Starting phenix.real_space_refine on Sat Jul 4 17:16:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gwi_34313/07_2026/8gwi_34313.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gwi_34313/07_2026/8gwi_34313.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8gwi_34313/07_2026/8gwi_34313.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gwi_34313/07_2026/8gwi_34313.cif" model { file = "/net/cci-nas-00/data/ceres_data/8gwi_34313/07_2026/8gwi_34313.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gwi_34313/07_2026/8gwi_34313.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gwi_34313/07_2026/8gwi_34313.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gwi_34313/07_2026/8gwi_34313.map" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 55 5.49 5 S 158 5.16 5 C 13735 2.51 5 N 3694 2.21 5 O 4305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21955 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 7492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 931, 7492 Classifications: {'peptide': 931} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 900} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1396 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 600 Classifications: {'peptide': 78} Link IDs: {'TRANS': 77} Chain: "D" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1422 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 545 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 16, 'rna3p_pyr': 8} Link IDs: {'rna3p': 24} Chain: "J" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 565 Classifications: {'RNA': 27} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 25} Chain: "F" Number of atoms: 4513 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4598 Chain: "E" Number of atoms: 4513 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4598 Chain: "G" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 868 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' ZN': 2, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2465 SG CYS A 301 75.578 55.650 121.844 1.00 86.97 S ATOM 2506 SG CYS A 306 75.567 57.180 125.354 1.00 84.94 S ATOM 2538 SG CYS A 310 76.856 53.605 124.773 1.00 84.77 S ATOM 3946 SG CYS A 487 78.264 69.779 106.107 1.00 95.87 S ATOM 5199 SG CYS A 645 77.470 71.834 109.252 1.00 97.77 S ATOM 5205 SG CYS A 646 76.146 68.218 108.904 1.00 89.00 S ATOM 12129 SG CYS F 16 102.478 65.216 50.524 1.00183.45 S ATOM 12144 SG CYS F 19 103.212 62.542 47.852 1.00198.14 S ATOM 12047 SG CYS F 5 114.925 66.378 50.337 1.00183.01 S ATOM 12068 SG CYS F 8 115.808 69.235 47.969 1.00185.13 S ATOM 12206 SG CYS F 26 114.614 70.148 51.170 1.00172.26 S ATOM 12223 SG CYS F 29 112.090 68.304 48.775 1.00175.19 S ATOM 12388 SG CYS F 50 93.154 76.836 65.675 1.00158.72 S ATOM 12418 SG CYS F 55 89.756 76.042 64.216 1.00164.97 S ATOM 12551 SG CYS F 72 91.926 78.390 62.448 1.00168.17 S ATOM 16642 SG CYS E 16 61.349 74.627 65.591 1.00165.58 S ATOM 16657 SG CYS E 19 58.755 72.126 64.275 1.00179.24 S ATOM 16560 SG CYS E 5 70.232 70.535 57.925 1.00188.71 S ATOM 16581 SG CYS E 8 70.961 72.499 54.838 1.00197.10 S ATOM 16719 SG CYS E 26 72.392 73.907 58.159 1.00186.39 S ATOM 16736 SG CYS E 29 68.780 74.086 57.029 1.00167.57 S ATOM 16901 SG CYS E 50 66.240 87.403 79.620 1.00176.08 S ATOM 16931 SG CYS E 55 63.011 88.887 81.055 1.00192.48 S ATOM 17064 SG CYS E 72 65.078 90.922 78.545 1.00187.74 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AMET F 474 " occ=0.42 ... (14 atoms not shown) pdb=" CE BMET F 474 " occ=0.58 residue: pdb=" N AMET E 474 " occ=0.11 ... (14 atoms not shown) pdb=" CE BMET E 474 " occ=0.89 Time building chain proxies: 5.93, per 1000 atoms: 0.27 Number of scatterers: 21955 At special positions: 0 Unit cell: (154.98, 136.94, 186.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 158 16.00 P 55 15.00 O 4305 8.00 N 3694 7.00 C 13735 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 19 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 16 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 29 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 5 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 26 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 55 " pdb=" ZN F 701 " pdb="ZN ZN F 701 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F 701 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 19 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 16 " pdb=" ZN F 702 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 8 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 26 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 5 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 29 " pdb=" ZN F 703 " pdb="ZN ZN F 703 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 72 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 55 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 50 " Number of angles added : 27 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5094 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 30 sheets defined 39.9% alpha, 10.3% beta 21 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 3.07 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 removed outlier: 3.974A pdb=" N ASN A 9 " --> pdb=" O GLN A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 91 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.649A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.622A pdb=" N TYR A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.815A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A 159 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.630A pdb=" N ASN A 209 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 206 through 210' Processing helix chain 'A' and resid 234 through 242 removed outlier: 3.528A pdb=" N TYR A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.865A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.569A pdb=" N HIS A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 removed outlier: 3.558A pdb=" N ARG A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 280 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.616A pdb=" N CYS A 301 " --> pdb=" O CYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.645A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.554A pdb=" N SER A 325 " --> pdb=" O PRO A 322 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 322 through 326' Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.506A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 425 Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 4.154A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.622A pdb=" N TRP A 509 " --> pdb=" O PHE A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.867A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 removed outlier: 3.610A pdb=" N THR A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 580 removed outlier: 4.033A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 removed outlier: 3.589A pdb=" N SER A 607 " --> pdb=" O LYS A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 removed outlier: 3.572A pdb=" N ARG A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 647 through 663 removed outlier: 3.586A pdb=" N ARG A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.525A pdb=" N ALA A 690 " --> pdb=" O THR A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 733 removed outlier: 3.504A pdb=" N ARG A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.792A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 