --> pdb=" O ARG E 560 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 5.374A pdb=" N TYR A 69 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 114 " --> pdb=" O LYS A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.687A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 355 removed outlier: 3.551A pdb=" N ILE A 333 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 9.675A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 355 removed outlier: 3.551A pdb=" N ILE A 333 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.970A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA8, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AA9, first strand: chain 'A' and resid 816 through 822 Processing sheet with id=AB1, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.344A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU D 189 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 15 through 16 Processing sheet with id=AB3, first strand: chain 'F' and resid 64 through 65 Processing sheet with id=AB4, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AB5, first strand: chain 'F' and resid 152 through 154 Processing sheet with id=AB6, first strand: chain 'F' and resid 186 through 187 Processing sheet with id=AB7, first strand: chain 'F' and resid 200 through 202 Processing sheet with id=AB8, first strand: chain 'F' and resid 304 through 305 removed outlier: 5.091A pdb=" N VAL F 305 " --> pdb=" O VAL F 372 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 330 through 331 removed outlier: 3.532A pdb=" N SER F 331 " --> pdb=" O TYR F 355 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 472 through 473 Processing sheet with id=AC2, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AC3, first strand: chain 'E' and resid 24 through 25 removed outlier: 4.432A pdb=" N LEU E 14 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 69 through 71 Processing sheet with id=AC5, first strand: chain 'E' and resid 152 through 154 removed outlier: 3.672A pdb=" N PHE E 225 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 182 through 187 removed outlier: 6.958A pdb=" N PHE E 182 " --> pdb=" O GLU E 197 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLU E 197 " --> pdb=" O PHE E 182 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLY E 184 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE E 195 " --> pdb=" O GLY E 184 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 330 through 332 removed outlier: 6.593A pdb=" N SER E 331 " --> pdb=" O PHE E 357 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL E 356 " --> pdb=" O ILE E 304 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL E 305 " --> pdb=" O VAL E 372 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 481 through 482 removed outlier: 3.854A pdb=" N THR E 481 " --> pdb=" O ILE E 488 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 511 through 512 removed outlier: 6.087A pdb=" N PHE E 511 " --> pdb=" O GLN E 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'E' and resid 544 through 546 removed outlier: 3.552A pdb=" N LEU E 573 " --> pdb=" O VAL E 544 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 16 through 17 removed outlier: 3.737A pdb=" N ALA G 54 " --> pdb=" O THR G 67 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE G 56 " --> pdb=" O ILE G 65 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE G 65 " --> pdb=" O PHE G 56 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 29 through 31 removed outlier: 3.535A pdb=" N SER G 46 " --> pdb=" O TYR G 87 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS G 86 " --> pdb=" O PHE G 75 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE G 75 " --> pdb=" O LYS G 86 " (cutoff:3.500A) 799 hydrogen bonds defined for protein. 2226 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 4.42 Time building geometry restraints manager: 2.34 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: 12705 33.29 - 66.58: 642 66.58 - 99.87: 21 99.87 - 133.16: 0 133.16 - 166.45: 2 Dihedral angle restraints: 13370 sinusoidal: 5476 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 13367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.321: 3575 0.321 - 0.642: 2 0.642 - 0.963: 0 0.963 - 1.284: 2 1.284 - 1.605: 2 Chirality restraints: 3581 Sorted by residual: chirality pdb=" CA CYS G 14 " pdb=" N CYS G 14 " pdb=" C CYS G 14 " pdb=" CB CYS G 14 " both_signs ideal model delta sigma weight residual False 2.51 0.91 1.61 2.00e-01 2.50e+01 6.44e+01 chirality pdb=" CA TYR G 32 " pdb=" N TYR G 32 " pdb=" C TYR G 32 " pdb=" CB TYR G 32 " both_signs ideal model delta sigma weight residual False 2.51 1.18 1.33 2.00e-01 2.50e+01 4.42e+01 chirality pdb=" CA GLN G 11 " pdb=" N GLN G 11 " pdb=" C GLN G 11 " pdb=" CB GLN G 11 " both_signs ideal model delta sigma weight residual False 2.51 1.49 1.02 2.00e-01 2.50e+01 2.60e+01 ... (remaining 3578 not shown) Planarity restraints: 3748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 72 " -0.030 2.00e-02 2.50e+03 5.97e-02 3.57e+01 pdb=" C VAL A 72 " 0.103 2.00e-02 2.50e+03 pdb=" O VAL A 72 " -0.039 2.00e-02 2.50e+03 pdb=" N LYS A 73 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 363 " 0.106 5.00e-02 4.00e+02 1.40e-01 3.15e+01 pdb=" N PRO E 364 " -0.241 5.00e-02 4.00e+02 pdb=" CA PRO E 364 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO E 364 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 490 " 0.092 5.00e-02 4.00e+02 1.20e-01 2.31e+01 pdb=" N PRO F 491 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO F 491 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO F 491 " 0.062 5.00e-02 4.00e+02 ... (remaining 3745 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 299 2.62 - 3.19: 18637 3.19 - 3.76: 34097 3.76 - 4.33: 46279 4.33 - 4.90: 74396 Nonbonded interactions: 173708 Sorted by model distance: nonbonded pdb=" O SER D 173 " pdb=" OG SER D 177 " model vdw 2.045 3.040 nonbonded pdb=" OD1 ASN F 381 " pdb=" OG SER F 424 " model vdw 2.140 3.040 nonbonded pdb=" O PRO E 77 " pdb=" OG SER E 80 " model vdw 2.141 3.040 nonbonded pdb=" N2 G I 12 " pdb=" O2 C J 48 " model vdw 2.148 2.496 nonbonded pdb=" O CYS E 471 " pdb=" OG1 THR E 588 " model vdw 2.171 3.040 ... (remaining 173703 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 6 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 192)) selection = (chain 'D' and (resid 6 through 21 or (resid 22 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 42 or (resid 43 and (name N or name CA or name C or na \ me O or name CB )) or resid 44 through 46 or (resid 47 and (name