Starting phenix.real_space_refine on Sat Jul 4 15:43:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gwm_34316/07_2026/8gwm_34316.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gwm_34316/07_2026/8gwm_34316.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gwm_34316/07_2026/8gwm_34316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gwm_34316/07_2026/8gwm_34316.map" model { file = "/net/cci-nas-00/data/ceres_data/8gwm_34316/07_2026/8gwm_34316.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gwm_34316/07_2026/8gwm_34316.cif" } resolution = 2.64 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= -0.001 sd= 0.078 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: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 55 5.49 5 S 157 5.16 5 C 13693 2.51 5 N 3683 2.21 5 O 4289 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 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: 21886 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 7473 Classifications: {'peptide': 928} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 897} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1400 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 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': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 553 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "D" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1418 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 179} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 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: "E" Number of atoms: 4508 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} 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: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} 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: 4593 Chain: "F" Number of atoms: 4508 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} 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: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} 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: 4593 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: "I" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 545 Classifications: {'RNA': 25} Modifications used: {'rna3p_pur': 17, 'rna3p_pyr': 8} Link IDs: {'rna3p': 24} Chain: "J" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 545 Classifications: {'RNA': 26} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 16} Link IDs: {'rna2p': 1, 'rna3p': 24} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' ZN': 2, 'GNP': 1} 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: "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: "G" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'6GS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 7 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "G" 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 2446 SG CYS A 301 68.202 53.571 123.983 1.00 13.11 S ATOM 2487 SG CYS A 306 68.098 55.327 127.352 1.00 14.48 S ATOM 2519 SG CYS A 310 69.484 51.694 127.026 1.00 16.76 S ATOM 3927 SG CYS A 487 71.195 67.933 108.375 1.00 20.66 S ATOM 5180 SG CYS A 645 70.179 70.036 111.413 1.00 21.54 S ATOM 5186 SG CYS A 646 69.133 66.354 111.156 1.00 21.49 S ATOM 10948 SG CYS E 16 102.769 62.885 52.931 1.00128.84 S ATOM 10963 SG CYS E 19 101.561 59.834 50.490 1.00110.07 S ATOM 10866 SG CYS E 5 113.104 64.356 55.785 1.00117.50 S ATOM 10887 SG CYS E 8 114.967 67.840 54.857 1.00133.06 S ATOM 11025 SG CYS E 26 112.665 67.140 57.280 1.00127.78 S ATOM 11042 SG CYS E 29 111.283 66.753 53.404 1.00118.27 S ATOM 11207 SG CYS E 50 87.235 71.750 62.455 1.00107.33 S ATOM 11237 SG CYS E 55 83.833 71.775 61.374 1.00121.95 S ATOM 11370 SG CYS E 72 86.125 74.616 60.179 1.00140.80 S ATOM 15456 SG CYS F 16 55.899 70.746 64.648 1.00105.86 S ATOM 15471 SG CYS F 19 53.289 68.207 63.943 1.00108.67 S ATOM 15374 SG CYS F 5 65.772 66.312 59.009 1.00123.49 S ATOM 15395 SG CYS F 8 67.987 68.307 55.968 1.00145.89 S ATOM 15533 SG CYS F 26 67.901 68.530 59.564 1.00126.32 S ATOM 15550 SG CYS F 29 64.712 69.699 57.437 1.00107.47 S ATOM 15715 SG CYS F 50 59.135 85.007 79.792 1.00137.05 S ATOM 15745 SG CYS F 55 55.443 85.538 80.386 1.00136.72 S ATOM 15878 SG CYS F 72 56.961 87.138 77.289 1.00155.86 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AMET E 474 " occ=0.02 ... (14 atoms not shown) pdb=" CE BMET E 474 " occ=0.98 residue: pdb=" N AMET F 474 " occ=0.60 ... (14 atoms not shown) pdb=" CE BMET F 474 " occ=0.40 Time building chain proxies: 5.04, per 1000 atoms: 0.23 Number of scatterers: 21886 At special positions: 0 Unit cell: (153.6, 135.36, 190.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 157 16.00 P 55 15.00 F 1 9.00 O 4289 8.00 N 3683 7.00 C 13693 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 1.0 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 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " 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=" ND1 HIS E 39 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 33 " 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 26 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 5 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 29 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 72 " pdb=" ZN F 701 " pdb="ZN ZN F 701 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 16 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 19 " pdb="ZN ZN F 701 " - pdb=" ND1 HIS F 39 " pdb=" ZN F 702 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 26 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 29 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 5 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 8 " pdb=" ZN F 703 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 55 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 72 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 50 " pdb="ZN ZN F 703 " - pdb=" ND1 HIS F 75 " Number of angles added : 27 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5070 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 32 sheets defined 41.6% alpha, 12.3% beta 18 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 14 through 16 No H-bonds generated for 'chain 'A' and resid 14 through 16' Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.536A pdb=" N TYR A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN A 81 " --> pdb=" O PHE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.628A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.769A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 159 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 176 removed outlier: 3.539A pdb=" N VAL A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 234 through 248 removed outlier: 3.664A pdb=" N TYR A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) Proline residue: A 243 - end of helix removed outlier: 4.346A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.564A pdb=" N HIS A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.732A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.876A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.293A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A 384 " --> pdb=" O MET A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 425 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.825A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.857A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (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: 3.756A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 removed outlier: 3.578A pdb=" N ASP A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 580 removed outlier: 4.261A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.523A pdb=" N MET A 626 " --> pdb=" O CYS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 