851 through 855 Processing helix chain 'A' and resid 856 through 866 Processing helix chain 'A' and resid 867 through 872 removed outlier: 3.581A pdb=" N LYS A 871 " --> pdb=" O PRO A 868 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS A 872 " --> pdb=" O LEU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 903 removed outlier: 4.388A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N MET A 902 " --> pdb=" O HIS A 898 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR A 903 " --> pdb=" O MET A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 917 removed outlier: 3.678A pdb=" N GLU A 917 " --> pdb=" O ARG A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 923 removed outlier: 3.608A pdb=" N ALA A 923 " --> pdb=" O GLU A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 11 through 28 Processing helix chain 'B' and resid 31 through 96 removed outlier: 3.645A pdb=" N LEU B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP B 52 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 109 removed outlier: 3.763A pdb=" N ASN B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.619A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 25 through 41 removed outlier: 3.665A pdb=" N LEU C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 61 removed outlier: 3.681A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 73 Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 31 through 80 removed outlier: 3.885A pdb=" N LEU D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA D 45 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP D 52 " --> pdb=" O GLU D 48 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA D 54 " --> pdb=" O ASP D 50 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 99 removed outlier: 3.842A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 134 through 142 removed outlier: 3.570A pdb=" N TYR D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'F' and resid 26 through 36 Processing helix chain 'F' and resid 104 through 110 Processing helix chain 'F' and resid 116 through 125 removed outlier: 4.231A pdb=" N TYR F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 147 Processing helix chain 'F' and resid 265 through 275 Processing helix chain 'F' and resid 290 through 299 Processing helix chain 'F' and resid 310 through 325 removed outlier: 3.684A pdb=" N ALA F 316 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU F 317 " --> pdb=" O ALA F 313 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N LYS F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU F 322 " --> pdb=" O CYS F 318 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N LYS F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 328 No H-bonds generated for 'chain 'F' and resid 326 through 328' Processing helix chain 'F' and resid 381 through 391 removed outlier: 3.632A pdb=" N LEU F 391 " --> pdb=" O VAL F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 433 removed outlier: 3.999A pdb=" N LYS F 430 " --> pdb=" O CYS F 426 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR F 431 " --> pdb=" O ARG F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 456 removed outlier: 3.616A pdb=" N VAL F 449 " --> pdb=" O PRO F 445 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR F 451 " --> pdb=" O GLU F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 501 Processing helix chain 'F' and resid 503 through 507 removed outlier: 3.912A pdb=" N TRP F 506 " --> pdb=" O ASN F 503 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG F 507 " --> pdb=" O PRO F 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 503 through 507' Processing helix chain 'F' and resid 516 through 523 Processing helix chain 'E' and resid 26 through 36 Processing helix chain 'E' and resid 103 through 112 Processing helix chain 'E' and resid 116 through 124 removed outlier: 4.094A pdb=" N TYR E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 148 Processing helix chain 'E' and resid 264 through 273 Processing helix chain 'E' and resid 290 through 299 removed outlier: 3.748A pdb=" N LEU E 297 " --> pdb=" O ILE E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 325 removed outlier: 4.509A pdb=" N LYS E 320 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ALA E 321 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU E 322 " --> pdb=" O CYS E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 391 Processing helix chain 'E' and resid 418 through 422 Processing helix chain 'E' and resid 423 through 432 removed outlier: 3.864A pdb=" N LYS E 430 " --> pdb=" O CYS E 426 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE E 432 " --> pdb=" O LEU E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 456 removed outlier: 4.497A pdb=" N VAL E 449 " --> pdb=" O PRO E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 494 Processing helix chain 'E' and resid 494 through 500 Processing helix chain 'E' and resid 505 through 509 removed outlier: 4.422A pdb=" N LYS E 508 " --> pdb=" O ALA E 505 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA E 509 " --> pdb=" O TRP E 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 505 through 509' Processing helix chain 'E' and resid 515 through 526 Processing helix chain 'E' and resid 560 through 565 removed outlier: 4.014A pdb=" N ALA E 564 " --> pdb=" O ARG E 560 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 5.374A pdb=" N TYR A 69 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 114 " --> pdb=" O LYS A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.687A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 355 removed outlier: 3.551A pdb=" N ILE A 333 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 9.675A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 355 removed outlier: 3.551A pdb=" N ILE A 333 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.970A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA8, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AA9, first strand: chain 'A' and resid 816 through 822 Processing sheet with id=AB1, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.344A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU D 189 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 15 through 16 Processing sheet with id=AB3, first strand: chain 'F' and resid 64 through 65 Processing sheet with id=AB4, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AB5, first strand: chain 'F' and resid 152 through 154 Processing sheet with id=AB6, first strand: chain 'F' and resid 186 through 187 Processing sheet with id=AB7, first strand: chain 'F' and resid 200 through 202 Processing sheet with id=AB8, first strand: chain 'F' and resid 304 through 305 removed outlier: 5.091A pdb=" N VAL F 305 " --> pdb=" O VAL F 372 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 330 through 331 removed outlier: 3.532A pdb=" N SER F 331 " --> pdb=" O TYR F 355 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 472 through 473 Processing sheet with id=AC2, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AC3, first strand: chain 'E' and resid 24 through 25 removed outlier: 4.432A pdb=" N LEU E 14 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 69 through 71 Processing sheet with id=AC5, first strand: chain 'E' and resid 152 through 154 removed outlier: 3.672A pdb=" N PHE E 225 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 182 through 187 removed outlier: 6.958A