N or name CA or \ name C or name O or name CB )) or resid 48 through 192)) } ncs_group { reference = (chain 'E' and (resid 1 through 473 or resid 475 through 703)) selection = (chain 'F' and (resid 1 through 473 or resid 475 through 703)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.11 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.650 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: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 26.770 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 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 : 17.821 166.450 8276 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.43 % Favored : 91.19 % Rotamer: Outliers : 5.14 % Allowed : 33.58 % Favored : 61.28 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.16), residues: 2650 helix: 0.34 (0.18), residues: 947 sheet: -1.60 (0.35), residues: 218 loop : -2.47 (0.15), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 303 TYR 0.022 0.001 TYR F 299 PHE 0.017 0.001 PHE F 437 TRP 0.037 0.002 TRP G 53 HIS 0.007 0.001 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00855 / 0.33 (22527) covalent geometry : angle 0.93982 / 0.55 (30879) hydrogen bonds : bond 0.18370 / 11.87 ( 842) hydrogen bonds : angle 6.41261 / 4.47 ( 2324) metal coordination : bond 0.01942 / 1.51 ( 32) metal coordination : angle 5.22093 / 2.92 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 296 time to evaluate : 0.831 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: 0.1703 time to fit residues: 102.9606 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 : 0.818 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.0980 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN A 534 ASN A 698 GLN A 725 HIS A 790 ASN B 73 GLN D 176 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN F 164 HIS 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 G 98 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.122573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.074554 restraints weight = 144422.517| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 7.06 r_work: 0.3077 rms_B_bonded: 5.98 restraints_weight: 2.0000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 22559 Z= 0.250 Angle : 0.824 19.087 30906 Z= 0.417 Chirality : 0.048 0.275 3581 Planarity : 0.006 0.059 3748 Dihedral : 8.860 147.773 3585 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.11 % Favored : 90.62 % Rotamer: Outliers : 5.75 % Allowed : 30.33 % Favored : 63.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.16), residues: 2650 helix: 0.02 (0.17), residues: 956 sheet: -1.37 (0.34), residues: 230 loop : -2.40 (0.15), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 75 TYR 0.020 0.002 TYR A 831 PHE 0.033 0.003 PHE E 422 TRP 0.026 0.002 TRP B 182 HIS 0.009 0.002 HIS A 810 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.25 (22527) covalent geometry : angle 0.80382 / 0.42 (30879) hydrogen bonds : bond 0.05788 / 3.71 ( 842) hydrogen bonds : angle 5.51847 / 3.86 ( 2324) metal coordination : bond 0.02015 / 1.43 ( 32) metal coordination : angle 6.20442 / 3.80 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 171 time to evaluate : 0.842 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: 0.7507 (tptt) cc_final: 0.7219 (tptp) REVERT: A 110 MET cc_start: 0.8114 (tpp) cc_final: 0.7724 (tpp) REVERT: A 114 ILE cc_start: 0.8335 (mt) cc_final: 0.8130 (mt) REVERT: A 258 ASP cc_start: 0.9164 (m-30) cc_final: 0.8590 (t0) REVERT: A 499 ASP cc_start: 0.9240 (OUTLIER) cc_final: 0.8996 (m-30) REVERT: A 603 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.9155 (mmtm) REVERT: A 665 GLU cc_start: 0.9050 (pm20) cc_final: 0.8753 (pm20) REVERT: A 734 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.8166 (t0) REVERT: A 924 MET cc_start: 0.8737 (mmm) cc_final: 0.8387 (mtt) REVERT: B 62 MET cc_start: 0.8672 (ttt) cc_final: 0.8077 (tpp) REVERT: B 174 MET cc_start: 0.9224 (tpp) cc_final: 0.8891 (tpp) REVERT: C 38 ASP cc_start: 0.9155 (t0) cc_final: 0.8856 (t0) REVERT: C 67 ASP cc_start: 0.8350 (t0) cc_final: 0.8031 (t0) REVERT: D 60 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8089 (pp20) REVERT: D 77 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8320 (tm-30) REVERT: D 189 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8396 (tt) REVERT: F 9 ASN cc_start: 0.8202 (t0) cc_final: 0.7929 (m110) REVERT: F 68 MET cc_start: 0.8300 (mtm) cc_final: 0.7045 (mmt) REVERT: F 233 MET cc_start: 0.8450 (mpp) cc_final: 0.7431 (tmm) REVERT: F 460 LYS cc_start: -0.2365 (OUTLIER) cc_final: -0.3212 (tttm) REVERT: F 531 GLN cc_start: 0.2085 (OUTLIER) cc_final: 0.1261 (mm-40) REVERT: F 576 MET cc_start: 0.1416 (mmt) cc_final: 0.0387 (mtt) REVERT: E 274 MET cc_start: 0.8297 (mmm) cc_final: 0.7645 (mmp) REVERT: G 31 TYR cc_start: 0.7902 (m-10) cc_final: 0.7627 (m-80) REVERT: G 35 THR cc_start: 0.8501 (OUTLIER) cc_final: 0.8248 (m) outliers start: 130 outliers final: 52 residues processed: 287 average time/residue: 0.1600 time to fit residues: 71.1010 Evaluate side-chains 192 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 133 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 111 VAL 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 404 ASN 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 603 LYS Chi-restraints excluded: chain A residue 615 MET 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 720 VAL Chi-restraints excluded: chain A residue 734 ASN 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 A residue 904 SER 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 22 VAL Chi-restraints excluded: chain D residue 90 MET 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 D residue 189 LEU 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 405 LEU 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 488 ILE Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 590 LEU 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 E residue 547 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 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 264 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 255 optimal weight: 30.0000 chunk 136 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 17 optimal weight: 0.0060 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN A 9 ASN A 113 HIS A 168 ASN A 447 ASN A 898 HIS ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** 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 116 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.123441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.075728 