Starting phenix.real_space_refine on Sun Aug 24 19:21:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gwi_34313/08_2025/8gwi_34313.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gwi_34313/08_2025/8gwi_34313.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gwi_34313/08_2025/8gwi_34313.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gwi_34313/08_2025/8gwi_34313.map" model { file = "/net/cci-nas-00/data/ceres_data/8gwi_34313/08_2025/8gwi_34313.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gwi_34313/08_2025/8gwi_34313.cif" } 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-2.0-5787/lib/python3.9/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: 7.14, per 1000 atoms: 0.33 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: 2.05 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 19 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 16 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 29 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 5 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 26 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 55 " pdb=" ZN F 701 " pdb="ZN ZN F 701 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F 701 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 19 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 16 " pdb=" ZN F 702 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 8 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 26 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 5 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 29 " pdb=" ZN F 703 " pdb="ZN ZN F 703 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 72 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 55 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 50 " Number of angles added : 27 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5094 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 30 sheets defined 39.9% alpha, 10.3% beta 21 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 2.92 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: 4.55 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.45 - 0.72: 1 0.72 - 1.00: 0 1.00 - 1.27: 3471 1.27 - 1.54: 18641 1.54 - 1.82: 414 Warning: very small bond lengths. Bond restraints: 22527 Sorted by residual: bond pdb=" CG PRO F 491 " pdb=" CD PRO F 491 " ideal model delta sigma weight residual 1.503 0.448 1.055 3.40e-02 8.65e+02 9.63e+02 bond pdb=" N PRO F 491 " pdb=" CD PRO F 491 " ideal model delta sigma weight residual 1.473 1.632 -0.159 1.40e-02 5.10e+03 1.29e+02 bond pdb=" CG PRO E 364 " pdb=" CD PRO E 364 " ideal model delta sigma weight residual 1.503 1.264 0.239 3.40e-02 8.65e+02 4.94e+01 bond pdb=" N PRO E 364 " pdb=" CD PRO E 364 " ideal model delta sigma weight residual 1.473 1.569 -0.096 1.40e-02 5.10e+03 4.66e+01 bond pdb=" N ALA G 15 " pdb=" CA ALA G 15 " ideal model delta sigma weight residual 1.458 1.541 -0.083 1.27e-02 6.20e+03 4.32e+01 ... (remaining 22522 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.85: 30820 6.85 - 13.71: 47 13.71 - 20.56: 6 20.56 - 27.41: 4 27.41 - 34.27: 2 Bond angle restraints: 30879 Sorted by residual: angle pdb=" N PRO F 491 " pdb=" CD PRO F 491 " pdb=" CG PRO F 491 " ideal model delta sigma weight residual 103.20 68.93 34.27 1.50e+00 4.44e-01 5.22e+02 angle pdb=" CA PRO E 364 " pdb=" N PRO E 364 " pdb=" CD PRO E 364 " ideal model delta sigma weight residual 112.00 89.87 22.13 1.40e+00 5.10e-01 2.50e+02 angle pdb=" CA PRO F 491 " pdb=" N PRO F 491 " pdb=" CD PRO F 491 " ideal model delta sigma weight residual 112.00 90.72 21.28 1.40e+00 5.10e-01 2.31e+02 angle pdb=" N TYR G 32 " pdb=" CA TYR G 32 " pdb=" C TYR G 32 " ideal model delta sigma weight residual 110.80 138.73 -27.93 2.13e+00 2.20e-01 1.72e+02 angle pdb=" CA PRO F 491 " pdb=" CB PRO F 491 " pdb=" CG PRO F 491 " ideal model delta sigma weight residual 104.50 80.58 23.92 1.90e+00 2.77e-01 1.58e+02 ... (remaining 30874 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.29: 12788 33.29 - 66.58: 741 66.58 - 99.87: 35 99.87 - 133.16: 0 133.16 - 166.45: 2 Dihedral angle restraints: 13566 sinusoidal: 5672 harmonic: 7894 Sorted by residual: dihedral pdb=" N CYS G 14 " pdb=" C CYS G 14 " pdb=" CA CYS G 14 " pdb=" CB CYS G 14 " ideal model delta harmonic sigma weight residual 122.80 159.42 -36.62 0 2.50e+00 1.60e-01 2.15e+02 dihedral