640 removed outlier: 3.520A pdb=" N ARG A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 663 removed outlier: 3.554A pdb=" N ARG A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 709 Processing helix chain 'A' and resid 717 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.892A pdb=" N PHE A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS A 783 " --> pdb=" O ILE A 779 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 removed outlier: 3.553A pdb=" N ILE A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 855 Processing helix chain 'A' and resid 856 through 867 Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 903 removed outlier: 4.147A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP A 879 " --> pdb=" O GLN A 875 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 917 removed outlier: 3.679A pdb=" N GLU A 917 " --> pdb=" O ARG A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 923 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 9 through 29 removed outlier: 4.073A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 45 removed outlier: 3.714A pdb=" N LYS B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 55 Processing helix chain 'B' and resid 55 through 96 removed outlier: 4.304A pdb=" N LEU B 59 " --> pdb=" O MET B 55 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU B 60 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 109 removed outlier: 4.072A pdb=" N ASN B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 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: 3.615A pdb=" N LEU C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 62 removed outlier: 3.910A pdb=" N GLU C 50 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 71 Processing helix chain 'D' and resid 10 through 29 removed outlier: 4.048A pdb=" N ALA D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 38 Processing helix chain 'D' and resid 44 through 49 Processing helix chain 'D' and resid 51 through 80 removed outlier: 3.676A pdb=" N MET D 55 " --> pdb=" O ARG D 51 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG D 80 " --> pdb=" O SER D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 99 removed outlier: 4.313A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 3.674A 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 141 removed outlier: 3.730A pdb=" N TYR D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 180 Processing helix chain 'E' and resid 26 through 37 removed outlier: 3.880A pdb=" N THR E 37 " --> pdb=" O HIS E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 112 Processing helix chain 'E' and resid 116 through 126 removed outlier: 3.952A pdb=" N TYR E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 147 Processing helix chain 'E' and resid 266 through 274 removed outlier: 4.236A pdb=" N GLN E 270 " --> pdb=" O VAL E 266 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LYS E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL E 272 " --> pdb=" O ASN E 268 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET E 274 " --> pdb=" O GLN E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 295 Processing helix chain 'E' and resid 296 through 299 removed outlier: 3.811A pdb=" N TYR E 299 " --> pdb=" O ALA E 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 296 through 299' Processing helix chain 'E' and resid 310 through 317 Processing helix chain 'E' and resid 359 through 363 removed outlier: 3.755A pdb=" N LEU E 363 " --> pdb=" O VAL E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 391 removed outlier: 3.506A pdb=" N SER E 385 " --> pdb=" O ASN E 381 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASN E 388 " --> pdb=" O LEU E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 428 removed outlier: 3.849A pdb=" N ARG E 427 " --> pdb=" O ASN E 423 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU E 428 " --> pdb=" O SER E 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 423 through 428' Processing helix chain 'E' and resid 445 through 449 removed outlier: 3.690A pdb=" N VAL E 449 " --> pdb=" O ALA E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 455 removed outlier: 3.605A pdb=" N ALA E 454 " --> pdb=" O THR E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 490 through 502 removed outlier: 3.775A pdb=" N VAL E 496 " --> pdb=" O GLN E 492 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU E 498 " --> pdb=" O GLY E 494 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR E 501 " --> pdb=" O ARG E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 503 through 507 removed outlier: 4.265A pdb=" N ARG E 507 " --> pdb=" O PRO E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 516 through 523 removed outlier: 3.668A pdb=" N SER E 523 " --> pdb=" O ASN E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 536 removed outlier: 3.666A pdb=" N SER E 535 " --> pdb=" O THR E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 557 removed outlier: 3.969A pdb=" N ASN E 557 " --> pdb=" O ALA E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 566 removed outlier: 4.305A pdb=" N VAL E 563 " --> pdb=" O ASN E 559 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ALA E 564 " --> pdb=" O ARG E 560 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR E 566 " --> pdb=" O ASN E 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 585 Processing helix chain 'F' and resid 26 through 37 removed outlier: 3.835A pdb=" N THR F 37 " --> pdb=" O HIS F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 76 Processing helix chain 'F' and resid 103 through 112 Processing helix chain 'F' and resid 116 through 126 removed outlier: 4.004A pdb=" N TYR F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 148 removed outlier: 3.510A pdb=" N LEU F 147 " --> pdb=" O GLU F 143 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER F 148 " --> pdb=" O THR F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 265 Processing helix chain 'F' and resid 266 through 273 removed outlier: 4.239A pdb=" N GLN F 270 " --> pdb=" O VAL F 266 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LYS F 271 " --> pdb=" O ALA F 267 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL F 272 " --> pdb=" O ASN F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 295 removed outlier: 3.646A pdb=" N ILE F 293 " --> pdb=" O SER F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 319 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 359 through 363 Processing helix chain 'F' and resid 380 through 391 removed outlier: 3.567A pdb=" N SER F 385 " --> pdb=" O ASN F 381 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASN F 388 " --> pdb=" O LEU F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 428 Processing helix chain 'F' and resid 445 through 449 removed outlier: 3.694A pdb=" N VAL F 449 " --> pdb=" O ALA F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 450 through 455 Processing helix chain 'F' and resid 489 through 502 removed outlier: 3.558A pdb=" N VAL F 496 " --> pdb=" O GLN F 492 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU F 498 " --> pdb=" O GLY F 494 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR F 501 " --> pdb=" O ARG F 497 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG F 502 " --> pdb=" O GLU F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 507 removed outlier: 4.287A pdb=" N ARG F 507 " --> pdb=" O PRO F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 516 through 523 removed outlier: 3.716A pdb=" N SER F 523 " --> pdb=" O ASN F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 536 removed outlier: 3.744A pdb=" N SER F 535 " --> pdb=" O THR F 532 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER F 536 " --> pdb=" O VAL F 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 532 through 