restraints weight = 132919.609| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 6.24 r_work: 0.3089 rms_B_bonded: 5.72 restraints_weight: 2.0000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 22559 Z= 0.146 Angle : 0.680 16.042 30906 Z= 0.342 Chirality : 0.043 0.223 3581 Planarity : 0.005 0.052 3748 Dihedral : 8.113 135.354 3560 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.68 % Favored : 92.06 % Rotamer: Outliers : 4.48 % Allowed : 30.60 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.16), residues: 2650 helix: 0.31 (0.17), residues: 959 sheet: -1.25 (0.34), residues: 228 loop : -2.26 (0.15), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 555 TYR 0.020 0.002 TYR F 299 PHE 0.023 0.001 PHE A 102 TRP 0.024 0.002 TRP B 182 HIS 0.013 0.001 HIS A 898 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (22527) covalent geometry : angle 0.66481 / 0.34 (30879) hydrogen bonds : bond 0.04957 / 3.16 ( 842) hydrogen bonds : angle 5.07763 / 3.55 ( 2324) metal coordination : bond 0.01631 / 1.26 ( 32) metal coordination : angle 4.88297 / 3.02 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 150 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.7540 (tptt) cc_final: 0.7252 (tptp) REVERT: A 63 ASP cc_start: 0.9198 (OUTLIER) cc_final: 0.8567 (t0) REVERT: A 110 MET cc_start: 0.8044 (tpp) cc_final: 0.7721 (tpp) REVERT: A 138 ASN cc_start: 0.9117 (OUTLIER) cc_final: 0.8450 (p0) REVERT: A 258 ASP cc_start: 0.9093 (m-30) cc_final: 0.8692 (t0) REVERT: A 380 MET cc_start: 0.7516 (mmt) cc_final: 0.7263 (mmm) REVERT: A 499 ASP cc_start: 0.9220 (OUTLIER) cc_final: 0.8966 (m-30) REVERT: A 618 ASP cc_start: 0.8617 (t0) cc_final: 0.8360 (t0) REVERT: A 665 GLU cc_start: 0.8998 (pm20) cc_final: 0.8710 (pm20) REVERT: A 734 ASN cc_start: 0.8459 (OUTLIER) cc_final: 0.8035 (t0) REVERT: A 736 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.8136 (p0) REVERT: A 737 VAL cc_start: 0.8283 (OUTLIER) cc_final: 0.8024 (t) REVERT: A 924 MET cc_start: 0.8791 (mmm) cc_final: 0.8303 (mtt) REVERT: B 57 ARG cc_start: 0.7052 (mpt180) cc_final: 0.6567 (mpt180) REVERT: C 19 GLN cc_start: 0.8322 (mp10) cc_final: 0.7547 (mp10) REVERT: C 38 ASP cc_start: 0.9197 (t0) cc_final: 0.8821 (t0) REVERT: D 71 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.7171 (t80) REVERT: D 77 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8297 (tm-30) REVERT: F 9 ASN cc_start: 0.8345 (t0) cc_final: 0.7950 (m110) REVERT: F 68 MET cc_start: 0.8044 (mtm) cc_final: 0.6808 (mmt) REVERT: F 460 LYS cc_start: -0.2206 (OUTLIER) cc_final: -0.2910 (tttm) REVERT: F 490 ARG cc_start: -0.0181 (OUTLIER) cc_final: -0.0775 (mtm-85) REVERT: F 531 GLN cc_start: 0.2509 (OUTLIER) cc_final: 0.1755 (mm-40) REVERT: F 576 MET cc_start: 0.1540 (mmt) cc_final: 0.0509 (mtt) REVERT: E 25 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.6557 (mm) REVERT: E 185 TYR cc_start: 0.8001 (OUTLIER) cc_final: 0.7548 (t80) REVERT: E 233 MET cc_start: 0.7454 (mmp) cc_final: 0.7240 (mmm) REVERT: E 274 MET cc_start: 0.8548 (mmm) cc_final: 0.8100 (mmp) REVERT: E 429 MET cc_start: 0.4723 (ptm) cc_final: 0.4394 (ppp) REVERT: E 576 MET cc_start: -0.3275 (tmm) cc_final: -0.3488 (ttp) REVERT: G 2 ASN cc_start: 0.9018 (OUTLIER) cc_final: 0.8768 (m-40) outliers start: 101 outliers final: 49 residues processed: 238 average time/residue: 0.1625 time to fit residues: 59.9834 Evaluate side-chains 193 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 131 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 138 ASN 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 499 ASP Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 768 SER 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 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 22 VAL Chi-restraints excluded: chain D residue 33 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 42 VAL Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 199 THR 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 428 LEU 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 E residue 25 LEU Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 350 SER 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 2 ASN Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 106 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 240 optimal weight: 8.9990 chunk 153 optimal weight: 9.9990 chunk 236 optimal weight: 30.0000 chunk 70 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 237 optimal weight: 0.9990 chunk 261 optimal weight: 9.9990 chunk 242 optimal weight: 8.9990 chunk 220 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 GLN A 312 ASN A 447 ASN A 489 ASN ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN ** F 33 HIS ** 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** E 519 ASN E 537 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.116307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.066687 restraints weight = 126633.772| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 6.92 r_work: 0.2964 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.4970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.075 22559 Z= 0.390 Angle : 0.888 22.357 30906 Z= 0.450 Chirality : 0.051 0.328 3581 Planarity : 0.006 0.068 3748 Dihedral : 8.675 143.971 3558 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.17 % Favored : 89.56 % Rotamer: Outliers : 5.84 % Allowed : 29.81 % Favored : 64.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.15), residues: 2650 helix: -0.39 (0.16), residues: 959 sheet: -1.19 (0.34), residues: 243 loop : -2.41 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG A 365 TYR 0.031 0.003 TYR E 71 PHE 0.029 0.003 PHE A 594 TRP 0.024 0.002 TRP A 916 HIS 0.010 0.002 HIS A 650 Details of bonding type rmsd/Z covalent geometry : bond 0.00887 / 0.39 (22527) covalent geometry : angle 0.86375 / 0.45 (30879) hydrogen bonds : bond 0.06738 / 4.39 ( 842) hydrogen bonds : angle 5.65083 / 3.94 ( 2324) metal coordination : bond 0.02333 / 1.52 ( 32) metal coordination : angle 7.04779 / 4.18 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 131 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.9136 (OUTLIER) cc_final: 0.8931 (p0) REVERT: A 63 ASP cc_start: 0.9347 (OUTLIER) cc_final: 0.8979 (t70) REVERT: A 110 MET cc_start: 0.8122 (tpp) cc_final: 0.7887 (mmm) REVERT: A 138 ASN cc_start: 0.9224 (OUTLIER) cc_final: 0.8488 (p0) REVERT: A 258 ASP cc_start: 0.9236 (OUTLIER) cc_final: 0.8891 (t0) REVERT: A 329 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8838 (mt) REVERT: A 380 MET cc_start: 0.7809 (mmt) cc_final: 0.7566 (mmm) REVERT: A 668 MET cc_start: 0.9054 (ttp) cc_final: 0.8582 (ttt) REVERT: A 734 ASN cc_start: 0.8772 (OUTLIER) cc_final: 0.8238 (t0) REVERT: A 798 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.9002 (mtmm) REVERT: A 924 MET cc_start: 0.8722 (mmm) cc_final: 0.8356 (mtt) REVERT: C 19 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8297 (mp10) REVERT: C 38 ASP cc_start: 0.9301 (t0) cc_final: 0.9034 (t0) REVERT: D 48 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8209 (tm-30) REVERT: D 62 MET cc_start: 0.8530 (tmm) cc_final: 0.8241 (tmm) REVERT: D 128 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6827 (tp) REVERT: F 68 MET cc_start: 0.8588 (mtm) cc_final: 0.7409 (mmt) REVERT: F 289 SER cc_start: 0.5857 (OUTLIER) cc_final: 0.5520 (p) REVERT: F 460 LYS cc_start: -0.2650 (OUTLIER) cc_final: -0.2967 (tttm) REVERT: F 576 MET cc_start: 0.1108 (mmt) cc_final: -0.0468 (mtt) REVERT: E 25 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7279 (mm) REVERT: E 274 MET cc_start: 0.8662 (mmm) cc_final: 0.8194 (mmp) REVERT: E 475 PHE cc_start: 0.4399 (OUTLIER) cc_final: 0.4177 (p90) outliers start: 132 outliers final: 77 residues processed: 254 average time/residue: 0.1496 time to fit residues: 60.4625 Evaluate side-chains 212 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 122 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 40 ASP 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 76 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 329 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 472 VAL Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 648 LEU 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 720 VAL Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 768 SER 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 845 ASP Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 148 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 128 LEU 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 215 THR 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 405 LEU Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 428 LEU 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 24 PHE 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 266 VAL Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 396 TYR 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 475 PHE Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain E residue 545 ILE Chi-restraints excluded: chain E residue 555 SER 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 29 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 106 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 163 optimal weight: 10.0000 chunk 23 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 199 optimal weight: 7.9990 chunk 263 optimal weight: 10.0000 chunk 176 optimal weight: 9.9990 chunk 231 optimal weight: 20.0000 chunk 82 optimal weight: 2.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 ASN A 447 ASN B 118 ASN C 63 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 62 GLN ** 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 = 0.4253 r_free = 0.4253 target = 0.118326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.068687 restraints weight = 122226.345| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 6.25 r_work: 0.3011 rms_B_bonded: 5.68 restraints_weight: 2.0000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22559 Z= 0.188 Angle : 0.689 20.192 30906 Z= 0.346 Chirality : 0.044 0.250 3581 Planarity : 0.005 0.056 3748 Dihedral : 8.103 132.798 3554 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.49 % Favored : 92.28 % Rotamer: Outliers : 3.95 % Allowed : 31.74 % Favored : 64.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.16), residues: 2650 helix: 0.01 (0.17), residues: 966 sheet: -1.21 (0.34), residues: 228 loop : -2.25 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 75 TYR 0.028 0.002 TYR F 457 PHE 0.019 0.002 PHE F 373 TRP 0.021 0.002 TRP B 182 HIS 0.004 0.001 HIS A 810 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (22527) covalent geometry : angle 0.67014 / 0.35 (30879) hydrogen bonds : bond 0.05116 / 3.26 ( 842) hydrogen bonds : angle 5.12419 / 3.58 ( 2324) metal coordination : bond 0.01372 / 0.97 ( 32) metal coordination : angle 5.44736 / 3.07 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 135 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.9007 (OUTLIER) cc_final: 0.8743 (p0) REVERT: A 63 ASP cc_start: 0.9324 (OUTLIER) cc_final: 0.8999 (t70) REVERT: A 110 MET cc_start: 0.8084 (tpp) cc_final: 0.7796 (tpp) REVERT: A 138 ASN cc_start: 0.9154 (OUTLIER) cc_final: 0.8392 (p0) REVERT: A 258 ASP cc_start: 0.9176 (m-30) cc_final: 0.8843 (t0) REVERT: A 380 MET cc_start: 0.7742 (mmt) cc_final: 0.7512 (mmm) REVERT: A 608 ASP cc_start: 0.8886 (p0) cc_final: 0.8659 (p0) REVERT: A 626 MET cc_start: 0.8435 (ttp) cc_final: 0.8212 (ttp) REVERT: A 633 MET cc_start: 0.9000 (tmm) cc_final: 0.8641 (tmm) REVERT: A 668 MET cc_start: 0.9005 (ttp) cc_final: 0.8543 (ttt) REVERT: A 734 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8164 (t0) REVERT: A 798 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8995 (mtmm) REVERT: A 924 MET cc_start: 0.8783 (mmm) cc_final: 0.8489 (mtp) REVERT: B 52 ASP cc_start: 0.8264 (m-30) cc_final: 0.7979 (t0) REVERT: B 75 ARG cc_start: 0.8534 (ttp80) cc_final: 0.8037 (tmm-80) REVERT: B 77 GLU cc_start: 0.8483 (tp30) cc_final: 0.8076 (tp30) REVERT: C 19 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8163 (mt0) REVERT: C 38 ASP cc_start: 0.9239 (t0) cc_final: 0.8921 (t0) REVERT: D 48 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8280 (tm-30) REVERT: D 60 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8131 (pp20) REVERT: D 62 MET cc_start: 0.8299 (tmm) cc_final: 0.7990 (tmm) REVERT: D 129 MET cc_start: 0.7597 (mpp) cc_final: 0.7349 (mpp) REVERT: F 9 ASN cc_start: 0.8702 (t0) cc_final: 0.8296 (m-40) REVERT: F 68 MET cc_start: 0.8297 (mtm) cc_final: 0.7206 (mmt) REVERT: F 289 SER cc_start: 0.5822 (OUTLIER) cc_final: 0.5498 (p) REVERT: F 460 LYS cc_start: -0.1973 (OUTLIER) cc_final: -0.2641 (tttm) REVERT: F 576 MET cc_start: 0.1544 (mmt) cc_final: 0.0242 (mtt) REVERT: E 25 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.7109 (mm) REVERT: E 233 MET cc_start: 0.8008 (mmp) cc_final: 0.7298 (mmm) REVERT: E 274 MET cc_start: 0.8646 (mmm) cc_final: 0.8111 (mmp) REVERT: E 475 PHE cc_start: 0.4106 (OUTLIER) cc_final: 0.3898 (p90) REVERT: G 44 LEU cc_start: 0.6056 (OUTLIER) cc_final: 0.5846 (tt) REVERT: G 52 LYS cc_start: 0.7894 (mmtp) cc_final: 0.7670 (tppt) outliers