pdb=" C CYS G 14 " pdb=" N CYS G 14 " pdb=" CA CYS G 14 " pdb=" CB CYS G 14 " ideal model delta harmonic sigma weight residual -122.60 -158.49 35.89 0 2.50e+00 1.60e-01 2.06e+02 dihedral pdb=" N TYR G 32 " pdb=" C TYR G 32 " pdb=" CA TYR G 32 " pdb=" CB TYR G 32 " ideal model delta harmonic sigma weight residual 122.80 147.41 -24.61 0 2.50e+00 1.60e-01 9.69e+01 ... (remaining 13563 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.321: 3575 0.321 - 0.642: 2 0.642 - 0.963: 0 0.963 - 1.284: 2 1.284 - 1.605: 2 Chirality restraints: 3581 Sorted by residual: chirality pdb=" CA CYS G 14 " pdb=" N CYS G 14 " pdb=" C CYS G 14 " pdb=" CB CYS G 14 " both_signs ideal model delta sigma weight residual False 2.51 0.91 1.61 2.00e-01 2.50e+01 6.44e+01 chirality pdb=" CA TYR G 32 " pdb=" N TYR G 32 " pdb=" C TYR G 32 " pdb=" CB TYR G 32 " both_signs ideal model delta sigma weight residual False 2.51 1.18 1.33 2.00e-01 2.50e+01 4.42e+01 chirality pdb=" CA GLN G 11 " pdb=" N GLN G 11 " pdb=" C GLN G 11 " pdb=" CB GLN G 11 " both_signs ideal model delta sigma weight residual False 2.51 1.49 1.02 2.00e-01 2.50e+01 2.60e+01 ... (remaining 3578 not shown) Planarity restraints: 3748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 72 " -0.030 2.00e-02 2.50e+03 5.97e-02 3.57e+01 pdb=" C VAL A 72 " 0.103 2.00e-02 2.50e+03 pdb=" O VAL A 72 " -0.039 2.00e-02 2.50e+03 pdb=" N LYS A 73 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 363 " 0.106 5.00e-02 4.00e+02 1.40e-01 3.15e+01 pdb=" N PRO E 364 " -0.241 5.00e-02 4.00e+02 pdb=" CA PRO E 364 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO E 364 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 490 " 0.092 5.00e-02 4.00e+02 1.20e-01 2.31e+01 pdb=" N PRO F 491 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO F 491 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO F 491 " 0.062 5.00e-02 4.00e+02 ... (remaining 3745 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 299 2.62 - 3.19: 18637 3.19 - 3.76: 34097 3.76 - 4.33: 46279 4.33 - 4.90: 74396 Nonbonded interactions: 173708 Sorted by model distance: nonbonded pdb=" O SER D 173 " pdb=" OG SER D 177 " model vdw 2.045 3.040 nonbonded pdb=" OD1 ASN F 381 " pdb=" OG SER F 424 " model vdw 2.140 3.040 nonbonded pdb=" O PRO E 77 " pdb=" OG SER E 80 " model vdw 2.141 3.040 nonbonded pdb=" N2 G I 12 " pdb=" O2 C J 48 " model vdw 2.148 2.496 nonbonded pdb=" O CYS E 471 " pdb=" OG1 THR E 588 " model vdw 2.171 3.040 ... (remaining 173703 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 6 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 192)) selection = (chain 'D' and (resid 6 through 21 or (resid 22 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 42 or (resid 43 and (name N or name CA or name C or na \ me O or name CB )) or resid 44 through 46 or (resid 47 and (name N or name CA or \ name C or name O or name CB )) or resid 48 through 192)) } ncs_group { reference = (chain 'E' and (resid 1 through 473 or resid 475 through 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: 7.390 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: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 29.090 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5008 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.055 22559 Z= 0.327 Angle : 0.952 34.266 30906 Z= 0.546 Chirality : 0.063 1.605 3581 Planarity : 0.006 0.140 3748 Dihedral : 18.826 166.450 8472 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.49 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 aren 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 covalent geometry : bond 0.00855 (22527) covalent geometry : angle 0.93982 (30879) hydrogen bonds : bond 0.18370 ( 842) hydrogen bonds : angle 6.41261 ( 2324) metal coordination : bond 0.01942 ( 32) metal coordination : angle 5.22093 ( 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 : 1.007 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: 0.1690 time to fit residues: 148.9211 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 : 0.835 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 113 HIS A 168 ASN A 752 HIS B 100 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS 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** G 27 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.232496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.204570 