536' Processing helix chain 'F' and resid 552 through 557 removed outlier: 3.561A pdb=" N CYS F 556 " --> pdb=" O THR F 552 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASN F 557 " --> pdb=" O ALA F 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 552 through 557' Processing helix chain 'F' and resid 557 through 566 removed outlier: 4.095A pdb=" N VAL F 563 " --> pdb=" O ASN F 559 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ALA F 564 " --> pdb=" O ARG F 560 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR F 566 " --> pdb=" O ASN F 562 " (cutoff:3.500A) Processing helix chain 'F' and resid 579 through 585 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: 5.380A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL A 71 " --> pdb=" O GLN A 117 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N GLN A 117 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LYS A 73 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N SER A 115 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS A 98 " --> pdb=" O GLN A 117 " (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: 6.475A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.829A 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: 3.548A pdb=" N GLY A 352 " --> pdb=" O PHE A 348 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 334 through 335 Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.733A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.733A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL B 159 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA9, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AB1, first strand: chain 'A' and resid 816 through 822 removed outlier: 3.798A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.712A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 3 through 4 removed outlier: 3.513A pdb=" N GLY E 3 " --> pdb=" O THR E 12 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 70 through 71 removed outlier: 3.816A pdb=" N PHE E 81 " --> pdb=" O LEU E 65 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 84 through 85 Processing sheet with id=AB6, first strand: chain 'E' and resid 152 through 153 removed outlier: 3.920A pdb=" N TYR E 224 " --> pdb=" O TYR E 185 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG E 186 " --> pdb=" O GLN E 194 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N GLN E 194 " --> pdb=" O ARG E 186 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 162 through 163 Processing sheet with id=AB8, first strand: chain 'E' and resid 330 through 332 removed outlier: 6.086A pdb=" N SER E 331 " --> pdb=" O PHE E 357 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL E 356 " --> pdb=" O ILE E 304 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL E 305 " --> pdb=" O VAL E 372 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 472 through 473 Processing sheet with id=AC1, first strand: chain 'E' and resid 480 through 482 removed outlier: 3.912A pdb=" N THR E 481 " --> pdb=" O ILE E 488 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE E 488 " --> pdb=" O THR E 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 510 through 512 removed outlier: 4.283A pdb=" N THR E 547 " --> pdb=" O ILE E 512 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL E 544 " --> pdb=" O LEU E 573 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N ILE E 575 " --> pdb=" O VAL E 544 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N PHE E 546 " --> pdb=" O ILE E 575 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 3 through 4 removed outlier: 3.582A pdb=" N GLY F 3 " --> pdb=" O THR F 12 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 24 through 25 removed outlier: 3.750A pdb=" N LEU F 25 " --> pdb=" O LEU F 14 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU F 14 " --> pdb=" O LEU F 25 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 64 through 65 Processing sheet with id=AC6, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AC7, first strand: chain 'F' and resid 152 through 153 removed outlier: 4.055A pdb=" N TYR F 224 " --> pdb=" O TYR F 185 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ARG F 186 " --> pdb=" O GLN F 194 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLN F 194 " --> pdb=" O ARG F 186 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 162 through 163 Processing sheet with id=AC9, first strand: chain 'F' and resid 330 through 332 removed outlier: 6.161A pdb=" N SER F 331 " --> pdb=" O PHE F 357 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL F 356 " --> pdb=" O ILE F 304 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 510 through 512 removed outlier: 5.810A pdb=" N VAL F 510 " --> pdb=" O ILE F 545 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL F 544 " --> pdb=" O LEU F 573 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N PHE F 472 " --> pdb=" O CYS F 574 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 481 through 482 removed outlier: 3.988A pdb=" N THR F 481 " --> pdb=" O ILE F 488 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE F 488 " --> pdb=" O THR F 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'G' and resid 10 through 11 Processing sheet with id=AD4, first strand: chain 'G' and resid 15 through 17 removed outlier: 4.067A pdb=" N ALA G 15 " --> pdb=" O ARG G 55 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 43 through 46 removed outlier: 3.603A pdb=" N THR G 79 " --> pdb=" O GLY G 82 " (cutoff:3.500A) 789 hydrogen bonds defined for protein. 2136 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 4.47 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.11: 1 1.11 - 1.36: 7033 1.36 - 1.61: 15189 1.61 - 1.86: 228 1.86 - 2.12: 1 Bond restraints: 22452 Sorted by residual: bond pdb=" N PRO E 254 " pdb=" CD PRO E 254 " ideal model delta sigma weight residual 1.473 1.804 -0.331 1.40e-02 5.10e+03 5.58e+02 bond pdb=" CG PRO E 254 " pdb=" CD PRO E 254 " ideal model delta sigma weight residual 1.503 0.858 0.645 3.40e-02 8.65e+02 3.60e+02 bond pdb=" CB PRO E 254 " pdb=" CG PRO E 254 " ideal model delta sigma weight residual 1.492 2.116 -0.624 5.00e-02 4.00e+02 1.56e+02 bond pdb=" CA PRO E 254 " pdb=" CB PRO E 254 " ideal model delta sigma weight residual 1.533 1.374 0.160 1.42e-02 4.96e+03 1.26e+02 bond pdb=" CG PRO F 408 " pdb=" CD PRO F 408 " ideal model delta sigma weight residual 1.503 1.145 0.358 3.40e-02 8.65e+02 1.11e+02 ... (remaining 22447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.22: 30771 21.22 - 42.44: 3 42.44 - 63.65: 1 63.65 - 84.87: 0 84.87 - 106.09: 1 Bond angle restraints: 30776 Sorted by residual: angle pdb=" CB PRO E 254 " pdb=" CG PRO E 254 " pdb=" CD PRO E 254 " ideal model delta sigma weight residual 106.10 0.01 106.09 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CA PRO E 254 " pdb=" N PRO E 254 " pdb=" CD PRO E 254 " ideal model delta sigma weight residual 112.00 72.78 39.22 1.40e+00 5.10e-01 7.85e+02 angle pdb=" CA TYR E 253 " pdb=" C TYR E 253 " pdb=" O TYR E 253 " ideal model delta sigma weight residual 120.03 101.79 18.24 1.08e+00 8.57e-01 2.85e+02 angle pdb=" CA TYR E 253 " pdb=" C TYR E 253 " pdb=" N PRO E 254 " ideal model delta sigma weight residual 117.94 135.78 -17.84 1.37e+00 5.33e-01 1.70e+02 angle pdb=" CA PRO F 408 " pdb=" N PRO F 408 " pdb=" CD PRO F 408 " ideal model delta sigma weight residual 112.00 94.49 17.51 1.40e+00 5.10e-01 1.56e+02 ... (remaining 30771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.21: 12298 25.21 - 50.41: 1057 50.41 - 75.62: 185 75.62 - 100.83: 15 100.83 - 126.04: 3 Dihedral angle restraints: 13558 sinusoidal: 5699 harmonic: 7859 Sorted by residual: dihedral pdb=" CA TRP B 182 " pdb=" C TRP B 182 " pdb=" N PRO B 183 " pdb=" CA PRO B 183 " ideal model delta harmonic sigma weight residual 180.00 129.62 