pdb=" N PHE E 182 " --> pdb=" O GLU E 197 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLU E 197 " --> pdb=" O PHE E 182 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLY E 184 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE E 195 " --> pdb=" O GLY E 184 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 330 through 332 removed outlier: 6.593A pdb=" N SER E 331 " --> pdb=" O PHE E 357 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL E 356 " --> pdb=" O ILE E 304 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL E 305 " --> pdb=" O VAL E 372 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 481 through 482 removed outlier: 3.854A pdb=" N THR E 481 " --> pdb=" O ILE E 488 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 511 through 512 removed outlier: 6.087A pdb=" N PHE E 511 " --> pdb=" O GLN E 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'E' and resid 544 through 546 removed outlier: 3.552A pdb=" N LEU E 573 " --> pdb=" O VAL E 544 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 16 through 17 removed outlier: 3.737A pdb=" N ALA G 54 " --> pdb=" O THR G 67 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE G 56 " --> pdb=" O ILE G 65 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE G 65 " --> pdb=" O PHE G 56 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 29 through 31 removed outlier: 3.535A pdb=" N SER G 46 " --> pdb=" O TYR G 87 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS G 86 " --> pdb=" O PHE G 75 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE G 75 " --> pdb=" O LYS G 86 " (cutoff:3.500A) 799 hydrogen bonds defined for protein. 2226 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 4.75 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.45 - 0.72: 1 0.72 - 1.00: 0 1.00 - 1.27: 3471 1.27 - 1.54: 18641 1.54 - 1.82: 414 Warning: very small bond lengths. Bond restraints: 22527 Sorted by residual: bond pdb=" CG PRO F 491 " pdb=" CD PRO F 491 " ideal model delta sigma weight residual 1.503 0.448 1.055 3.40e-02 8.65e+02 9.63e+02 bond pdb=" N PRO F 491 " pdb=" CD PRO F 491 " ideal model delta sigma weight residual 1.473 1.632 -0.159 1.40e-02 5.10e+03 1.29e+02 bond pdb=" CG PRO E 364 " pdb=" CD PRO E 364 " ideal model delta sigma weight residual 1.503 1.264 0.239 3.40e-02 8.65e+02 4.94e+01 bond pdb=" N PRO E 364 " pdb=" CD PRO E 364 " ideal model delta sigma weight residual 1.473 1.569 -0.096 1.40e-02 5.10e+03 4.66e+01 bond pdb=" N ALA G 15 " pdb=" CA ALA G 15 " ideal model delta sigma weight residual 1.458 1.541 -0.083 1.27e-02 6.20e+03 4.32e+01 ... (remaining 22522 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.85: 30820 6.85 - 13.71: 47 13.71 - 20.56: 6 20.56 - 27.41: 4 27.41 - 34.27: 2 Bond angle restraints: 30879 Sorted by residual: angle pdb=" N PRO F 491 " pdb=" CD PRO F 491 " pdb=" CG PRO F 491 " ideal model delta sigma weight residual 103.20 68.93 34.27 1.50e+00 4.44e-01 5.22e+02 angle pdb=" CA PRO E 364 " pdb=" N PRO E 364 " pdb=" CD PRO E 364 " ideal model delta sigma weight residual 112.00 89.87 22.13 1.40e+00 5.10e-01 2.50e+02 angle pdb=" CA PRO F 491 " pdb=" N PRO F 491 " pdb=" CD PRO F 491 " ideal model delta sigma weight residual 112.00 90.72 21.28 1.40e+00 5.10e-01 2.31e+02 angle pdb=" N TYR G 32 " pdb=" CA TYR G 32 " pdb=" C TYR G 32 " ideal model delta sigma weight residual 110.80 138.73 -27.93 2.13e+00 2.20e-01 1.72e+02 angle pdb=" CA PRO F 491 " pdb=" CB PRO F 491 " pdb=" CG PRO F 491 " ideal model delta sigma weight residual 104.50 80.58 23.92 1.90e+00 2.77e-01 1.58e+02 ... (remaining 30874 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.29: 12705 33.29 - 66.58: 642 66.58 - 99.87: 21 99.87 - 133.16: 0 133.16 - 166.45: 2 Dihedral angle restraints: 13370 sinusoidal: 5476 harmonic: 7894 Sorted by residual: dihedral pdb=" N CYS G 14 " pdb=" C CYS G 14 " pdb=" CA CYS G 14 " pdb=" CB CYS G 14 " ideal model delta harmonic sigma weight residual 122.80 159.42 -36.62 0 2.50e+00 1.60e-01 2.15e+02 dihedral pdb=" C CYS G 14 " pdb=" N CYS G 14 " pdb=" CA CYS G 14 " pdb=" CB CYS G 14 " ideal model delta harmonic sigma weight residual -122.60 -158.49 35.89 0 2.50e+00 1.60e-01 2.06e+02 dihedral pdb=" N TYR G 32 " pdb=" C TYR G 32 " pdb=" CA TYR G 32 " pdb=" CB TYR G 32 " ideal model delta harmonic sigma weight residual 122.80 147.41 -24.61 0 2.50e+00 1.60e-01 9.69e+01 ... (remaining 13367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.321: 3575 0.321 - 0.642: 2 0.642 - 0.963: 0 0.963 - 1.284: 2 1.284 - 1.605: 2 Chirality restraints: 3581 Sorted by residual: chirality pdb=" CA CYS G 14 " pdb=" N CYS G 14 " pdb=" C CYS G 14 " pdb=" CB CYS G 14 " both_signs ideal model delta sigma weight residual False 2.51 0.91 1.61 2.00e-01 2.50e+01 6.44e+01 chirality pdb=" CA TYR G 32 " pdb=" N TYR G 32 " pdb=" C TYR G 32 " pdb=" CB TYR G 32 " both_signs ideal model delta sigma weight residual False 2.51 1.18 1.33 2.00e-01 2.50e+01 4.42e+01 chirality pdb=" CA GLN G 11 " pdb=" N GLN G 11 " pdb=" C GLN G 11 " pdb=" CB GLN G 11 " both_signs ideal model delta sigma weight residual False 2.51 1.49 1.02 2.00e-01 2.50e+01 2.60e+01 ... (remaining 3578 not shown) Planarity restraints: 3748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 72 " -0.030 2.00e-02 2.50e+03 5.97e-02 3.57e+01 pdb=" C VAL A 72 " 0.103 2.00e-02 2.50e+03 pdb=" O VAL A 72 " -0.039 2.00e-02 2.50e+03 pdb=" N LYS A 73 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 363 " 0.106 5.00e-02 4.00e+02 1.40e-01 3.15e+01 pdb=" N PRO E 364 " -0.241 5.00e-02 4.00e+02 pdb=" CA PRO E 364 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO E 364 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 490 " 0.092 5.00e-02 4.00e+02 1.20e-01 2.31e+01 pdb=" N PRO F 491 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO F 491 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO F 491 " 0.062 5.00e-02 4.00e+02 ... (remaining 3745 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 299 2.62 - 3.19: 18637 3.19 - 3.76: 34097 3.76 - 4.33: 46279 4.33 - 4.90: 74396 Nonbonded interactions: 173708 Sorted by model distance: nonbonded pdb=" O SER D 173 " pdb=" OG SER D 177 " model vdw 2.045 3.040 nonbonded pdb=" OD1 ASN F 381 " pdb=" OG SER F 424 " model vdw 2.140 3.040 nonbonded pdb=" O PRO E 77 " pdb=" OG SER E 80 " model vdw 2.141 3.040 nonbonded pdb=" N2 G I 12 " pdb=" O2 C J 48 " model vdw 2.148 2.496 nonbonded pdb=" O CYS E 471 " pdb=" OG1 THR E 588 " model vdw 2.171 3.040 ... (remaining 173703 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 6 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 192)) selection = (chain 'D' and (resid 6 through 21 or (resid 22 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 42 or (resid 43 and (name N or name CA or name C or na \ me O or name CB )) or resid 44 through 46 or (resid 47 and (name N or name CA or \ name C or name O or name CB )) or resid 48 through 192)) } ncs_group { reference = (chain 'E' and (resid 1 through 473 or resid 475 through 703)) selection = (chain 'F' and (resid 1 through 473 or resid 475 through 703)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.11 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.180 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: 0.550 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 28.570 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5170 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.055 22559 Z= 0.327 Angle : 0.952 34.266 