restraints weight = 76511.477| |-----------------------------------------------------------------------------| r_work (start): 0.4472 rms_B_bonded: 2.90 r_work: 0.3872 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3841 r_free = 0.3841 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3841 r_free = 0.3841 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6105 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 22559 Z= 0.160 Angle : 0.761 14.369 30906 Z= 0.385 Chirality : 0.044 0.279 3581 Planarity : 0.005 0.057 3748 Dihedral : 12.753 146.309 3769 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.43 % Favored : 91.30 % Rotamer: Outliers : 4.74 % Allowed : 30.51 % Favored : 64.75 % 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 aren not related in a simple way. whole: -1.90 (0.16), residues: 2650 helix: 0.21 (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 0.023 0.002 TYR G 89 PHE 0.023 0.002 PHE E 373 TRP 0.023 0.002 TRP B 182 HIS 0.009 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00352 (22527) covalent geometry : angle 0.74473 (30879) hydrogen bonds : bond 0.05408 ( 842) hydrogen bonds : angle 5.21316 ( 2324) metal coordination : bond 0.01959 ( 32) metal coordination : angle 5.27817 ( 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 409 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 302 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 666 MET cc_start: 0.6727 (mmt) cc_final: 0.6520 (mmt) REVERT: A 757 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7451 (mm) REVERT: B 61 LYS cc_start: 0.8469 (tmmt) cc_final: 0.8175 (tppt) REVERT: B 143 ASP cc_start: 0.4691 (p0) cc_final: 0.4261 (t0) REVERT: B 166 ILE cc_start: 0.3351 (OUTLIER) cc_final: 0.3104 (pt) REVERT: C 44 ASP cc_start: 0.7653 (p0) cc_final: 0.7360 (p0) REVERT: D 31 SER cc_start: 0.6421 (p) cc_final: 0.5920 (t) REVERT: F 14 LEU cc_start: 0.5937 (mt) cc_final: 0.4835 (tp) REVERT: F 61 THR cc_start: 0.5074 (OUTLIER) cc_final: 0.4802 (p) REVERT: F 122 LEU cc_start: 0.6370 (tt) cc_final: 0.6125 (tp) REVERT: F 460 LYS cc_start: -0.2097 (OUTLIER) cc_final: -0.2352 (mtmt) REVERT: F 531 GLN cc_start: -0.0703 (OUTLIER) cc_final: -0.1328 (mt0) REVERT: E 183 THR cc_start: 0.5748 (m) cc_final: 0.5301 (p) REVERT: E 437 PHE cc_start: 0.5578 (OUTLIER) cc_final: 0.5153 (p90) REVERT: E 460 LYS cc_start: 0.0506 (pttp) cc_final: 0.0027 (pttm) REVERT: E 480 ILE cc_start: 0.0359 (OUTLIER) cc_final: -0.0705 (tp) REVERT: E 579 ARG cc_start: 0.3055 (mmp80) cc_final: 0.2404 (mmm160) outliers start: 107 outliers final: 36 residues processed: 391 average time/residue: 0.1607 time to fit residues: 97.4958 Evaluate side-chains 268 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 225 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 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 602 LEU 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 42 LEU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 166 ILE 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 422 PHE Chi-restraints excluded: chain F residue 460 LYS Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 480 ILE Chi-restraints excluded: chain G residue 9 LEU 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: 7.9990 chunk 108 optimal weight: 0.5980 chunk 150 optimal weight: 8.9990 chunk 103 optimal weight: 0.2980 chunk 255 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS A 297 ASN A 309 HIS A 381 HIS A 698 GLN A 752 HIS ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN E 275 GLN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.219879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.183921 restraints weight = 70278.993| |-----------------------------------------------------------------------------| r_work (start): 0.4287 rms_B_bonded: 3.25 r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4286 r_free = 0.4286 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4286 r_free = 0.4286 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.6082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 22559 Z= 0.212 Angle : 0.811 14.361 30906 Z= 0.415 Chirality : 0.048 0.496 3581 Planarity : 0.005 0.051 3748 Dihedral : 12.400 132.779 3744 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.09 % Favored : 91.68 % Rotamer: Outliers : 4.92 % Allowed : 29.41 % 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 