50.38 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA PHE A 504 " pdb=" C PHE A 504 " pdb=" N PRO A 505 " pdb=" CA PRO A 505 " ideal model delta harmonic sigma weight residual 180.00 -133.42 -46.58 0 5.00e+00 4.00e-02 8.68e+01 dihedral pdb=" CA TYR A 903 " pdb=" C TYR A 903 " pdb=" N SER A 904 " pdb=" CA SER A 904 " ideal model delta harmonic sigma weight residual 180.00 141.78 38.22 0 5.00e+00 4.00e-02 5.84e+01 ... (remaining 13555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.937: 3566 0.937 - 1.874: 0 1.874 - 2.810: 0 2.810 - 3.747: 0 3.747 - 4.684: 1 Chirality restraints: 3567 Sorted by residual: chirality pdb=" C3' 6GS G 201 " pdb=" C2' 6GS G 201 " pdb=" C4' 6GS G 201 " pdb=" O3' 6GS G 201 " both_signs ideal model delta sigma weight residual False -2.36 2.32 -4.68 2.00e-01 2.50e+01 5.49e+02 chirality pdb=" CA PRO E 254 " pdb=" N PRO E 254 " pdb=" C PRO E 254 " pdb=" CB PRO E 254 " both_signs ideal model delta sigma weight residual False 2.72 2.10 0.62 2.00e-01 2.50e+01 9.63e+00 chirality pdb=" CA ALA F 407 " pdb=" N ALA F 407 " pdb=" C ALA F 407 " pdb=" CB ALA F 407 " both_signs ideal model delta sigma weight residual False 2.48 2.88 -0.40 2.00e-01 2.50e+01 3.94e+00 ... (remaining 3564 not shown) Planarity restraints: 3734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 504 " 0.122 5.00e-02 4.00e+02 1.86e-01 5.52e+01 pdb=" N PRO A 505 " -0.321 5.00e-02 4.00e+02 pdb=" CA PRO A 505 " 0.113 5.00e-02 4.00e+02 pdb=" CD PRO A 505 " 0.087 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 167 " -0.053 2.00e-02 2.50e+03 3.80e-02 3.60e+01 pdb=" CG TRP F 167 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP F 167 " 0.087 2.00e-02 2.50e+03 pdb=" CD2 TRP F 167 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP F 167 " -0.047 2.00e-02 2.50e+03 pdb=" CE2 TRP F 167 " -0.026 2.00e-02 2.50e+03 pdb=" CE3 TRP F 167 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 167 " -0.019 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 167 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP F 167 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 90 " -0.034 2.00e-02 2.50e+03 3.31e-02 1.92e+01 pdb=" CG PHE E 90 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 PHE E 90 " 0.050 2.00e-02 2.50e+03 pdb=" CD2 PHE E 90 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE E 90 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE E 90 " 0.036 2.00e-02 2.50e+03 pdb=" CZ PHE E 90 " -0.050 2.00e-02 2.50e+03 ... (remaining 3731 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.21: 16 2.21 - 2.88: 8381 2.88 - 3.55: 29328 3.55 - 4.23: 50957 4.23 - 4.90: 84523 Nonbonded interactions: 173205 Sorted by model distance: nonbonded pdb=" O3A 6GS G 201 " pdb=" O HOH G 301 " model vdw 1.536 3.040 nonbonded pdb=" OE1 GLN F 354 " pdb=" OH TYR F 355 " model vdw 1.822 3.040 nonbonded pdb=" OD1 ASN F 489 " pdb=" N GLN F 492 " model vdw 1.917 3.120 nonbonded pdb=" NZ LYS A 73 " pdb=" NE2 HIS A 75 " model vdw 1.979 3.200 nonbonded pdb=" SG CYS F 318 " pdb=" NH2 ARG F 332 " model vdw 2.025 3.480 ... (remaining 173200 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 191)) 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 191)) } ncs_group { reference = (chain 'E' and (resid 2 through 473 or resid 475 through 703)) selection = (chain 'F' and (resid 2 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=0.02 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: 6.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 23.310 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.070 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:6.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 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 : 0.012 0.792 22485 Z= 0.444 Angle : 1.152 106.091 30803 Z= 0.563 Chirality : 0.091 4.684 3567 Planarity : 0.006 0.186 3734 Dihedral : 18.457 126.035 8488 Min Nonbonded Distance : 1.536 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.21 % Favored : 92.63 % Rotamer: Outliers : 0.26 % Allowed : 27.16 % Favored : 72.58 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.16 % 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: -2.81 (0.15), residues: 2640 helix: -0.77 (0.17), residues: 920 sheet: -1.86 (0.29), residues: 273 loop : -2.70 (0.14), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG G 55 TYR 0.036 0.002 TYR A 903 PHE 0.050 0.002 PHE E 90 TRP 0.087 0.003 TRP F 167 HIS 0.023 0.002 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00919 / 0.38 (22452) covalent geometry : angle 1.11162 / 0.56 (30776) hydrogen bonds : bond 0.19668 / 13.30 ( 810) hydrogen bonds : angle 6.85228 / 4.89 ( 2222) metal coordination : bond 0.17879 / 7.17 ( 32) metal coordination : angle 10.23390 / 7.16 ( 27) Misc. bond : bond 0.27991 / 14.73 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 184 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 906 MET cc_start: 0.5849 (mpp) cc_final: 0.4518 (pp-130) REVERT: E 68 MET cc_start: 0.5511 (mmm) cc_final: 0.5296 (mmm) REVERT: E 217 TYR cc_start: 0.2325 (m-80) cc_final: 0.1910 (p90) REVERT: F 224 TYR cc_start: 0.4418 (m-10) cc_final: 0.3684 (m-10) REVERT: F 443 ARG cc_start: 0.1967 (ptt-90) cc_final: 0.1571 (ptt90) REVERT: F 576 MET cc_start: 0.2590 (ppp) cc_final: 0.0948 (pmm) REVERT: G 12 MET cc_start: 0.3757 (mpp) cc_final: 0.3428 (mpt) outliers start: 5 outliers final: 1 residues processed: 186 average time/residue: 0.6312 time to fit residues: 133.2197 Evaluate side-chains 172 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 790 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 197 optimal weight: 0.1980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 GLN E 395 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.210996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.119597 restraints weight = 48102.940| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 4.89 r_work: 0.2989 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.220 22485 Z= 0.183 Angle : 0.796 27.225 30803 Z= 0.390 Chirality : 0.046 0.346 3567 Planarity : 0.006 0.168 3734 Dihedral : 12.785 114.288 3763 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.72 % Favored : 93.13 % Rotamer: Outliers : 3.08 % Allowed : 26.58 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.16 % 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: -2.56 (0.15), residues: 2640 helix: -0.47 (0.17), residues: 930 sheet: -1.79 (0.28), residues: 299 loop : -2.63 (0.15), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 74 TYR 0.027 0.002 TYR F 185 PHE 0.022 0.002 PHE A 652 TRP 0.016 0.002 TRP F 167 HIS 0.019 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (22452) covalent geometry : angle 0.73473 / 0.39 (30776) hydrogen bonds : bond 0.06811 / 4.59 ( 810) hydrogen bonds : angle 5.25598 / 3.71 ( 2222) metal coordination : bond 0.05235 / 2.30 ( 32) metal coordination : angle 10.41067 / 7.31 ( 27) Misc. bond : bond 0.01064 / 0.56 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 189 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: A 548 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8884 (tt) REVERT: A 790 ASN cc_start: 0.9198 (OUTLIER) cc_final: 0.8630 (t0) REVERT: A 906 MET cc_start: 0.6119 (mpp) cc_final: 0.4670 (pp-130) REVERT: B 48 GLU cc_start: 0.6194 (tp30) cc_final: 0.5664 (mt-10) REVERT: B 112 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7898 (m-30) REVERT: D 67 MET cc_start: 0.7204 (tpp) cc_final: 0.6992 (ttp) REVERT: D 83 VAL cc_start: 0.8443 (m) cc_final: 0.8128 (t) REVERT: D 155 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7212 (pt0) REVERT: E 217 TYR cc_start: 0.2357 (OUTLIER) cc_final: 0.1967 (p90) REVERT: F 576 MET cc_start: 0.2047 (ppp) cc_final: 0.1136 (pmm) REVERT: G 12 MET cc_start: 0.4175 (mpp) cc_final: 0.3931 (mpt) outliers start: 69 outliers