start: 89 outliers final: 57 residues processed: 216 average time/residue: 0.1518 time to fit residues: 51.2756 Evaluate side-chains 193 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 125 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 40 ASP 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 89 LEU Chi-restraints excluded: chain A residue 138 ASN 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 404 ASN Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 768 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 904 SER Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 87 MET 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 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 136 ASN 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 289 SER Chi-restraints excluded: chain F residue 318 CYS Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 428 LEU 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 199 THR Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 396 TYR 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 475 PHE Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain G residue 2 ASN Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 106 LEU 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 23 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 263 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 196 optimal weight: 50.0000 chunk 64 optimal weight: 0.4980 chunk 225 optimal weight: 5.9990 chunk 42 optimal weight: 0.3980 chunk 204 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN A 381 HIS A 447 ASN A 898 HIS C 34 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.118901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.069912 restraints weight = 133688.079| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 6.61 r_work: 0.3023 rms_B_bonded: 5.52 restraints_weight: 2.0000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22559 Z= 0.151 Angle : 0.656 18.902 30906 Z= 0.329 Chirality : 0.043 0.236 3581 Planarity : 0.004 0.062 3748 Dihedral : 7.749 118.797 3552 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.70 % Favored : 91.07 % Rotamer: Outliers : 4.21 % Allowed : 30.99 % Favored : 64.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.16), residues: 2650 helix: 0.18 (0.17), residues: 976 sheet: -1.15 (0.34), residues: 226 loop : -2.13 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 443 TYR 0.020 0.002 TYR F 457 PHE 0.018 0.001 PHE A 753 TRP 0.021 0.001 TRP B 182 HIS 0.005 0.001 HIS F 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (22527) covalent geometry : angle 0.63909 / 0.33 (30879) hydrogen bonds : bond 0.04778 / 3.05 ( 842) hydrogen bonds : angle 4.91833 / 3.44 ( 2324) metal coordination : bond 0.01314 / 0.97 ( 32) metal coordination : angle 5.09089 / 2.91 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 128 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.9055 (OUTLIER) cc_final: 0.8798 (p0) REVERT: A 63 ASP cc_start: 0.9347 (OUTLIER) cc_final: 0.9012 (t70) REVERT: A 110 MET cc_start: 0.8081 (tpp) cc_final: 0.7817 (mmm) REVERT: A 138 ASN cc_start: 0.9175 (OUTLIER) cc_final: 0.8451 (p0) REVERT: A 161 ASP cc_start: 0.8254 (m-30) cc_final: 0.7945 (t0) REVERT: A 258 ASP cc_start: 0.9186 (m-30) cc_final: 0.8837 (t0) REVERT: A 396 PHE cc_start: 0.8546 (t80) cc_final: 0.8288 (t80) REVERT: A 608 ASP cc_start: 0.8856 (p0) cc_final: 0.8628 (p0) REVERT: A 626 MET cc_start: 0.8446 (ttp) cc_final: 0.8199 (ttp) REVERT: A 668 MET cc_start: 0.8962 (ttp) cc_final: 0.8459 (ttt) REVERT: A 734 ASN cc_start: 0.8606 (OUTLIER) cc_final: 0.8143 (t0) REVERT: A 924 MET cc_start: 0.8770 (mmm) cc_final: 0.8463 (mtp) REVERT: C 19 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8166 (mt0) REVERT: C 38 ASP cc_start: 0.9234 (t0) cc_final: 0.8885 (t0) REVERT: D 48 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8340 (tm-30) REVERT: D 60 GLU cc_start: 0.8439 (tm-30) cc_final: 0.8132 (pp20) REVERT: D 62 MET cc_start: 0.8329 (tmm) cc_final: 0.8000 (tmm) REVERT: D 129 MET cc_start: 0.7629 (mpp) cc_final: 0.7373 (mpp) REVERT: F 9 ASN cc_start: 0.8720 (t0) cc_final: 0.8307 (m-40) REVERT: F 68 MET cc_start: 0.8302 (mtm) cc_final: 0.7104 (mmt) REVERT: F 289 SER cc_start: 0.5829 (OUTLIER) cc_final: 0.5498 (p) REVERT: F 460 LYS cc_start: -0.2330 (OUTLIER) cc_final: -0.3005 (tttm) REVERT: F 576 MET cc_start: 0.1167 (mmt) cc_final: -0.0306 (mtt) REVERT: E 233 MET cc_start: 0.8042 (mmp) cc_final: 0.7446 (mmm) REVERT: E 274 MET cc_start: 0.8566 (mmm) cc_final: 0.8010 (mmp) REVERT: E 475 PHE cc_start: 0.4226 (OUTLIER) cc_final: 0.3994 (p90) outliers start: 95 outliers final: 57 residues processed: 213 average time/residue: 0.1504 time to fit residues: 49.6534 Evaluate side-chains 189 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 124 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 40 ASP 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 261 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 353 VAL 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 563 CYS Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 621 LYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 734 ASN 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 883 LEU Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 79 LYS 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 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 57 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 289 SER Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 428 LEU 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 29 CYS Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 396 TYR 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 475 PHE Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain E residue 555 SER 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 29 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 106 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 86 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 156 optimal weight: 0.0040 chunk 101 optimal weight: 6.9990 chunk 263 optimal weight: 8.9990 chunk 212 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 82 optimal weight: 0.6980 chunk 241 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 overall best weight: 1.