aren not related in a simple way. whole: -2.04 (0.16), residues: 2650 helix: -0.06 (0.16), residues: 996 sheet: -1.23 (0.34), residues: 242 loop : -2.43 (0.15), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 490 TYR 0.037 0.003 TYR D 135 PHE 0.068 0.003 PHE A 528 TRP 0.017 0.002 TRP B 182 HIS 0.012 0.002 HIS E 290 Details of bonding type rmsd covalent geometry : bond 0.00460 (22527) covalent geometry : angle 0.79927 (30879) hydrogen bonds : bond 0.06019 ( 842) hydrogen bonds : angle 5.17031 ( 2324) metal coordination : bond 0.01711 ( 32) metal coordination : angle 4.69816 ( 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 394 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 283 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASP cc_start: 0.7102 (p0) cc_final: 0.6701 (m-30) REVERT: A 906 MET cc_start: 0.5406 (ppp) cc_final: 0.5196 (ppp) REVERT: B 148 THR cc_start: 0.8182 (OUTLIER) cc_final: 0.7943 (t) REVERT: F 378 MET cc_start: 0.0787 (mpp) cc_final: -0.1720 (mmt) REVERT: F 460 LYS cc_start: -0.1286 (OUTLIER) cc_final: -0.2292 (mtmt) REVERT: F 531 GLN cc_start: -0.0014 (OUTLIER) cc_final: -0.0722 (mt0) REVERT: F 551 GLU cc_start: -0.0280 (pt0) cc_final: -0.0725 (mm-30) REVERT: F 554 HIS cc_start: -0.0822 (OUTLIER) cc_final: -0.1496 (m-70) REVERT: E 460 LYS cc_start: 0.1053 (pttp) cc_final: 0.0296 (pttm) REVERT: E 579 ARG cc_start: 0.3563 (mmp80) cc_final: 0.3319 (mmp-170) outliers start: 111 outliers final: 49 residues processed: 373 average time/residue: 0.1622 time to fit residues: 94.3356 Evaluate side-chains 252 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 199 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 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 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 563 CYS Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 928 HIS 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 146 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 170 SER 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 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 181 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 460 LYS 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 199 THR 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 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 G residue 23 CYS Chi-restraints excluded: chain G residue 73 CYS 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: 5.9990 chunk 153 optimal weight: 5.9990 chunk 236 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 137 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 237 optimal weight: 7.9990 chunk 261 optimal weight: 7.9990 chunk 242 optimal weight: 8.9990 chunk 220 optimal weight: 6.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS A 158 ASN A 168 ASN A 752 HIS B 88 GLN B 109 ASN ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN D 65 GLN D 192 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 GLN E 51 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 586 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.203063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.162662 restraints weight = 66217.092| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 3.08 r_work: 0.3179 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.8918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.104 22559 Z= 0.468 Angle : 1.003 19.831 30906 Z= 0.511 Chirality : 0.059 0.359 3581 Planarity : 0.006 0.060 3748 Dihedral : 12.624 108.387 3741 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.53 % Favored : 90.24 % Rotamer: Outliers : 5.18 % Allowed : 29.54 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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 aren not related in a simple way. whole: -2.66 (0.15), residues: 2650 helix: -0.75 (0.16), residues: 996 sheet: -1.71 (0.33), residues: 242 loop : -2.61 (0.15), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 569 TYR 0.032 0.003 TYR D 135 PHE 0.030 0.004 PHE E 422 TRP 0.018 0.003 TRP A 268 HIS 0.018 0.002 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.01121 (22527) covalent geometry : angle 0.98571 (30879) hydrogen bonds : bond 0.08834 ( 842) hydrogen bonds : angle 5.40428 ( 2324) metal coordination : bond 0.02913 ( 32) metal coordination : angle 6.31472 ( 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 348 