final: 20 residues processed: 237 average time/residue: 0.5481 time to fit residues: 148.7546 Evaluate side-chains 207 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 185 TYR Chi-restraints excluded: chain G residue 48 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 242 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 192 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 200 optimal weight: 0.0000 chunk 20 optimal weight: 1.9990 chunk 235 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 218 optimal weight: 8.9990 chunk 21 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 395 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.212802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.134975 restraints weight = 48768.971| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 4.82 r_work: 0.3008 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.359 22485 Z= 0.140 Angle : 0.707 25.697 30803 Z= 0.344 Chirality : 0.043 0.334 3567 Planarity : 0.005 0.157 3734 Dihedral : 12.405 115.450 3763 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.26 % Favored : 93.58 % Rotamer: Outliers : 3.30 % Allowed : 26.76 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.12 % 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: -2.24 (0.16), residues: 2640 helix: -0.07 (0.17), residues: 917 sheet: -1.68 (0.27), residues: 297 loop : -2.50 (0.15), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 443 TYR 0.019 0.001 TYR E 185 PHE 0.023 0.001 PHE E 561 TRP 0.015 0.001 TRP D 182 HIS 0.037 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (22452) covalent geometry : angle 0.64497 / 0.34 (30776) hydrogen bonds : bond 0.05421 / 3.68 ( 810) hydrogen bonds : angle 4.88139 / 3.46 ( 2222) metal coordination : bond 0.06952 / 2.58 ( 32) metal coordination : angle 9.78020 / 6.95 ( 27) Misc. bond : bond 0.00852 / 0.45 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 187 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 548 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8733 (tt) REVERT: A 790 ASN cc_start: 0.9114 (OUTLIER) cc_final: 0.8906 (t160) REVERT: A 902 MET cc_start: 0.5661 (OUTLIER) cc_final: 0.4997 (tpp) REVERT: B 48 GLU cc_start: 0.6243 (tp30) cc_final: 0.5755 (mt-10) REVERT: B 78 ASP cc_start: 0.7909 (t70) cc_final: 0.7694 (t0) REVERT: B 112 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7859 (m-30) REVERT: D 83 VAL cc_start: 0.8274 (m) cc_final: 0.7922 (t) REVERT: D 155 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6980 (pt0) REVERT: E 83 LEU cc_start: 0.6272 (OUTLIER) cc_final: 0.5936 (mt) REVERT: E 395 HIS cc_start: 0.1913 (OUTLIER) cc_final: 0.1473 (p90) REVERT: E 429 MET cc_start: 0.2175 (OUTLIER) cc_final: 0.1868 (ptp) REVERT: E 436 MET cc_start: 0.1036 (mmm) cc_final: -0.0510 (mmm) REVERT: E 540 GLU cc_start: -0.0146 (OUTLIER) cc_final: -0.1051 (tm-30) REVERT: F 576 MET cc_start: 0.2042 (ppp) cc_final: 0.1143 (pmm) outliers start: 74 outliers final: 25 residues processed: 234 average time/residue: 0.5845 time to fit residues: 156.4859 Evaluate side-chains 206 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 395 HIS Chi-restraints excluded: chain E residue 429 MET Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 185 TYR Chi-restraints excluded: chain F residue 523 SER Chi-restraints excluded: chain G residue 86 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 38 optimal weight: 0.0980 chunk 85 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 82 optimal weight: 0.0060 chunk 184 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.0050 overall best weight: 0.3812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 349 ASN E 395 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 518 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.213678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.124618 restraints weight = 52686.305| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 4.43 r_work: 0.3058 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.375 22485 Z= 0.130 Angle : 0.679 24.096 30803 Z= 0.331 Chirality : 0.043 0.462 3567 Planarity : 0.005 0.150 3734 Dihedral : 12.250 114.983 3763 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.85 % Favored : 94.00 % Rotamer: Outliers : 3.35 % Allowed : 26.41 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % 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: -1.99 (0.16), residues: 2640 helix: 0.22 (0.18), residues: 909 sheet: -1.49 (0.27), residues: 293 loop : -2.41 (0.15), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 74 TYR 0.037 0.001 TYR E 396 PHE 0.019 0.001 PHE E 561 TRP 0.016 0.001 TRP E 167 HIS 0.044 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (22452) covalent geometry : angle 0.62122 / 0.33 (30776) hydrogen bonds : bond 0.04854 / 3.32 ( 810) hydrogen bonds : angle 4.69458 / 3.33 ( 2222) metal coordination : bond 0.07039 / 2.54 ( 32) metal coordination : angle 9.25299 / 6.57 ( 27) Misc. bond : bond 0.00137 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 179 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: A 758 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7901 (mt) REVERT: A 790 ASN cc_start: 0.9119 (OUTLIER) cc_final: 0.8890 (t160) REVERT: A 902 MET cc_start: 0.5624 (OUTLIER) cc_final: 0.5109 (tpp) REVERT: B 48 GLU cc_start: 0.6262 (tp30) cc_final: 0.5798 (mt-10) REVERT: B 112 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7902 (m-30) REVERT: C 50 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7603 (pt0) REVERT: D 48 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6520 (tm-30) REVERT: D 83 VAL cc_start: 0.8352 (m) cc_final: 0.7976 (t) REVERT: D 155 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7122 (pt0) REVERT: E 83 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.6306 (tp) REVERT: E 271 LYS cc_start: -0.0302 (OUTLIER) cc_final: -0.0518 (pttt) REVERT: E 345 LYS cc_start: 0.2048 (tmtt) cc_final: 0.1675 (tptt) REVERT: E 395 HIS cc_start: 0.2080 (OUTLIER) cc_final: 0.1365 (p90) REVERT: E 436 MET cc_start: 0.1059 (mmm) cc_final: 0.0466 (mmm) REVERT: E 540 GLU cc_start: -0.0134 (OUTLIER) cc_final: -0.1043 (tm-30) REVERT: F 576 MET cc_start: 0.2395 (ppp) cc_final: 0.1643 (pmm) outliers start: 75 outliers final: 31 residues processed: 231 average time/residue: 0.6076 time to fit residues: 161.0863 Evaluate side-chains 209 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 168 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain E residue 19 CYS Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 395 HIS Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain F residue 24 PHE Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 185 TYR Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 523 SER Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 86 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 202 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 169 optimal weight: 0.0870 chunk 8 optimal weight: 0.7980 chunk 118 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 103 optimal weight: 0.4980 chunk 210 optimal weight: 9.9990 chunk 241 optimal weight: 8.