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 ASN 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** G 11 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.119013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.069551 restraints weight = 127942.546| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 6.66 r_work: 0.3030 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.5432 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= 0.147 Angle : 0.652 17.969 30906 Z= 0.324 Chirality : 0.042 0.243 3581 Planarity : 0.004 0.066 3748 Dihedral : 7.420 95.421 3551 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.75 % Favored : 92.10 % Rotamer: Outliers : 4.08 % Allowed : 30.82 % Favored : 65.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.16), residues: 2650 helix: 0.31 (0.17), residues: 971 sheet: -1.09 (0.34), residues: 226 loop : -2.04 (0.16), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 443 TYR 0.018 0.001 TYR F 457 PHE 0.016 0.001 PHE A 753 TRP 0.019 0.001 TRP B 182 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (22527) covalent geometry : angle 0.63491 / 0.32 (30879) hydrogen bonds : bond 0.04622 / 2.95 ( 842) hydrogen bonds : angle 4.77859 / 3.35 ( 2324) metal coordination : bond 0.01045 / 0.77 ( 32) metal coordination : angle 5.04436 / 2.93 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 130 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8954 (OUTLIER) cc_final: 0.8685 (p0) REVERT: A 63 ASP cc_start: 0.9339 (OUTLIER) cc_final: 0.9009 (t70) REVERT: A 110 MET cc_start: 0.8152 (tpp) cc_final: 0.7817 (mmm) REVERT: A 138 ASN cc_start: 0.9145 (OUTLIER) cc_final: 0.8417 (p0) REVERT: A 161 ASP cc_start: 0.8286 (m-30) cc_final: 0.7952 (t0) REVERT: A 258 ASP cc_start: 0.9169 (m-30) cc_final: 0.8828 (t0) REVERT: A 380 MET cc_start: 0.7717 (mmt) cc_final: 0.7470 (mmm) REVERT: A 396 PHE cc_start: 0.8550 (t80) cc_final: 0.8283 (t80) REVERT: A 608 ASP cc_start: 0.8832 (p0) cc_final: 0.8629 (p0) REVERT: A 626 MET cc_start: 0.8403 (ttp) cc_final: 0.8135 (ttp) REVERT: A 668 MET cc_start: 0.8966 (ttp) cc_final: 0.8465 (ttt) REVERT: A 734 ASN cc_start: 0.8612 (OUTLIER) cc_final: 0.8112 (t0) REVERT: A 924 MET cc_start: 0.8765 (mmm) cc_final: 0.8379 (mtt) REVERT: B 52 ASP cc_start: 0.8382 (m-30) cc_final: 0.8108 (t0) REVERT: B 75 ARG cc_start: 0.8592 (ttp80) cc_final: 0.8382 (ttp80) REVERT: B 77 GLU cc_start: 0.8463 (tp30) cc_final: 0.8031 (tp30) REVERT: B 157 GLN cc_start: 0.8315 (mm110) cc_final: 0.8069 (mm110) REVERT: C 19 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8164 (mt0) REVERT: C 38 ASP cc_start: 0.9236 (t0) cc_final: 0.8880 (t0) REVERT: D 48 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8319 (tm-30) REVERT: D 62 MET cc_start: 0.8466 (tmm) cc_final: 0.8163 (tmm) REVERT: D 129 MET cc_start: 0.7645 (mpp) cc_final: 0.7386 (mpp) REVERT: F 9 ASN cc_start: 0.8523 (t0) cc_final: 0.8156 (m-40) REVERT: F 68 MET cc_start: 0.8372 (mtm) cc_final: 0.7224 (mmt) REVERT: F 460 LYS cc_start: -0.3195 (OUTLIER) cc_final: -0.3688 (tttm) REVERT: F 576 MET cc_start: 0.0938 (mmt) cc_final: -0.0805 (mtt) REVERT: E 233 MET cc_start: 0.8053 (mmp) cc_final: 0.7479 (mmm) REVERT: E 274 MET cc_start: 0.8522 (mmm) cc_final: 0.7889 (mmm) REVERT: E 475 PHE cc_start: 0.4637 (OUTLIER) cc_final: 0.4202 (p90) REVERT: G 2 ASN cc_start: 0.8971 (OUTLIER) cc_final: 0.8710 (m-40) REVERT: G 64 THR cc_start: 0.7603 (OUTLIER) cc_final: 0.7255 (m) outliers start: 92 outliers final: 60 residues processed: 213 average time/residue: 0.1541 time to fit residues: 51.4242 Evaluate side-chains 189 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 120 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 40 ASP 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 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 353 VAL 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 447 ASN Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 621 LYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 734 ASN 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 883 LEU Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 79 LYS 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 12 THR Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 57 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 318 CYS Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 428 LEU 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 350 SER Chi-restraints excluded: chain E residue 396 TYR 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 475 PHE Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 555 SER 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 18 THR Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 64 THR 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 252 optimal weight: 0.0570 chunk 204 optimal weight: 7.9990 chunk 216 optimal weight: 8.9990 chunk 190 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 240 optimal weight: 0.3980 chunk 193 optimal weight: 30.0000 chunk 189 optimal weight: 8.9990 overall best weight: 2.4904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 HIS 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 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.117526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.068095 restraints weight = 138116.537| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 7.24 r_work: 0.2980 rms_B_bonded: 5.45 restraints_weight: 2.0000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 22559 Z= 0.208 Angle : 0.693 18.680 30906 Z= 0.346 Chirality : 0.044 0.267 3581 Planarity : 0.005 0.067 3748 Dihedral : 7.220 79.019 3551 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.15 % Favored : 90.70 % Rotamer: Outliers : 4.04 % Allowed : 30.51 % Favored : 65.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.16), residues: 2650 helix: 0.21 (0.17), residues: 971 sheet: -1.22 (0.34), residues: 244 loop : -2.07 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 75 TYR 0.021 0.002 TYR E 421 PHE 0.017 0.002 PHE E 422 TRP 0.017 0.001 TRP A 916 HIS 0.006 0.001 HIS F 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 (22527) covalent geometry : angle 0.67494 / 0.35 (30879) hydrogen bonds : bond 0.05075 / 3.27 ( 842) hydrogen bonds : angle 4.90516 / 3.44 ( 2324) metal coordination : bond 0.01228 / 0.83 ( 32) metal coordination : angle 5.29414 / 3.06 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 125 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.9014 (OUTLIER) cc_final: 0.8755 (p0) REVERT: A 63 ASP cc_start: 0.9366 (OUTLIER) cc_final: 0.9036 (t70) REVERT: A 110 MET cc_start: 0.8094 (tpp) cc_final: 0.7793 (mmm) REVERT: A 138 ASN cc_start: 0.9155 (OUTLIER) cc_final: 0.8422 (p0) REVERT: A 161 ASP cc_start: 0.8405 (m-30) cc_final: 0.8062 (t0) REVERT: A 258 ASP cc_start: 0.9177 (OUTLIER) cc_final: 0.8840 (t0) REVERT: A 380 MET cc_start: 