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 231 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8055 (m-80) REVERT: A 197 ARG cc_start: 0.8649 (ttp-170) cc_final: 0.8435 (ttm-80) REVERT: A 277 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7557 (mp0) REVERT: A 477 ASP cc_start: 0.8440 (t70) cc_final: 0.8137 (t0) REVERT: A 499 ASP cc_start: 0.8498 (m-30) cc_final: 0.8185 (t0) REVERT: A 623 ASP cc_start: 0.8798 (p0) cc_final: 0.8565 (p0) REVERT: A 855 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7800 (ttp) REVERT: A 906 MET cc_start: 0.5557 (ppp) cc_final: 0.5290 (ppp) REVERT: B 109 ASN cc_start: 0.7990 (OUTLIER) cc_final: 0.7630 (t0) REVERT: B 158 GLN cc_start: 0.8171 (tp40) cc_final: 0.7927 (tt0) REVERT: D 65 GLN cc_start: 0.7266 (tm130) cc_final: 0.6940 (tt0) REVERT: D 75 ARG cc_start: 0.8535 (tpp-160) cc_final: 0.8297 (tpt90) REVERT: D 77 GLU cc_start: 0.8400 (tp30) cc_final: 0.8110 (mt-10) REVERT: D 78 ASP cc_start: 0.8408 (t70) cc_final: 0.8181 (t70) REVERT: D 87 MET cc_start: 0.8487 (tpp) cc_final: 0.8239 (mmt) REVERT: F 68 MET cc_start: 0.6213 (mmm) cc_final: 0.5751 (mmt) REVERT: F 120 TYR cc_start: 0.5049 (OUTLIER) cc_final: 0.4586 (m-80) REVERT: F 192 LYS cc_start: 0.1189 (OUTLIER) cc_final: 0.0630 (ptmt) REVERT: F 531 GLN cc_start: -0.0107 (OUTLIER) cc_final: -0.0726 (mt0) REVERT: F 554 HIS cc_start: -0.0509 (OUTLIER) cc_final: -0.1267 (m90) REVERT: E 233 MET cc_start: 0.5043 (OUTLIER) cc_final: 0.3872 (mtt) REVERT: E 243 GLN cc_start: 0.4254 (pt0) cc_final: 0.3974 (pt0) REVERT: E 579 ARG cc_start: 0.3369 (mmp80) cc_final: 0.2598 (mmp-170) outliers start: 117 outliers final: 57 residues processed: 329 average time/residue: 0.1636 time to fit residues: 83.8273 Evaluate side-chains 254 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 188 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 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 101 PHE Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 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 563 CYS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 730 CYS Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 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 899 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 928 HIS 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 146 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 398 TYR Chi-restraints excluded: chain F residue 482 HIS 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 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 410 THR Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 576 MET 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 Chi-restraints excluded: chain G residue 106 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 163 optimal weight: 0.0570 chunk 23 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 179 optimal weight: 0.1980 chunk 143 optimal weight: 9.9990 chunk 199 optimal weight: 0.2980 chunk 263 optimal weight: 8.9990 chunk 176 optimal weight: 20.0000 chunk 231 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 HIS ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.206487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.143104 restraints weight = 63173.623| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 4.84 r_work: 0.3056 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.8999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 22559 Z= 0.135 Angle : 0.670 17.259 30906 Z= 0.342 Chirality : 0.042 0.234 3581 Planarity : 0.004 0.047 3748 Dihedral : 12.031 73.678 3740 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.30 % Favored : 92.47 % 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 aren not related in a simple way. whole: -2.02 (0.16), residues: 2650 helix: -0.03 (0.17), residues: 993 sheet: -1.46 (0.33), residues: 250 loop : -2.37 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 490 TYR 0.043 0.002 TYR E 421 PHE 0.020 0.001 PHE E 373 TRP 0.023 0.002 TRP B 182 HIS 0.005 0.001 HIS E 290 Details of bonding type rmsd covalent geometry : bond 0.00270 (22527) covalent geometry : angle 0.65550 (30879) hydrogen bonds : bond 0.05275 ( 842) hydrogen bonds : angle 4.83226 ( 2324) metal coordination : bond 0.01847 ( 32) metal coordination : angle 4.79971 ( 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 270 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 