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 69 ASN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.213872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.125643 restraints weight = 35426.648| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 4.03 r_work: 0.3053 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.246 22485 Z= 0.123 Angle : 0.664 23.121 30803 Z= 0.323 Chirality : 0.042 0.412 3567 Planarity : 0.005 0.147 3734 Dihedral : 12.124 114.853 3763 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.73 % Favored : 94.12 % Rotamer: Outliers : 3.26 % Allowed : 26.41 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % 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: -1.82 (0.16), residues: 2640 helix: 0.37 (0.18), residues: 908 sheet: -1.33 (0.28), residues: 283 loop : -2.33 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 443 TYR 0.020 0.001 TYR A 903 PHE 0.020 0.001 PHE E 561 TRP 0.013 0.001 TRP A 916 HIS 0.027 0.001 HIS E 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (22452) covalent geometry : angle 0.60684 / 0.32 (30776) hydrogen bonds : bond 0.04757 / 3.25 ( 810) hydrogen bonds : angle 4.60692 / 3.27 ( 2222) metal coordination : bond 0.05275 / 2.15 ( 32) metal coordination : angle 9.10567 / 6.46 ( 27) Misc. bond : bond 0.00055 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 175 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 548 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8760 (tt) REVERT: A 758 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7884 (mt) REVERT: A 790 ASN cc_start: 0.9085 (OUTLIER) cc_final: 0.8842 (t160) REVERT: A 902 MET cc_start: 0.5431 (OUTLIER) cc_final: 0.3591 (ptm) REVERT: B 48 GLU cc_start: 0.6253 (tp30) cc_final: 0.5797 (mt-10) REVERT: B 112 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7901 (m-30) REVERT: C 50 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7596 (pt0) REVERT: D 59 LEU cc_start: 0.5401 (OUTLIER) cc_final: 0.4997 (tt) REVERT: D 83 VAL cc_start: 0.8313 (OUTLIER) cc_final: 0.7907 (t) REVERT: D 155 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7103 (pt0) REVERT: E 83 LEU cc_start: 0.6489 (OUTLIER) cc_final: 0.6148 (tp) REVERT: E 271 LYS cc_start: -0.0581 (OUTLIER) cc_final: -0.0855 (pttt) REVERT: E 345 LYS cc_start: 0.2100 (tmtt) cc_final: 0.1733 (tptt) REVERT: E 436 MET cc_start: 0.0849 (mmm) cc_final: 0.0335 (mmm) REVERT: E 540 GLU cc_start: -0.0258 (OUTLIER) cc_final: -0.1144 (tm-30) REVERT: F 429 MET cc_start: -0.0353 (mmt) cc_final: -0.0755 (mmt) REVERT: F 443 ARG cc_start: -0.0986 (ptp90) cc_final: -0.1296 (ptp90) REVERT: F 576 MET cc_start: 0.2385 (ppp) cc_final: 0.1627 (pmm) outliers start: 73 outliers final: 40 residues processed: 226 average time/residue: 0.5945 time to fit residues: 154.2304 Evaluate side-chains 213 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 162 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain E residue 19 CYS Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 395 HIS Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain F residue 24 PHE Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 185 TYR Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 523 SER Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 31 TYR Chi-restraints excluded: chain G residue 86 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 184 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 262 optimal weight: 30.0000 chunk 92 optimal weight: 0.2980 chunk 58 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 163 optimal weight: 20.0000 chunk 230 optimal weight: 6.9990 chunk 147 optimal weight: 20.0000 chunk 138 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN B 88 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 349 ASN E 395 HIS ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** 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 = 0.4530 r_free = 0.4530 target = 0.211296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.129750 restraints weight = 44014.456| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 4.36 r_work: 0.2984 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.218 22485 Z= 0.151 Angle : 0.680 22.029 30803 Z= 0.333 Chirality : 0.044 0.392 3567 Planarity : 0.005 0.148 3734 Dihedral : 12.106 114.403 3763 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.69 % Favored : 94.15 % Rotamer: Outliers : 3.65 % Allowed : 25.92 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % 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: -1.77 (0.16), residues: 2640 helix: 0.38 (0.18), residues: 910 sheet: -1.24 (0.29), residues: 274 loop : -2.29 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 443 TYR 0.029 0.002 TYR A 903 PHE 0.019 0.002 PHE A 504 TRP 0.013 0.002 TRP A 916 HIS 0.016 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (22452) covalent geometry : angle 0.62757 / 0.33 (30776) hydrogen bonds : bond 0.05731 / 3.86 ( 810) hydrogen bonds : angle 4.63330 / 3.28 ( 2222) metal coordination : bond 0.04720 / 1.95 ( 32) metal coordination : angle 8.85916 / 6.23 ( 27) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 175 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.7881 (ttm170) cc_final: 0.7544 (mtt-85) REVERT: A 161 ASP cc_start: 0.8284 (m-30) cc_final: 0.8070 (m-30) REVERT: A 548 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8861 (tt) REVERT: A 790 ASN cc_start: 0.9179 (OUTLIER) cc_final: 0.8975 (t160) REVERT: A 903 TYR cc_start: 0.3126 (OUTLIER) cc_final: 0.1825 (m-10) REVERT: B 48 GLU cc_start: 0.6221 (tp30) cc_final: 0.5777 (mt-10) REVERT: B 112 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7958 (m-30) REVERT: C 50 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7649 (pt0) REVERT: D 48 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6430 (tm-30) REVERT: D 83 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.7978 (t) REVERT: D 155 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7303 (pt0) REVERT: E 83 LEU cc_start: 0.6616 (OUTLIER) cc_final: 0.6295 (tp) REVERT: E 345 LYS cc_start: 0.2073 (tmtt) cc_final: 0.1696 (tptt) REVERT: E 395 HIS cc_start: 0.1619 (OUTLIER) cc_final: 0.1026 (p90) REVERT: E 540 GLU cc_start: -0.0254 (OUTLIER) cc_final: -0.1121 (tm-30) REVERT: F 429 MET cc_start: -0.0015 (mmt) cc_final: -0.0389 (mmt) REVERT: F 443 ARG cc_start: -0.0940 (ptp90) cc_final: -0.1216 (ptp90) REVERT: F 576 MET cc_start: 0.2389 (ppp) cc_final: 0.1530 (pmm) outliers start: 82 outliers final: 44 residues processed: 232 average time/residue: 0.5885 time to fit residues: 155.9024 Evaluate side-chains 224 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 170 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 903 TYR Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 19 CYS Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 395 HIS Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 24 PHE Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 185 TYR Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 523 SER Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 31 TYR Chi-restraints excluded: chain G residue 86 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 21 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 200 optimal weight: 0.3980 chunk 211 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 214 optimal weight: 8.9990 chunk 216 optimal weight: 0.4980 chunk 193 optimal weight: 10.0000 chunk 112 optimal weight: 0.5980 chunk 249 optimal weight: 40.0000 chunk 127 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 395 HIS ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.212001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.124747 restraints weight = 52454.894| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 4.51 r_work: 0.3018 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2898 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.198 22485 Z= 0.130 Angle : 0.660 21.705 30803 Z= 0.323 Chirality : 0.042 0.380 3567 Planarity : 0.005 0.147 3734 Dihedral : 12.046 114.000 3763 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.50 % Favored : 94.34 % Rotamer: Outliers : 3.61 % Allowed : 26.50 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % 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: -1.70 (0.16), residues: 2640 helix: 0.33 (0.17), residues: 937 sheet: -1.16 (0.29), residues: 274 loop : -2.22 (0.15), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 173 TYR 0.024 0.001 TYR A 903 PHE 0.028 0.001 PHE F 106 TRP 0.013 0.001 TRP A 916 HIS 0.013 