30906 Z= 0.546 Chirality : 0.063 1.605 3581 Planarity : 0.006 0.140 3748 Dihedral : 17.821 166.450 8276 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.43 % Favored : 91.19 % Rotamer: Outliers : 5.14 % Allowed : 33.58 % Favored : 61.28 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.16), residues: 2650 helix: 0.34 (0.18), residues: 947 sheet: -1.60 (0.35), residues: 218 loop : -2.47 (0.15), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 303 TYR 0.022 0.001 TYR F 299 PHE 0.017 0.001 PHE F 437 TRP 0.037 0.002 TRP G 53 HIS 0.007 0.001 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00855 / 0.33 (22527) covalent geometry : angle 0.93982 / 0.55 (30879) hydrogen bonds : bond 0.18370 / 11.87 ( 842) hydrogen bonds : angle 6.41261 / 4.47 ( 2324) metal coordination : bond 0.01942 / 1.51 ( 32) metal coordination : angle 5.22093 / 2.92 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 476 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.5122 (tt0) cc_final: 0.4615 (tm-30) REVERT: A 73 LYS cc_start: 0.5142 (OUTLIER) cc_final: 0.4814 (pttp) REVERT: A 76 THR cc_start: 0.2705 (OUTLIER) cc_final: 0.1344 (m) REVERT: A 248 THR cc_start: 0.5941 (p) cc_final: 0.5736 (t) REVERT: A 548 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7936 (tt) REVERT: A 731 LEU cc_start: 0.4636 (OUTLIER) cc_final: 0.4251 (mt) REVERT: A 750 ARG cc_start: 0.6290 (mtp85) cc_final: 0.5789 (ttp-110) REVERT: A 857 GLU cc_start: 0.6351 (pm20) cc_final: 0.5877 (tp30) REVERT: B 58 LYS cc_start: 0.7337 (tppp) cc_final: 0.7127 (tppt) REVERT: B 148 THR cc_start: 0.5665 (p) cc_final: 0.5425 (t) REVERT: D 57 ARG cc_start: 0.5446 (mmt-90) cc_final: 0.5208 (ttp80) REVERT: D 60 GLU cc_start: 0.5644 (tm-30) cc_final: 0.5201 (mm-30) REVERT: D 182 TRP cc_start: 0.5387 (m100) cc_final: 0.4428 (m100) REVERT: F 14 LEU cc_start: 0.5261 (mt) cc_final: 0.4069 (tp) REVERT: F 133 PHE cc_start: 0.3553 (t80) cc_final: 0.3321 (t80) REVERT: F 194 GLN cc_start: 0.3459 (tm-30) cc_final: 0.3070 (tp-100) REVERT: F 396 TYR cc_start: 0.7297 (m-80) cc_final: 0.6932 (m-10) REVERT: F 419 PRO cc_start: 0.6605 (Cg_exo) cc_final: 0.6270 (Cg_endo) REVERT: F 430 LYS cc_start: 0.0919 (mtmm) cc_final: 0.0426 (mmtp) REVERT: F 576 MET cc_start: 0.2990 (mmt) cc_final: 0.2121 (mtp) REVERT: E 48 TYR cc_start: 0.5937 (m-10) cc_final: 0.5510 (m-10) REVERT: E 64 TYR cc_start: 0.6720 (m-80) cc_final: 0.6482 (m-80) REVERT: E 156 GLU cc_start: 0.2354 (pp20) cc_final: 0.1886 (mm-30) REVERT: E 175 PRO cc_start: 0.3467 (Cg_exo) cc_final: 0.2995 (Cg_endo) REVERT: E 180 TYR cc_start: 0.3908 (m-80) cc_final: 0.3699 (m-80) REVERT: E 183 THR cc_start: 0.6263 (OUTLIER) cc_final: 0.5962 (p) REVERT: E 263 SER cc_start: 0.5471 (m) cc_final: 0.5080 (p) REVERT: E 436 MET cc_start: 0.2753 (ttm) cc_final: 0.2447 (ttt) REVERT: E 460 LYS cc_start: 0.0426 (pttp) cc_final: 0.0054 (pttm) REVERT: E 572 ILE cc_start: 0.2184 (mp) cc_final: 0.1960 (mp) REVERT: E 579 ARG cc_start: 0.2913 (mmp80) cc_final: 0.2138 (mmm160) REVERT: G 33 ASN cc_start: 0.1922 (OUTLIER) cc_final: 0.1186 (t0) REVERT: G 36 LYS cc_start: 0.5719 (mppt) cc_final: 0.5078 (mppt) outliers start: 116 outliers final: 19 residues processed: 578 average time/residue: 0.1493 time to fit residues: 132.9332 Evaluate side-chains 287 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 262 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 102 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.0980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.0070 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.3980 chunk 111 optimal weight: 0.4980 overall best weight: 0.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS A 168 ASN A 752 HIS A 790 ASN B 100 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 GLN F 516 ASN ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 562 ASN G 27 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.232201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.204114 restraints weight = 76215.064| |-----------------------------------------------------------------------------| r_work (start): 0.4477 rms_B_bonded: 3.05 r_work: 0.3796 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3767 r_free = 0.3767 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3767 r_free = 0.3767 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 22559 Z= 0.161 Angle : 0.773 14.527 30906 Z= 0.390 Chirality : 0.045 0.371 3581 Planarity : 0.005 0.067 3748 Dihedral : 8.393 143.751 3573 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.43 % Favored : 91.30 % Rotamer: Outliers : 5.09 % Allowed : 29.94 % Favored : 64.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.16), residues: 2650 helix: 0.15 (0.17), residues: 964 sheet: -1.49 (0.32), residues: 256 loop : -2.36 (0.15), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 390 TYR 0.024 0.002 TYR G 89 PHE 0.026 0.002 PHE E 373 TRP 0.022 0.002 TRP B 182 HIS 0.010 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (22527) covalent geometry : angle 0.75749 / 0.39 (30879) hydrogen bonds : bond 0.05209 / 3.31 ( 842) hydrogen bonds : angle 5.20994 / 3.66 ( 2324) metal coordination : bond 0.02034 / 1.56 ( 32) metal coordination : angle 5.27870 / 3.54 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 310 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 600 ASN cc_start: 0.7771 (m-40) cc_final: 0.7523 (m110) REVERT: A 757 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7641 (mm) REVERT: B 61 LYS cc_start: 0.8335 (tmmt) cc_final: 0.7952 (tppt) REVERT: B 143 ASP cc_start: 0.4783 (p0) cc_final: 0.4216 (t0) REVERT: C 44 ASP cc_start: 0.7700 (p0) cc_final: 0.7470 (p0) REVERT: D 31 SER cc_start: 0.6850 (p) cc_final: 0.6404 (t) REVERT: D 60 GLU cc_start: 0.6250 (tm-30) cc_final: 0.5968 (mm-30) REVERT: F 61 THR cc_start: 0.5159 (OUTLIER) cc_final: 0.4953 (p) REVERT: F 297 LEU cc_start: 0.4829 (pp) cc_final: 0.4617 (tt) REVERT: F 531 GLN cc_start: -0.0794 (OUTLIER) cc_final: -0.1298 (mt0) REVERT: F 576 MET cc_start: 0.1738 (mmt) cc_final: 0.1265 (mtp) REVERT: E 183 THR cc_start: 0.5922 (m) cc_final: 0.5466 (p) REVERT: E 233 MET cc_start: 0.3037 (OUTLIER) cc_final: 0.1991 (tmm) REVERT: E 437 PHE cc_start: 0.5844 (OUTLIER) cc_final: 0.5318 (p90) REVERT: E 460 LYS cc_start: 0.0283 (pttp) cc_final: -0.0142 (pttm) REVERT: E 480 ILE cc_start: 0.0964 (OUTLIER) cc_final: -0.0115 (tp) REVERT: E 579 ARG cc_start: 0.2979 (mmp80) cc_final: 0.2331 (mmm160) REVERT: G 12 MET cc_start: 0.2456 (pmm) cc_final: 0.2145 (pmm) REVERT: G 94 LEU cc_start: 0.4669 (tt) cc_final: 0.4362 (tp) outliers start: 115 outliers final: 36 residues processed: 407 average time/residue: 0.1427 time to fit residues: 90.2438 Evaluate side-chains 275 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 233 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 480 ILE Chi-restraints excluded: chain G residue 73 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 264 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 chunk 150 optimal weight: 5.9990 chunk 103 optimal weight: 0.0370 chunk 255 optimal weight: 0.8980 chunk 136 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 HIS A 297 ASN A 309 HIS A 381 HIS A 698 GLN A 752 HIS ** A 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN E 51 ASN E 275 GLN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 562 ASN G 11 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.218188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.180267 