211 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: 0.7676 (OUTLIER) cc_final: 0.7368 (p) REVERT: A 81 GLN cc_start: 0.8527 (mm-40) cc_final: 0.8081 (mt0) REVERT: A 197 ARG cc_start: 0.8270 (ttp-170) cc_final: 0.7623 (ttm-80) REVERT: A 477 ASP cc_start: 0.8006 (t70) cc_final: 0.7673 (t0) REVERT: A 499 ASP cc_start: 0.8355 (m-30) cc_final: 0.7705 (t0) REVERT: A 542 MET cc_start: 0.8628 (mtm) cc_final: 0.8318 (mtp) REVERT: A 623 ASP cc_start: 0.8774 (p0) cc_final: 0.8374 (p0) REVERT: A 898 HIS cc_start: 0.7003 (t70) cc_final: 0.6491 (t70) REVERT: B 67 MET cc_start: 0.7670 (tpt) cc_final: 0.7380 (tpt) REVERT: D 65 GLN cc_start: 0.7057 (tm130) cc_final: 0.6280 (mm110) REVERT: D 73 GLN cc_start: 0.7592 (tp40) cc_final: 0.7292 (tt0) REVERT: D 77 GLU cc_start: 0.8355 (tp30) cc_final: 0.7674 (mt-10) REVERT: D 79 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7578 (ttmm) REVERT: D 106 ILE cc_start: 0.7770 (mt) cc_final: 0.7451 (pt) REVERT: D 165 LYS cc_start: 0.6840 (mtmm) cc_final: 0.6570 (ptpt) REVERT: F 68 MET cc_start: 0.5613 (mmm) cc_final: 0.5248 (mmp) REVERT: F 192 LYS cc_start: 0.0736 (OUTLIER) cc_final: 0.0356 (ptmt) REVERT: F 531 GLN cc_start: 0.0075 (OUTLIER) cc_final: -0.0246 (mt0) REVERT: F 554 HIS cc_start: -0.0466 (OUTLIER) cc_final: -0.1203 (m-70) REVERT: E 233 MET cc_start: 0.4524 (OUTLIER) cc_final: 0.3623 (mtt) REVERT: E 579 ARG cc_start: 0.3380 (mmp80) cc_final: 0.2696 (mmp-170) outliers start: 59 outliers final: 32 residues processed: 255 average time/residue: 0.1721 time to fit residues: 67.4598 Evaluate side-chains 225 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 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 434 SER Chi-restraints excluded: chain A residue 648 LEU 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 7 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 97 LYS 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 25 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 398 TYR Chi-restraints excluded: chain F residue 495 VAL 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 256 LEU Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 86 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 23 optimal weight: 0.7980 chunk 191 optimal weight: 8.9990 chunk 215 optimal weight: 0.0770 chunk 263 optimal weight: 0.0060 chunk 66 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 chunk 196 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 225 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 204 optimal weight: 8.9990 overall best weight: 1.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN E 459 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.203611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.141246 restraints weight = 67039.797| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 5.15 r_work: 0.2983 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 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 = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.9247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 22559 Z= 0.184 Angle : 0.695 17.722 30906 Z= 0.353 Chirality : 0.044 0.273 3581 Planarity : 0.005 0.050 3748 Dihedral : 11.853 73.799 3740 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.09 % Favored : 91.68 % Rotamer: Outliers : 3.07 % Allowed : 29.85 % Favored : 67.08 % 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 aren not related in a simple way. whole: -1.89 (0.16), residues: 2650 helix: 0.10 (0.17), residues: 990 sheet: -1.48 (0.33), residues: 253 loop : -2.31 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 21 TYR 0.035 0.002 TYR F 396 PHE 0.030 0.002 PHE F 373 TRP 0.018 0.001 TRP B 182 HIS 0.010 0.001 HIS E 290 Details of bonding type rmsd covalent geometry : bond 0.00433 (22527) covalent geometry : angle 0.67899 (30879) hydrogen bonds : bond 0.05836 ( 842) hydrogen bonds : angle 4.73444 ( 2324) metal coordination : bond 0.01741 ( 32) metal coordination : angle 5.00318 ( 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 269 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 200 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: 0.7744 (OUTLIER) cc_final: 0.7368 (p) REVERT: A 81 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8222 (mt0) REVERT: A 197 ARG cc_start: 0.8490 (ttp-170) cc_final: 0.7845 (ttm-80) REVERT: A 