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (22452) covalent geometry : angle 0.61041 / 0.32 (30776) hydrogen bonds : bond 0.05227 / 3.55 ( 810) hydrogen bonds : angle 4.57424 / 3.24 ( 2222) metal coordination : bond 0.04222 / 1.74 ( 32) metal coordination : angle 8.54328 / 5.99 ( 27) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 178 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.7884 (ttm170) cc_final: 0.7574 (mtt-85) REVERT: A 548 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8833 (tt) REVERT: A 790 ASN cc_start: 0.9140 (OUTLIER) cc_final: 0.8916 (t160) REVERT: A 903 TYR cc_start: 0.3657 (OUTLIER) cc_final: 0.2315 (m-10) REVERT: B 48 GLU cc_start: 0.6232 (tp30) cc_final: 0.5828 (mt-10) REVERT: B 75 ARG cc_start: 0.7749 (ttp-110) cc_final: 0.7334 (mtm-85) REVERT: B 112 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7936 (m-30) REVERT: C 50 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7706 (pt0) REVERT: D 48 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6428 (tm-30) REVERT: D 59 LEU cc_start: 0.5422 (OUTLIER) cc_final: 0.5052 (tt) REVERT: D 83 VAL cc_start: 0.8380 (OUTLIER) cc_final: 0.7958 (t) REVERT: D 129 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8855 (mtm) REVERT: D 155 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7223 (pt0) REVERT: E 83 LEU cc_start: 0.6759 (OUTLIER) cc_final: 0.6414 (tp) REVERT: E 271 LYS cc_start: -0.0494 (OUTLIER) cc_final: -0.0793 (tppt) REVERT: E 345 LYS cc_start: 0.2126 (tmtt) cc_final: 0.1756 (tptt) REVERT: E 395 HIS cc_start: 0.2056 (OUTLIER) cc_final: 0.1399 (p90) REVERT: E 436 MET cc_start: 0.0079 (mmm) cc_final: -0.1435 (mmm) REVERT: E 540 GLU cc_start: -0.0273 (OUTLIER) cc_final: -0.1364 (pp20) REVERT: F 429 MET cc_start: -0.0170 (mmt) cc_final: -0.0606 (mmt) REVERT: F 443 ARG cc_start: -0.0803 (ptp90) cc_final: -0.1069 (ptp90) REVERT: F 576 MET cc_start: 0.2383 (ppp) cc_final: 0.1520 (pmm) outliers start: 81 outliers final: 45 residues processed: 231 average time/residue: 0.6169 time to fit residues: 163.3028 Evaluate side-chains 231 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 173 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 903 TYR Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 19 CYS Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 299 TYR Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 395 HIS Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 24 PHE Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 185 TYR Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 523 SER Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 27 ASN Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 86 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 211 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 252 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 238 optimal weight: 0.6980 chunk 202 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 69 ASN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 518 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.210197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.124236 restraints weight = 54598.911| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 3.86 r_work: 0.2980 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.192 22485 Z= 0.184 Angle : 0.699 21.281 30803 Z= 0.346 Chirality : 0.045 0.348 3567 Planarity : 0.005 0.148 3734 Dihedral : 12.081 113.497 3763 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.07 % Favored : 93.77 % Rotamer: Outliers : 3.26 % Allowed : 26.98 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % 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: -1.76 (0.16), residues: 2640 helix: 0.29 (0.17), residues: 923 sheet: -1.18 (0.29), residues: 285 loop : -2.25 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 443 TYR 0.020 0.002 TYR A 149 PHE 0.029 0.002 PHE F 106 TRP 0.013 0.002 TRP A 916 HIS 0.032 0.002 HIS E 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (22452) covalent geometry : angle 0.64893 / 0.34 (30776) hydrogen bonds : bond 0.06372 / 4.28 ( 810) hydrogen bonds : angle 4.65823 / 3.29 ( 2222) metal coordination : bond 0.04330 / 1.86 ( 32) metal coordination : angle 8.75580 / 6.12 ( 27) Misc. bond : bond 0.00010 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 173 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8892 (tt) REVERT: A 790 ASN cc_start: 0.9195 (OUTLIER) cc_final: 0.8925 (t160) REVERT: A 903 TYR cc_start: 0.4702 (OUTLIER) cc_final: 0.3201 (m-80) REVERT: B 48 GLU cc_start: 0.6232 (tp30) cc_final: 0.5831 (mt-10) REVERT: B 112 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7904 (m-30) REVERT: D 48 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6482 (tm-30) REVERT: D 83 VAL cc_start: 0.8425 (OUTLIER) cc_final: 0.7990 (t) REVERT: D 129 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8850 (mtm) REVERT: D 155 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7299 (pt0) REVERT: E 83 LEU cc_start: 0.6694 (OUTLIER) cc_final: 0.6269 (mt) REVERT: E 271 LYS cc_start: -0.0511 (OUTLIER) cc_final: -0.0814 (tppt) REVERT: E 345 LYS cc_start: 0.2138 (tmtt) cc_final: 0.1775 (tptt) REVERT: E 395 HIS cc_start: 0.2077 (OUTLIER) cc_final: 0.1510 (p-80) REVERT: E 436 MET cc_start: 0.0396 (mmm) cc_final: -0.1254 (mmm) REVERT: E 540 GLU cc_start: -0.0342 (OUTLIER) cc_final: -0.1479 (pp20) REVERT: F 429 MET cc_start: 0.0175 (mmt) cc_final: -0.0087 (mmp) REVERT: F 443 ARG cc_start: -0.0778 (ptp90) cc_final: -0.1197 (ptp90) REVERT: F 576 MET cc_start: 0.2296 (ppp) cc_final: 0.1461 (pmm) REVERT: G 86 LYS cc_start: 0.3263 (OUTLIER) cc_final: 0.2938 (mttt) outliers start: 73 outliers final: 46 residues processed: 222 average time/residue: 0.6060 time to fit residues: 153.2245 Evaluate side-chains 229 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 170 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 903 TYR Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 19 CYS Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 395 HIS Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 24 PHE Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 185 TYR Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 523 SER Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 86 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 139 optimal weight: 20.0000 chunk 157 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 229 optimal weight: 10.0000 chunk 145 optimal weight: 0.9990 chunk 243 optimal weight: 7.9990 chunk 230 optimal weight: 6.9990 chunk 163 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 216 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 69 ASN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 395 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.210128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.119150 restraints weight = 47169.661| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 4.01 r_work: 0.3003 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.188 22485 Z= 0.170 Angle : 0.690 21.581 30803 Z= 0.341 Chirality : 0.044 0.332 3567 Planarity : 0.005 0.148 3734 Dihedral : 12.079 112.645 3763 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.85 % Favored : 94.00 % Rotamer: Outliers : 3.12 % Allowed : 27.42 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % 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: -1.78 (0.16), residues: 2640 helix: 0.26 (0.17), residues: 935 sheet: -1.33 (0.28), residues: 311 loop : -2.24 (0.15), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 74 TYR 0.019 0.002 TYR A 149 PHE 0.031 0.002 PHE F 106 TRP 0.013 0.002 TRP A 916 HIS 0.010 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (22452) covalent geometry : angle 0.64146 / 0.34 (30776) hydrogen bonds : bond 0.06175 / 4.16 ( 810) hydrogen bonds : angle 4.65028 / 3.29 ( 