0.7740 (mmt) cc_final: 0.7439 (mmm) REVERT: A 396 PHE cc_start: 0.8674 (t80) cc_final: 0.8402 (t80) REVERT: A 608 ASP cc_start: 0.8877 (p0) cc_final: 0.8654 (p0) REVERT: A 626 MET cc_start: 0.8442 (ttp) cc_final: 0.8184 (ttp) REVERT: A 668 MET cc_start: 0.9000 (ttp) cc_final: 0.8524 (ttt) REVERT: A 734 ASN cc_start: 0.8673 (OUTLIER) cc_final: 0.8114 (t0) REVERT: A 924 MET cc_start: 0.8751 (mmm) cc_final: 0.8433 (mtp) REVERT: B 77 GLU cc_start: 0.8409 (tp30) cc_final: 0.7945 (tp30) REVERT: C 19 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8259 (mt0) REVERT: C 38 ASP cc_start: 0.9291 (t0) cc_final: 0.8947 (t0) REVERT: D 48 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8310 (tm-30) REVERT: D 62 MET cc_start: 0.8338 (tmm) cc_final: 0.8008 (tmm) REVERT: D 94 MET cc_start: 0.8615 (mtp) cc_final: 0.8206 (mtp) REVERT: D 129 MET cc_start: 0.7707 (mpp) cc_final: 0.7435 (mpp) REVERT: F 68 MET cc_start: 0.8386 (mtm) cc_final: 0.7351 (mmt) REVERT: F 422 PHE cc_start: 0.5760 (OUTLIER) cc_final: 0.5492 (m-10) REVERT: F 576 MET cc_start: 0.1425 (mmt) cc_final: -0.0005 (mtt) REVERT: E 233 MET cc_start: 0.8135 (mmp) cc_final: 0.7466 (mmm) REVERT: G 29 LEU cc_start: 0.4563 (OUTLIER) cc_final: 0.4020 (tp) REVERT: G 52 LYS cc_start: 0.7640 (mmtt) cc_final: 0.7197 (tppt) outliers start: 91 outliers final: 71 residues processed: 205 average time/residue: 0.1490 time to fit residues: 47.9843 Evaluate side-chains 198 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 119 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 40 ASP 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 166 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 258 ASP 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 353 VAL 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 472 VAL Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 621 LYS Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 739 THR 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 904 SER Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 79 LYS 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 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 318 CYS Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 428 LEU 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 113 ASP Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 396 TYR 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 495 VAL Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 555 SER 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 18 THR Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 106 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 131 optimal weight: 0.4980 chunk 117 optimal weight: 4.9990 chunk 256 optimal weight: 0.0270 chunk 152 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 245 optimal weight: 0.8980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 447 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.119710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.069343 restraints weight = 115385.272| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 6.34 r_work: 0.3059 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.5788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22559 Z= 0.115 Angle : 0.639 16.296 30906 Z= 0.317 Chirality : 0.042 0.233 3581 Planarity : 0.004 0.070 3748 Dihedral : 6.818 78.493 3549 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.07 % Favored : 92.78 % Rotamer: Outliers : 2.94 % Allowed : 31.69 % Favored : 65.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.16), residues: 2650 helix: 0.48 (0.17), residues: 966 sheet: -0.91 (0.35), residues: 229 loop : -1.95 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 75 TYR 0.017 0.001 TYR F 457 PHE 0.025 0.001 PHE F 373 TRP 0.024 0.001 TRP B 182 HIS 0.004 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (22527) covalent geometry : angle 0.62490 / 0.32 (30879) hydrogen bonds : bond 0.04344 / 2.76 ( 842) hydrogen bonds : angle 4.62368 / 3.25 ( 2324) metal coordination : bond 0.01058 / 0.82 ( 32) metal coordination : angle 4.56870 / 2.62 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 122 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8880 (OUTLIER) cc_final: 0.8606 (p0) REVERT: A 50 LYS cc_start: 0.8014 (tptp) cc_final: 0.7710 (tptp) REVERT: A 63 ASP cc_start: 0.9350 (OUTLIER) cc_final: 0.9000 (t70) REVERT: A 110 MET cc_start: 0.8037 (tpp) cc_final: 0.7721 (mmm) REVERT: A 138 ASN cc_start: 0.9086 (OUTLIER) cc_final: 0.8374 (p0) REVERT: A 161 ASP cc_start: 0.8192 (m-30) cc_final: 0.7894 (t0) REVERT: A 258 ASP cc_start: 0.9128 (m-30) cc_final: 0.8816 (t0) REVERT: A 380 MET cc_start: 0.7581 (mmt) cc_final: 0.7337 (mmm) REVERT: A 396 PHE cc_start: 0.8515 (t80) cc_final: 0.8265 (t80) REVERT: A 626 MET cc_start: 0.8305 (ttp) cc_final: 0.8026 (ttp) REVERT: A 668 MET cc_start: 0.8887 (ttp) cc_final: 0.8394 (ttt) REVERT: A 734 ASN cc_start: 0.8620 (OUTLIER) cc_final: 0.8112 (t0) REVERT: A 924 MET cc_start: 0.8769 (mmm) cc_final: 0.8403 (mtp) REVERT: B 52 ASP cc_start: 0.8321 (m-30) cc_final: 0.8098 (t0) REVERT: B 75 ARG cc_start: 0.8521 (ttp80) cc_final: 0.8032 (tmm-80) REVERT: B 77 GLU cc_start: 0.8383 (tp30) cc_final: 0.7966 (tp30) REVERT: B 88 GLN cc_start: 0.8045 (tp40) cc_final: 0.7709 (tp40) REVERT: C 38 ASP cc_start: 0.9161 (t0) cc_final: 0.8784 (t0) REVERT: D 62 MET cc_start: 0.8458 (tmm) cc_final: 0.8166 (tmm) REVERT: D 94 MET cc_start: 0.8527 (mtp) cc_final: 0.8118 (mtp) REVERT: D 129 MET cc_start: 0.7618 (mpp) cc_final: 0.7355 (mpp) REVERT: F 68 MET cc_start: 0.8463 (mtm) cc_final: 0.7305 (mmt) REVERT: F 460 LYS cc_start: -0.2380 (OUTLIER) cc_final: -0.3054 (ttpt) REVERT: F 576 MET cc_start: 0.1455 (mmt) cc_final: 0.0066 (mtt) REVERT: E 68 MET cc_start: 0.8937 (pmm) cc_final: 0.8427 (mmm) REVERT: E 233 MET cc_start: 0.7830 (mmp) cc_final: 0.7610 (mmm) REVERT: E 274 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8215 (tpp) REVERT: G 2 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8689 (m-40) REVERT: G 52 LYS cc_start: 0.7471 (mmtt) cc_final: 0.6979 (tppt) outliers start: 66 outliers final: 51 residues processed: 179 average time/residue: 0.1578 time to fit residues: 44.6747 Evaluate side-chains 175 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 117 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 40 ASP 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 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 362 HIS 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 586 THR Chi-restraints excluded: chain A residue 621 LYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 