restraints weight = 69878.606| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 3.48 r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4248 r_free = 0.4248 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4248 r_free = 0.4248 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.6589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 22559 Z= 0.216 Angle : 0.846 14.243 30906 Z= 0.431 Chirality : 0.049 0.289 3581 Planarity : 0.006 0.055 3748 Dihedral : 7.973 131.168 3546 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.40 % Favored : 91.38 % Rotamer: Outliers : 4.70 % Allowed : 29.63 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.08 (0.16), residues: 2650 helix: -0.16 (0.16), residues: 996 sheet: -1.20 (0.36), residues: 219 loop : -2.40 (0.15), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 390 TYR 0.035 0.002 TYR F 396 PHE 0.040 0.002 PHE E 422 TRP 0.017 0.002 TRP A 216 HIS 0.012 0.002 HIS E 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.22 (22527) covalent geometry : angle 0.83434 / 0.43 (30879) hydrogen bonds : bond 0.06485 / 4.13 ( 842) hydrogen bonds : angle 5.24881 / 3.66 ( 2324) metal coordination : bond 0.01865 / 1.37 ( 32) metal coordination : angle 4.79718 / 3.21 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 290 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 768 SER cc_start: 0.8255 (OUTLIER) cc_final: 0.7852 (p) REVERT: A 854 LEU cc_start: 0.8184 (tt) cc_final: 0.7735 (mt) REVERT: A 883 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8128 (tp) REVERT: B 148 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8203 (t) REVERT: B 156 ILE cc_start: 0.8682 (mt) cc_final: 0.8432 (mp) REVERT: C 51 LYS cc_start: 0.8644 (mttm) cc_final: 0.8402 (mttt) REVERT: D 182 TRP cc_start: 0.4699 (OUTLIER) cc_final: 0.4333 (m100) REVERT: F 192 LYS cc_start: 0.0989 (OUTLIER) cc_final: 0.0766 (ptpt) REVERT: F 378 MET cc_start: 0.0777 (mpp) cc_final: -0.1659 (mmt) REVERT: F 531 GLN cc_start: 0.0042 (OUTLIER) cc_final: -0.0667 (mt0) REVERT: F 551 GLU cc_start: -0.0225 (pt0) cc_final: -0.0656 (mm-30) REVERT: F 554 HIS cc_start: -0.0850 (OUTLIER) cc_final: -0.1500 (m-70) REVERT: E 233 MET cc_start: 0.3212 (OUTLIER) cc_final: 0.2245 (mtt) REVERT: E 432 ILE cc_start: 0.2977 (OUTLIER) cc_final: 0.2449 (pt) REVERT: E 460 LYS cc_start: 0.0991 (pttp) cc_final: 0.0183 (pttm) REVERT: E 579 ARG cc_start: 0.3565 (mmp80) cc_final: 0.3300 (mmp-170) outliers start: 106 outliers final: 49 residues processed: 376 average time/residue: 0.1318 time to fit residues: 78.2781 Evaluate side-chains 274 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 216 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 432 ILE Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 105 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 240 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 236 optimal weight: 30.0000 chunk 70 optimal weight: 0.5980 chunk 137 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 237 optimal weight: 0.0870 chunk 261 optimal weight: 6.9990 chunk 242 optimal weight: 7.9990 chunk 220 optimal weight: 9.9990 overall best weight: 3.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 HIS A 158 ASN A 168 ASN A 611 ASN ** A 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 GLN B 88 GLN B 109 ASN B 157 GLN C 63 GLN D 43 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 GLN ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 ASN E 586 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.203218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.152738 restraints weight = 67531.735| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 4.28 r_work: 0.3014 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.8588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.090 22559 Z= 0.362 Angle : 0.904 17.871 30906 Z= 0.463 Chirality : 0.052 0.302 3581 Planarity : 0.006 0.059 3748 Dihedral : 8.034 134.756 3545 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.27 % Favored : 90.51 % Rotamer: Outliers : 4.78 % Allowed : 29.94 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.15), residues: 2650 helix: -0.35 (0.16), residues: 983 sheet: -1.58 (0.33), residues: 247 loop : -2.51 (0.15), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 427 TYR 0.029 0.003 TYR A 674 PHE 0.028 0.003 PHE E 422 TRP 0.020 0.003 TRP A 290 HIS 0.014 0.002 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00854 / 0.36 (22527) covalent geometry : angle 0.88947 / 0.46 (30879) hydrogen bonds : bond 0.07554 / 4.86 ( 842) hydrogen bonds : angle 5.15830 / 3.60 ( 2324) metal coordination : bond 0.02550 / 1.84 ( 32) metal coordination : angle 5.52763 / 3.41 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 236 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8415 (ttp-170) REVERT: A 197 ARG cc_start: 0.8606 (ttp-170) cc_final: 0.8196 (ttm-80) REVERT: A 477 ASP cc_start: 0.8524 (t70) cc_final: 0.8266 (t0) REVERT: A 623 ASP cc_start: 0.8858 (p0) cc_final: 0.8522 (p0) REVERT: A 750 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8576 (ttm110) REVERT: A 755 MET cc_start: 0.9379 (mtt) cc_final: 0.9105 (mtt) REVERT: A 768 SER cc_start: 0.8892 (OUTLIER) cc_final: 0.8567 (p) REVERT: A 883 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8723 (tp) REVERT: A 902 MET cc_start: 0.5674 (pmm) cc_final: 0.5413 (pmm) REVERT: B 109 ASN cc_start: 0.8138 (OUTLIER) cc_final: 0.7697 (t0) REVERT: B 127 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8603 (ttpt) REVERT: B 158 GLN cc_start: 0.8411 (tp40) cc_final: 0.8070 (tt0) REVERT: C 19 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7717 (mt0) REVERT: D 87 MET cc_start: 0.8632 (tpp) cc_final: 0.8400 (mmt) REVERT: D 165 LYS cc_start: 0.7061 (mtmm) cc_final: 0.6829 (ptpt) REVERT: F 414 LYS cc_start: 0.3103 (OUTLIER) cc_final: 0.2334 (pttp) REVERT: F 508 LYS cc_start: 0.3459 (OUTLIER) cc_final: 0.3103 (pttt) REVERT: F 531 GLN cc_start: -0.0234 (OUTLIER) cc_final: -0.0636 (mt0) REVERT: F 554 HIS cc_start: -0.0590 (OUTLIER) cc_final: -0.1290 (m90) REVERT: E 233 MET cc_start: 0.4621 (OUTLIER) cc_final: 0.3548 (mtt) REVERT: E 290 HIS cc_start: 0.3784 (m-70) cc_final: 0.3488 (m170) REVERT: E 485 SER cc_start: 0.0587 (OUTLIER) cc_final: 0.0289 (t) REVERT: E 579 ARG cc_start: 0.3148 (mmp80) cc_final: 0.2407 (mmp-170) outliers start: 108 outliers final: 54 residues processed: 320 average time/residue: 0.1405 time to fit residues: 69.7807 Evaluate side-chains 263 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 197 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 398 TYR Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 508 LYS Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 102 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 163 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 179 optimal weight: 3.9990 chunk 143 optimal weight: 20.0000 chunk 199 optimal weight: 1.9990 chunk 263 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 231 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN A 297 ASN ** A 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.205955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.141745 restraints weight = 62827.360| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 4.73 r_work: 0.3044 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.8799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 22559 Z= 0.141 Angle : 0.682 16.466 30906 Z= 0.346 Chirality : 0.043 0.258 