2222) metal coordination : bond 0.04693 / 2.08 ( 32) metal coordination : angle 8.62370 / 6.02 ( 27) Misc. bond : bond 0.00024 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 178 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8870 (tt) REVERT: A 553 ARG cc_start: 0.8107 (ttp80) cc_final: 0.7617 (ptm-80) REVERT: A 790 ASN cc_start: 0.9173 (OUTLIER) cc_final: 0.8923 (t160) REVERT: A 903 TYR cc_start: 0.4779 (OUTLIER) cc_final: 0.3488 (m-80) REVERT: B 48 GLU cc_start: 0.6352 (tp30) cc_final: 0.5946 (mt-10) REVERT: B 75 ARG cc_start: 0.7710 (ttp-110) cc_final: 0.7295 (mtm-85) REVERT: B 112 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.8000 (m-30) REVERT: C 50 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7750 (pt0) REVERT: D 48 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6526 (tm-30) REVERT: D 59 LEU cc_start: 0.5553 (mm) cc_final: 0.5106 (tt) REVERT: D 83 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.7977 (t) REVERT: D 129 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8831 (mtm) REVERT: D 155 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7310 (pt0) REVERT: E 83 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.6239 (mt) REVERT: E 86 ASN cc_start: 0.7119 (OUTLIER) cc_final: 0.6808 (m110) REVERT: E 345 LYS cc_start: 0.2165 (tmtt) cc_final: 0.1800 (tptt) REVERT: E 395 HIS cc_start: 0.1352 (OUTLIER) cc_final: 0.0663 (p90) REVERT: E 436 MET cc_start: 0.0298 (mmm) cc_final: -0.0297 (mmm) REVERT: E 540 GLU cc_start: -0.0069 (OUTLIER) cc_final: -0.1160 (pp20) REVERT: F 429 MET cc_start: 0.0139 (mmt) cc_final: -0.0146 (mmp) REVERT: F 436 MET cc_start: 0.1476 (tpp) cc_final: 0.0261 (mtt) REVERT: G 86 LYS cc_start: 0.3408 (OUTLIER) cc_final: 0.3086 (mttt) outliers start: 70 outliers final: 44 residues processed: 225 average time/residue: 0.6185 time to fit residues: 158.9780 Evaluate side-chains 231 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 174 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 903 TYR Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 19 CYS Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 395 HIS Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 24 PHE Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 185 TYR Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 523 SER Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 86 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 137 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 247 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 126 optimal weight: 0.1980 chunk 139 optimal weight: 6.9990 chunk 219 optimal weight: 0.0570 chunk 12 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 140 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 69 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.211975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.120842 restraints weight = 36385.516| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 4.37 r_work: 0.2990 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.604 22485 Z= 0.148 Angle : 0.707 26.908 30803 Z= 0.336 Chirality : 0.042 0.319 3567 Planarity : 0.005 0.147 3734 Dihedral : 12.014 112.428 3763 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.58 % Favored : 94.27 % Rotamer: Outliers : 2.55 % Allowed : 27.95 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % 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: -1.62 (0.16), residues: 2640 helix: 0.34 (0.17), residues: 950 sheet: -1.06 (0.30), residues: 276 loop : -2.17 (0.15), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 443 TYR 0.018 0.001 TYR E 382 PHE 0.031 0.001 PHE F 106 TRP 0.014 0.001 TRP A 916 HIS 0.023 0.001 HIS E 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (22452) covalent geometry : angle 0.62345 / 0.33 (30776) hydrogen bonds : bond 0.05231 / 3.55 ( 810) hydrogen bonds : angle 4.56435 / 3.23 ( 2222) metal coordination : bond 0.11325 / 5.58 ( 32) metal coordination : angle 11.26700 / 7.55 ( 27) Misc. bond : bond 0.00016 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 176 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.7849 (ttp-110) cc_final: 0.7319 (mtt-85) REVERT: A 548 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8754 (tt) REVERT: A 790 ASN cc_start: 0.9153 (OUTLIER) cc_final: 0.8915 (t160) REVERT: A 903 TYR cc_start: 0.4494 (OUTLIER) cc_final: 0.3359 (m-80) REVERT: B 48 GLU cc_start: 0.6232 (tp30) cc_final: 0.5785 (mt-10) REVERT: B 75 ARG cc_start: 0.7447 (ttp-110) cc_final: 0.7032 (mtm-85) REVERT: B 112 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7894 (m-30) REVERT: D 48 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6489 (tm-30) REVERT: D 59 LEU cc_start: 0.5311 (mm) cc_final: 0.4919 (tt) REVERT: D 83 VAL cc_start: 0.8236 (OUTLIER) cc_final: 0.7827 (t) REVERT: D 155 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7060 (pt0) REVERT: E 83 LEU cc_start: 0.6216 (OUTLIER) cc_final: 0.5892 (mt) REVERT: E 345 LYS cc_start: 0.2156 (tmtt) cc_final: 0.1839 (tptt) REVERT: E 383 ASP cc_start: 0.5299 (p0) cc_final: 0.4868 (t0) REVERT: E 540 GLU cc_start: -0.0083 (OUTLIER) cc_final: -0.1160 (pp20) REVERT: E 580 ASP cc_start: 0.2111 (t70) cc_final: 0.1527 (m-30) REVERT: F 260 ASP cc_start: 0.4409 (p0) cc_final: 0.3620 (m-30) REVERT: F 429 MET cc_start: 0.0071 (mmt) cc_final: -0.0195 (mmp) REVERT: F 436 MET cc_start: 0.1096 (tpp) cc_final: -0.0026 (mtt) REVERT: G 86 LYS cc_start: 0.3083 (OUTLIER) cc_final: 0.2826 (mttt) outliers start: 57 outliers final: 39 residues processed: 217 average time/residue: 0.6357 time to fit residues: 157.1863 Evaluate side-chains 223 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 174 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 903 TYR Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 19 CYS Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 24 PHE Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 185 TYR Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 523 SER Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 86 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 119 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 232 optimal weight: 0.0170 chunk 241 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 143 optimal weight: 0.0670 chunk 26 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 254 optimal weight: 5.9990 chunk 228 optimal weight: 4.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 69 ASN E 557 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.211592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.131999 restraints weight = 42577.064| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 3.83 r_work: 0.3031 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.415 22485 Z= 0.144 Angle : 0.685 20.394 30803 Z= 0.329 Chirality : 0.042 0.287 3567 Planarity : 0.005 0.147 3734 Dihedral : 11.949 112.106 3763 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.47 % Favored : 94.34 % Rotamer: Outliers : 2.51 % Allowed : 28.12 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % 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: -1.52 (0.16), residues: 2640 helix: 0.42 (0.17), residues: 950 sheet: -0.97 (0.30), residues: 276 loop : -2.11 (0.15), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 15 TYR 0.021 0.001 TYR E 396 PHE 0.023 0.001 PHE F 561 TRP 0.014 0.002 TRP A 916 HIS 0.031 0.001 HIS F 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (22452) covalent geometry : angle 0.61461 / 0.32 (30776) hydrogen bonds : bond 0.05106 / 3.46 ( 810) hydrogen bonds : angle 4.51068 / 3.20 ( 2222) metal coordination : bond 0.09485 / 4.67 ( 32) metal coordination : angle 10.21524 / 7.15 ( 27) Misc. bond : bond 0.00006 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13206.16 seconds wall clock time: 224 minutes 11.82 seconds (13451.82 seconds total)