734 ASN 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 907 LEU Chi-restraints excluded: chain A residue 929 THR 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 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 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 318 CYS Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 428 LEU 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 113 ASP Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 396 TYR 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 2 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 89 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 265 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 chunk 173 optimal weight: 0.8980 chunk 197 optimal weight: 9.9990 chunk 260 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN 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 194 GLN ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.118033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.068440 restraints weight = 139628.617| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 6.87 r_work: 0.3013 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.5937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22559 Z= 0.193 Angle : 0.684 17.082 30906 Z= 0.339 Chirality : 0.044 0.264 3581 Planarity : 0.005 0.071 3748 Dihedral : 6.893 79.400 3549 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.47 % Favored : 91.38 % Rotamer: Outliers : 2.90 % Allowed : 31.56 % Favored : 65.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.16), residues: 2650 helix: 0.36 (0.17), residues: 966 sheet: -1.03 (0.34), residues: 238 loop : -1.95 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 365 TYR 0.016 0.002 TYR F 457 PHE 0.016 0.002 PHE A 753 TRP 0.018 0.001 TRP A 916 HIS 0.005 0.001 HIS F 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (22527) covalent geometry : angle 0.66840 / 0.34 (30879) hydrogen bonds : bond 0.04772 / 3.08 ( 842) hydrogen bonds : angle 4.74674 / 3.34 ( 2324) metal coordination : bond 0.01238 / 0.90 ( 32) metal coordination : angle 4.94944 / 2.89 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 119 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8972 (OUTLIER) cc_final: 0.8696 (p0) REVERT: A 63 ASP cc_start: 0.9350 (OUTLIER) cc_final: 0.9001 (t70) REVERT: A 110 MET cc_start: 0.8140 (tpp) cc_final: 0.7815 (mmm) REVERT: A 138 ASN cc_start: 0.9136 (OUTLIER) cc_final: 0.8410 (p0) REVERT: A 161 ASP cc_start: 0.8340 (m-30) cc_final: 0.8011 (t0) REVERT: A 258 ASP cc_start: 0.9162 (m-30) cc_final: 0.8838 (t0) REVERT: A 380 MET cc_start: 0.7703 (mmt) cc_final: 0.7439 (mmm) REVERT: A 396 PHE cc_start: 0.8615 (t80) cc_final: 0.8379 (t80) REVERT: A 626 MET cc_start: 0.8426 (ttp) cc_final: 0.8142 (ttp) REVERT: A 668 MET cc_start: 0.8983 (ttp) cc_final: 0.8505 (ttt) REVERT: A 734 ASN cc_start: 0.8625 (OUTLIER) cc_final: 0.8091 (t0) REVERT: A 924 MET cc_start: 0.8769 (mmm) cc_final: 0.8441 (mtp) REVERT: B 88 GLN cc_start: 0.8151 (tp40) cc_final: 0.7747 (tp40) REVERT: C 38 ASP cc_start: 0.9215 (t0) cc_final: 0.8875 (t0) REVERT: D 62 MET cc_start: 0.8437 (tmm) cc_final: 0.8121 (tmm) REVERT: D 94 MET cc_start: 0.8594 (mtp) cc_final: 0.8193 (mtp) REVERT: D 129 MET cc_start: 0.7661 (mpp) cc_final: 0.7383 (mpp) REVERT: F 68 MET cc_start: 0.8619 (mtm) cc_final: 0.7466 (mmt) REVERT: F 378 MET cc_start: 0.5200 (mmt) cc_final: 0.4921 (mmm) REVERT: F 576 MET cc_start: 0.1054 (mmt) cc_final: -0.0958 (mtt) REVERT: E 68 MET cc_start: 0.8990 (pmm) cc_final: 0.8503 (mmm) REVERT: E 233 MET cc_start: 0.8048 (mmp) cc_final: 0.7476 (mmm) REVERT: E 274 MET cc_start: 0.8562 (mmm) cc_final: 0.8042 (mmp) REVERT: G 2 ASN cc_start: 0.9037 (OUTLIER) cc_final: 0.8748 (m-40) outliers start: 65 outliers final: 56 residues processed: 177 average time/residue: 0.1574 time to fit residues: 44.3737 Evaluate side-chains 178 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 117 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 40 ASP 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 166 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 257 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 434 SER Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 621 LYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 739 THR 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 904 SER Chi-restraints excluded: chain A residue 929 THR 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 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 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 318 CYS Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 428 LEU 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 113 ASP Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 396 TYR 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 2 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 130 optimal weight: 0.9980 chunk 157 optimal weight: 40.0000 chunk 39 optimal weight: 2.9990 chunk 163 optimal weight: 0.0570 chunk 250 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 194 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 181 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN A 447 ASN ** 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 = 0.4270 r_free = 0.4270 target = 0.118703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.069065 restraints weight = 108792.505| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 6.10 r_work: 0.3042 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.6023 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= 0.138 Angle : 0.648 16.267 30906 Z= 0.320 Chirality : 0.042 0.226 3581 Planarity : 0.004 0.069 3748 Dihedral : 6.766 75.116 3549 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.79 % Favored : 92.06 % Rotamer: Outliers : 3.16 % Allowed : 31.39 % Favored : 65.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.16), residues: 2650 helix: 0.44 (0.17), residues: 968 sheet: -0.73 (0.37), residues: 216 loop : -1.89 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 365 TYR 0.017 0.001 TYR E 421 PHE 0.016 0.001 PHE F 373 TRP 0.020 0.001 TRP B 182 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (22527) covalent geometry : angle 0.63333 / 0.32 (30879) hydrogen bonds : bond 0.04447 / 2.84 ( 842) hydrogen bonds : angle 4.63517 / 3.27 ( 2324) metal coordination : bond 0.01076 / 0.82 ( 32) metal coordination : angle 4.62993 / 2.66 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9893.29 seconds wall clock time: 169 minutes 5.75 seconds (10145.75 seconds total)