3581 Planarity : 0.004 0.049 3748 Dihedral : 7.414 124.479 3544 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.26 % Favored : 92.51 % Rotamer: Outliers : 3.20 % Allowed : 30.86 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.93 (0.16), residues: 2650 helix: 0.04 (0.17), residues: 995 sheet: -1.37 (0.33), residues: 252 loop : -2.33 (0.15), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 490 TYR 0.025 0.001 TYR F 31 PHE 0.020 0.002 PHE E 373 TRP 0.018 0.001 TRP B 182 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (22527) covalent geometry : angle 0.66779 / 0.35 (30879) hydrogen bonds : bond 0.05373 / 3.43 ( 842) hydrogen bonds : angle 4.77312 / 3.35 ( 2324) metal coordination : bond 0.01613 / 1.23 ( 32) metal coordination : angle 4.69773 / 2.86 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 219 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: 0.7656 (OUTLIER) cc_final: 0.7338 (p) REVERT: A 197 ARG cc_start: 0.8309 (ttp-170) cc_final: 0.7654 (ttm-80) REVERT: A 497 ASN cc_start: 0.8532 (t0) cc_final: 0.8199 (t0) REVERT: A 794 MET cc_start: 0.9017 (ttp) cc_final: 0.8694 (ttt) REVERT: A 902 MET cc_start: 0.5406 (pmm) cc_final: 0.5193 (pmm) REVERT: A 906 MET cc_start: 0.5171 (ppp) cc_final: 0.4965 (ppp) REVERT: B 67 MET cc_start: 0.7877 (tpt) cc_final: 0.7499 (tpt) REVERT: B 158 GLN cc_start: 0.8285 (tp40) cc_final: 0.7629 (tt0) REVERT: D 65 GLN cc_start: 0.6928 (tm-30) cc_final: 0.5966 (mm110) REVERT: D 182 TRP cc_start: 0.6686 (m100) cc_final: 0.6052 (m100) REVERT: F 414 LYS cc_start: 0.3284 (OUTLIER) cc_final: 0.3061 (pttp) REVERT: F 508 LYS cc_start: 0.3619 (OUTLIER) cc_final: 0.3344 (pttt) REVERT: F 531 GLN cc_start: 0.0017 (OUTLIER) cc_final: -0.0304 (mt0) REVERT: F 554 HIS cc_start: -0.0489 (OUTLIER) cc_final: -0.1226 (m-70) REVERT: E 233 MET cc_start: 0.4381 (OUTLIER) cc_final: 0.3437 (mtt) REVERT: E 290 HIS cc_start: 0.3257 (m-70) cc_final: 0.3053 (m170) REVERT: E 432 ILE cc_start: 0.4873 (OUTLIER) cc_final: 0.4608 (pt) REVERT: E 579 ARG cc_start: 0.3300 (mmp80) cc_final: 0.2599 (mmp-170) outliers start: 72 outliers final: 45 residues processed: 273 average time/residue: 0.1525 time to fit residues: 64.5534 Evaluate side-chains 251 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 199 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 398 TYR Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 508 LYS Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 432 ILE Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 23 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 215 optimal weight: 0.3980 chunk 263 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 196 optimal weight: 30.0000 chunk 64 optimal weight: 6.9990 chunk 225 optimal weight: 30.0000 chunk 42 optimal weight: 1.9990 chunk 204 optimal weight: 4.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 822 GLN ** A 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 459 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.202714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.139156 restraints weight = 66668.355| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 5.20 r_work: 0.2966 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.9318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 22559 Z= 0.209 Angle : 0.738 17.759 30906 Z= 0.374 Chirality : 0.046 0.291 3581 Planarity : 0.005 0.051 3748 Dihedral : 7.176 78.495 3544 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.36 % Favored : 91.41 % Rotamer: Outliers : 4.04 % Allowed : 29.85 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.16), residues: 2650 helix: 0.15 (0.17), residues: 986 sheet: -1.47 (0.33), residues: 245 loop : -2.36 (0.15), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 18 TYR 0.026 0.002 TYR F 31 PHE 0.030 0.002 PHE F 472 TRP 0.016 0.002 TRP A 916 HIS 0.011 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.21 (22527) covalent geometry : angle 0.72105 / 0.37 (30879) hydrogen bonds : bond 0.06275 / 4.03 ( 842) hydrogen bonds : angle 4.72872 / 3.32 ( 2324) metal coordination : bond 0.02082 / 1.53 ( 32) metal coordination : angle 5.31455 / 3.25 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 205 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: 0.7731 (OUTLIER) cc_final: 0.7353 (p) REVERT: A 221 ASP cc_start: 0.8588 (t0) cc_final: 0.8147 (t0) REVERT: A 336 ASP cc_start: 0.7892 (t0) cc_final: 0.7650 (t0) REVERT: A 350 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7650 (mt-10) REVERT: A 477 ASP cc_start: 0.8457 (t0) cc_final: 0.8212 (t0) REVERT: A 898 HIS cc_start: 0.7078 (t-90) cc_final: 0.6727 (t-90) REVERT: B 67 MET cc_start: 0.7969 (tpt) cc_final: 0.7551 (tpt) REVERT: B 69 GLN cc_start: 0.8750 (tp40) cc_final: 0.8397 (tp-100) REVERT: B 71 TYR cc_start: 0.8131 (t80) cc_final: 0.7764 (t80) REVERT: B 171 GLU cc_start: 0.7546 (pt0) cc_final: 0.7176 (pt0) REVERT: D 65 GLN cc_start: 0.7027 (tm-30) cc_final: 0.6121 (mm110) REVERT: D 77 GLU cc_start: 0.8472 (tp30) cc_final: 0.7792 (mt-10) REVERT: D 155 GLU cc_start: 0.7918 (pp20) cc_final: 0.7630 (pp20) REVERT: F 192 LYS cc_start: 0.0370 (OUTLIER) cc_final: 0.0023 (ptmt) REVERT: F 324 TYR cc_start: 0.3933 (m-10) cc_final: 0.3136 (t80) REVERT: F 414 LYS cc_start: 0.3469 (ptpp) cc_final: 0.3132 (pttp) REVERT: F 508 LYS cc_start: 0.3619 (OUTLIER) cc_final: 0.3367 (pttt) REVERT: F 531 GLN cc_start: 0.0003 (OUTLIER) cc_final: -0.0326 (mt0) REVERT: F 545 ILE cc_start: 0.2296 (mm) cc_final: 0.1951 (mt) REVERT: F 554 HIS cc_start: -0.0315 (OUTLIER) cc_final: -0.0953 (m-70) REVERT: E 233 MET cc_start: 0.4816 (OUTLIER) cc_final: 0.3960 (mtt) REVERT: E 290 HIS cc_start: 0.3488 (m-70) cc_final: 0.3276 (m170) REVERT: E 579 ARG cc_start: 0.3404 (mmp80) cc_final: 0.2648 (mmp-170) REVERT: G 5 SER cc_start: 0.7236 (OUTLIER) cc_final: 0.6828 (p) outliers start: 91 outliers final: 54 residues processed: 271 average time/residue: 0.1391 time to fit residues: 58.6201 Evaluate side-chains 251 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 189 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 398 TYR Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 508 LYS Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 86 optimal weight: 0.6980 chunk 121 optimal weight: 8.9990 chunk 156 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 chunk 263 optimal weight: 0.8980 chunk 212 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 241 optimal weight: 7.9990 chunk 16 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 537 GLN E 586 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.206989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.161916 restraints weight = 64677.897| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 3.67 r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4086 r_free = 0.4086 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4086 r_free = 0.4086 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.9496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 22559 Z= 0.130 Angle : 0.645 16.158 30906 Z= 0.325 Chirality : 0.042 0.241 3581 Planarity : 0.004 0.075 3748 Dihedral : 6.656 66.079 3544 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.22 % Favored : 92.59 % Rotamer: Outliers : 3.12 % Allowed : 30.51 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.16), residues: 2650 helix: 0.34 (0.17), residues: 992 sheet: -1.40 (0.33), residues: 248 loop : -2.23 (0.15), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 96 TYR 0.029 0.001 TYR E 421 PHE 0.020 0.001 PHE E 373 TRP 0.022 0.002 TRP E 114 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (22527) covalent geometry : angle 0.63138 / 0.32 (30879) hydrogen bonds : bond 0.05027 / 3.20 ( 842) hydrogen bonds : angle 4.54994 / 3.20 ( 2324) metal coordination : bond 0.01418 / 1.08 ( 32) metal coordination : angle 4.56358 / 2.72 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 204 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 183 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8202 (ttp-110) REVERT: A 221 ASP cc_start: 0.7699 (t0) cc_final: 0.7423 (t0) REVERT: A 350 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6463 (mp0) REVERT: A 545 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8583 (mtmt) REVERT: B 57 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.6921 (mtm110) REVERT: B 67 MET cc_start: 0.7800 (tpt) cc_final: 0.7546 (tpt) REVERT: B 79 LYS cc_start: 0.8188 (ttpt) cc_final: 0.7982 (mtmt) REVERT: B 171 GLU cc_start: 0.7158 (pt0) cc_final: 0.6940 (pt0) REVERT: D 65 GLN cc_start: 0.6978 (tm-30) cc_final: 0.6675 (mm110) REVERT: F 192 LYS cc_start: 0.1237 (OUTLIER) cc_final: 0.0916 (ptmt) REVERT: F 531 GLN cc_start: 0.0358 (OUTLIER) cc_final: -0.0376 (mt0) REVERT: E 233 MET cc_start: 0.4343 (OUTLIER) cc_final: 0.3758 (mtt) REVERT: E 432 ILE cc_start: 0.3042 (OUTLIER) cc_final: 0.2266 (pt) REVERT: E 576 MET cc_start: 0.4099 (ppp) cc_final: 0.3864 (ppp) REVERT: E 579 ARG cc_start: 0.4062 (mmp80) cc_final: 0.3465 (mmp-170) outliers start: 70 outliers final: 44 residues processed: 252 average time/residue: 0.1557 time to fit residues: 60.5388 Evaluate side-chains 244 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 192 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 145 PHE Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 398 TYR Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 432 ILE Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 86 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 252 optimal weight: 30.0000 chunk 204 optimal weight: 0.0970 chunk 216 optimal weight: 6.9990 chunk 190 optimal weight: 10.0000 chunk 103 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 240 optimal weight: 7.9990 chunk 193 optimal weight: 6.9990 chunk 189 optimal weight: 20.0000 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 63 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN ** E 220 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 = 0.4535 r_free = 0.4535 target = 0.203050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.153385 restraints weight = 70787.671| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 10.51 r_work: 0.2970 rms_B_bonded: 5.95 restraints_weight: 2.0000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.9890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 22559 Z= 0.263 Angle : 0.762 18.991 30906 Z= 0.384 Chirality : 0.047 0.312 3581 Planarity : 0.006 0.189 3748 Dihedral : 6.870 66.237 3542 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.62 % Favored : 91.23 % Rotamer: Outliers : 3.56 % Allowed : 29.94 % Favored : 66.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.16), residues: 2650 helix: 0.08 (0.17), residues: 989 sheet: -1.45 (0.34), residues: 235 loop : -2.30 (0.15), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 96 TYR 0.056 0.002 TYR E 421 PHE 0.041 0.002 PHE E 422 TRP 0.015 0.002 TRP A 916 HIS 0.013 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.26 (22527) covalent geometry : angle 0.73968 / 0.38 (30879) hydrogen bonds : bond 0.06626 / 4.26 ( 842) hydrogen bonds : angle 4.73051 / 3.32 ( 2324) metal coordination : bond 0.02009 / 1.44 ( 32) metal coordination : angle 6.20113 / 3.77 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 187 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: A 221 ASP cc_start: 0.8689 (t0) cc_final: 0.8279 (t0) REVERT: A 258 ASP cc_start: 0.8506 (t70) cc_final: 0.8220 (t0) REVERT: A 336 ASP cc_start: 0.7932 (t0) cc_final: 0.7718 (t0) REVERT: A 350 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7938 (mt-10) REVERT: A 750 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8605 (ttm110) REVERT: A 794 MET cc_start: 0.9080 (ttp) cc_final: 0.8715 (ttt) REVERT: A 898 HIS cc_start: 0.7317 (t-90) cc_final: 0.7021 (t-90) REVERT: B 67 MET cc_start: 0.8344 (tpt) cc_final: 0.7938 (tpt) REVERT: B 71 TYR cc_start: 0.8318 (t80) cc_final: 0.7938 (t80) REVERT: B 171 GLU cc_start: 0.7853 (pt0) cc_final: 0.7540 (pt0) REVERT: D 65 GLN cc_start: 0.7136 (tm-30) cc_final: 0.6345 (mm110) REVERT: F 49 VAL cc_start: 0.7094 (p) cc_final: 0.6871 (m) REVERT: F 192 LYS cc_start: 0.0228 (OUTLIER) cc_final: -0.0116 (ptmt) REVERT: F 343 PHE cc_start: 0.2318 (t80) cc_final: 0.1899 (m-80) REVERT: F 531 GLN cc_start: 0.0177 (OUTLIER) cc_final: -0.0188 (mt0) REVERT: E 233 MET cc_start: 0.4916 (OUTLIER) cc_final: 0.4114 (mtt) REVERT: E 373 PHE cc_start: 0.6779 (t80) cc_final: 0.6155 (t80) REVERT: E 432 ILE cc_start: 0.4910 (OUTLIER) cc_final: 0.4513 (pt) REVERT: E 485 SER cc_start: 0.1105 (OUTLIER) cc_final: 0.0645 (t) REVERT: E 576 MET cc_start: 0.3027 (ppp) cc_final: 0.2136 (pmm) REVERT: E 579 ARG cc_start: 0.3554 (mmp80) cc_final: 0.2740 (mmp-170) outliers start: 80 outliers final: 55 residues processed: 247 average time/residue: 0.1506 time to fit residues: 58.6527 Evaluate side-chains 241 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 179 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 145 PHE Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 398 TYR Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 432 ILE Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 131 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 chunk 256 optimal weight: 0.0050 chunk 152 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 166 optimal weight: 9.9990 chunk 135 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 245 optimal weight: 9.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 109 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 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 = 0.4565 r_free = 0.4565 target = 0.206253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.159240 restraints weight = 57627.019| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 3.65 r_work: 0.3201 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 1.0002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22559 Z= 0.127 Angle : 0.650 16.190 30906 Z= 0.326 Chirality : 0.042 0.231 3581 Planarity : 0.005 0.141 3748 Dihedral : 6.516 67.676 3542 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.53 % Favored : 92.32 % Rotamer: Outliers : 2.99 % Allowed : 30.47 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.16), residues: 2650 helix: 0.45 (0.17), residues: 970 sheet: -1.29 (0.33), residues: 244 loop : -2.17 (0.15), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 96 TYR 0.037 0.001 TYR E 421 PHE 0.033 0.001 PHE E 422 TRP 0.020 0.002 TRP B 182 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (22527) covalent geometry : angle 0.63308 / 0.32 (30879) hydrogen bonds : bond 0.04961 / 3.15 ( 842) hydrogen bonds : angle 4.51461 / 3.18 ( 2324) metal coordination : bond 0.01418 / 1.08 ( 32) metal coordination : angle 5.09034 / 3.02 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 187 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8466 (mm-40) cc_final: 0.8222 (mt0) REVERT: A 221 ASP cc_start: 0.8182 (t0) cc_final: 0.7860 (t0) REVERT: A 350 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7387 (mt-10) REVERT: A 794 MET cc_start: 0.8783 (ttp) cc_final: 0.8432 (ttt) REVERT: B 57 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7271 (mtm110) REVERT: B 67 MET cc_start: 0.8284 (tpt) cc_final: 0.7964 (tpt) REVERT: B 139 LYS cc_start: 0.8854 (ttpp) cc_final: 0.8531 (tttt) REVERT: B 171 GLU cc_start: 0.7680 (pt0) cc_final: 0.7441 (pt0) REVERT: D 65 GLN cc_start: 0.7043 (tm-30) cc_final: 0.6210 (mm110) REVERT: F 68 MET cc_start: 0.6676 (mmt) cc_final: 0.4312 (mtp) REVERT: F 192 LYS cc_start: 0.0357 (OUTLIER) cc_final: -0.0126 (ptmt) REVERT: F 270 GLN cc_start: 0.5494 (tp-100) cc_final: 0.4851 (mm110) REVERT: F 531 GLN cc_start: -0.0055 (OUTLIER) cc_final: -0.0498 (mt0) REVERT: E 233 MET cc_start: 0.4919 (OUTLIER) cc_final: 0.4116 (mtt) REVERT: E 373 PHE cc_start: 0.6604 (t80) cc_final: 0.5983 (t80) REVERT: E 432 ILE cc_start: 0.4563 (OUTLIER) cc_final: 0.3998 (pt) REVERT: E 576 MET cc_start: 0.3535 (ppp) cc_final: 0.2509 (pmm) REVERT: E 579 ARG cc_start: 0.3559 (mmp80) cc_final: 0.2777 (mmp-170) REVERT: G 86 LYS cc_start: 0.2106 (OUTLIER) cc_final: 0.1134 (mptt) outliers start: 67 outliers final: 51 residues processed: 236 average time/residue: 0.1570 time to fit residues: 57.6903 Evaluate side-chains 233 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 175 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 922 GLU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 145 PHE Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 398 TYR Chi-restraints excluded: chain F residue 430 LYS Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 432 ILE Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 86 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 89 optimal weight: 3.9990 chunk 203 optimal weight: 0.0970 chunk 265 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 80 optimal weight: 0.0170 chunk 130 optimal weight: 3.9990 chunk 140 optimal weight: 8.9990 chunk 173 optimal weight: 0.9990 chunk 197 optimal weight: 7.9990 chunk 260 optimal weight: 9.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 408 GLN B 109 ASN D 73 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN E 381 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.207067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.158538 restraints weight = 70388.372| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 10.97 r_work: 0.3047 rms_B_bonded: 6.01 restraints_weight: 2.0000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 1.0106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 22559 Z= 0.120 Angle : 0.640 14.651 30906 Z= 0.322 Chirality : 0.042 0.217 3581 Planarity : 0.005 0.122 3748 Dihedral : 6.375 67.370 3542 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.11 % Favored : 92.78 % Rotamer: Outliers : 2.63 % Allowed : 30.60 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.16), residues: 2650 helix: 0.63 (0.17), residues: 975 sheet: -1.21 (0.33), residues: 233 loop : -2.15 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 96 TYR 0.066 0.001 TYR E 421 PHE 0.017 0.001 PHE E 422 TRP 0.025 0.001 TRP B 182 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (22527) covalent geometry : angle 0.62456 / 0.32 (30879) hydrogen bonds : bond 0.04775 / 3.01 ( 842) hydrogen bonds : angle 4.44240 / 3.13 ( 2324) metal coordination : bond 0.01423 / 1.12 ( 32) metal coordination : angle 4.69305 / 2.81 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 197 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8246 (mt0) REVERT: A 221 ASP cc_start: 0.8484 (t0) cc_final: 0.8081 (t0) REVERT: A 336 ASP cc_start: 0.7610 (t0) cc_final: 0.7409 (t0) REVERT: A 350 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7693 (mt-10) REVERT: A 626 MET cc_start: 0.8671 (ptm) cc_final: 0.8170 (ttp) REVERT: A 794 MET cc_start: 0.8971 (ttp) cc_final: 0.8643 (ttt) REVERT: B 57 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.6999 (mtm110) REVERT: B 67 MET cc_start: 0.8256 (tpt) cc_final: 0.7967 (tpt) REVERT: B 171 GLU cc_start: 0.7781 (pt0) cc_final: 0.7462 (pt0) REVERT: D 65 GLN cc_start: 0.7043 (tm-30) cc_final: 0.6070 (mm110) REVERT: D 94 MET cc_start: 0.8826 (mtp) cc_final: 0.8591 (mtp) REVERT: D 101 ASP cc_start: 0.8071 (p0) cc_final: 0.7447 (t0) REVERT: F 68 MET cc_start: 0.6717 (mmt) cc_final: 0.4306 (mtp) REVERT: F 192 LYS cc_start: -0.0028 (OUTLIER) cc_final: -0.0393 (ptmt) REVERT: F 270 GLN cc_start: 0.5265 (tp-100) cc_final: 0.4856 (mm110) REVERT: F 349 ASN cc_start: 0.5540 (m-40) cc_final: 0.5153 (p0) REVERT: F 531 GLN cc_start: 0.0165 (OUTLIER) cc_final: -0.0191 (mt0) REVERT: E 51 ASN cc_start: 0.7091 (OUTLIER) cc_final: 0.6744 (m-40) REVERT: E 164 HIS cc_start: 0.6163 (m-70) cc_final: 0.5453 (p-80) REVERT: E 233 MET cc_start: 0.4785 (OUTLIER) cc_final: 0.4124 (mtp) REVERT: E 432 ILE cc_start: 0.5040 (OUTLIER) cc_final: 0.4689 (pt) REVERT: E 576 MET cc_start: 0.3151 (ppp) cc_final: 0.2339 (pmm) REVERT: E 579 ARG cc_start: 0.3400 (mmp80) cc_final: 0.2649 (mmp-170) REVERT: G 86 LYS cc_start: 0.2055 (OUTLIER) cc_final: 0.1119 (mptt) outliers start: 59 outliers final: 44 residues processed: 243 average time/residue: 0.1552 time to fit residues: 59.0771 Evaluate side-chains 234 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 182 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 922 GLU Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 145 PHE Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 398 TYR Chi-restraints excluded: chain F residue 430 LYS Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 432 ILE Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 86 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 130 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 163 optimal weight: 0.7980 chunk 250 optimal weight: 10.0000 chunk 3 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 181 optimal weight: 0.1980 chunk 55 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 408 GLN A 497 ASN B 109 ASN ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 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 = 0.4572 r_free = 0.4572 target = 0.206931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.159990 restraints weight = 54775.942| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 3.67 r_work: 0.3209 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 1.0117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 22559 Z= 0.168 Angle : 1.074 59.200 30906 Z= 0.582 Chirality : 0.043 0.400 3581 Planarity : 0.005 0.124 3748 Dihedral : 6.400 67.368 3542 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.22 % Favored : 92.66 % Rotamer: Outliers : 2.41 % Allowed : 31.08 % Favored : 66.51 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.16), residues: 2650 helix: 0.63 (0.17), residues: 975 sheet: -1.21 (0.33), residues: 233 loop : -2.13 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 96 TYR 0.060 0.001 TYR E 421 PHE 0.016 0.001 PHE E 422 TRP 0.023 0.001 TRP B 182 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.17 (22527) covalent geometry : angle 0.98101 / 0.58 (30879) hydrogen bonds : bond 0.04799 / 3.03 ( 842) hydrogen bonds : angle 4.45928 / 3.14 ( 2324) metal coordination : bond 0.02310 / 1.62 ( 32) metal coordination : angle 14.83356 / 8.27 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6838.89 seconds wall clock time: 117 minutes 44.24 seconds (7064.24 seconds total)