350 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: A 477 ASP cc_start: 0.8296 (t70) cc_final: 0.7947 (t0) REVERT: A 497 ASN cc_start: 0.8759 (t0) cc_final: 0.8500 (t0) REVERT: A 623 ASP cc_start: 0.8859 (p0) cc_final: 0.8482 (p0) REVERT: A 898 HIS cc_start: 0.7034 (t70) cc_final: 0.6652 (t70) REVERT: B 71 TYR cc_start: 0.8050 (t80) cc_final: 0.7728 (t80) REVERT: B 158 GLN cc_start: 0.8257 (tp40) cc_final: 0.7844 (tt0) REVERT: D 43 ASN cc_start: 0.7710 (OUTLIER) cc_final: 0.7506 (t0) REVERT: D 65 GLN cc_start: 0.7059 (tm130) cc_final: 0.6403 (mm110) REVERT: D 77 GLU cc_start: 0.8458 (tp30) cc_final: 0.7761 (mt-10) REVERT: F 68 MET cc_start: 0.5644 (mmm) cc_final: 0.5342 (mmm) REVERT: F 133 PHE cc_start: 0.6696 (m-80) cc_final: 0.6383 (m-80) REVERT: F 343 PHE cc_start: 0.2204 (t80) cc_final: 0.1929 (m-80) REVERT: F 531 GLN cc_start: -0.0045 (OUTLIER) cc_final: -0.0345 (mt0) REVERT: F 554 HIS cc_start: -0.0530 (OUTLIER) cc_final: -0.1242 (m-70) REVERT: E 233 MET cc_start: 0.4622 (OUTLIER) cc_final: 0.3767 (mtt) REVERT: E 579 ARG cc_start: 0.3405 (mmp80) cc_final: 0.2666 (mmp-170) outliers start: 69 outliers final: 47 residues processed: 253 average time/residue: 0.1677 time to fit residues: 65.2889 Evaluate side-chains 242 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 189 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 350 GLU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 648 LEU 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 7 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain D residue 43 ASN 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 D residue 157 GLN 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 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 495 VAL 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 250 THR Chi-restraints excluded: chain E residue 256 LEU 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 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: 0.8980 chunk 121 optimal weight: 0.9980 chunk 156 optimal weight: 6.9990 chunk 101 optimal weight: 0.0970 chunk 263 optimal weight: 5.9990 chunk 212 optimal weight: 7.9990 chunk 68 optimal weight: 0.0170 chunk 29 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 241 optimal weight: 0.0980 chunk 16 optimal weight: 0.9990 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN B 158 GLN ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.205585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.143236 restraints weight = 64083.292| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 5.12 r_work: 0.3051 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.9395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 22559 Z= 0.115 Angle : 0.633 15.798 30906 Z= 0.319 Chirality : 0.041 0.223 3581 Planarity : 0.004 0.051 3748 Dihedral : 11.704 73.688 3740 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.15 % Favored : 92.62 % Rotamer: Outliers : 2.77 % Allowed : 30.20 % Favored : 67.03 % 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 aren not related in a simple way. whole: -1.64 (0.16), residues: 2650 helix: 0.37 (0.17), residues: 993 sheet: -1.45 (0.32), residues: 254 loop : -2.18 (0.15), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG D 96 TYR 0.034 0.001 TYR F 396 PHE 0.028 0.001 PHE F 373 TRP 0.023 0.001 TRP B 182 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00244 (22527) covalent geometry : angle 0.62009 (30879) hydrogen bonds : bond 0.04756 ( 842) hydrogen bonds : angle 4.52719 ( 2324) metal coordination : bond 0.01480 ( 32) metal coordination : angle 4.31946 ( 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 279 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 217 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: 0.7753 (OUTLIER) cc_final: 0.7404 (p) REVERT: A 81 GLN cc_start: 0.8506 (mm-40) cc_final: 0.8115 (mt0) REVERT: A 197 ARG cc_start: 0.8324 (ttp-170) cc_final: 0.7704 (ttm-80) REVERT: A 258 ASP cc_start: 0.8166 (t70) cc_final: 0.7813 (t0) REVERT: A 267 LYS cc_start: 0.8785 (mmmt) cc_final: 0.8568 (mptt) REVERT: A 477 ASP cc_start: 0.8064 (t70) cc_final: 0.7730 (t0) REVERT: A 497 ASN cc_start: 0.8596 (t0) cc_final: 0.8327 (t0) REVERT: A 545 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8535 (mtmt) REVERT: A 623 ASP cc_start: 0.8807 (p0) cc_final: 0.8421 (p0) REVERT: A 898 HIS cc_start: 0.6923 (t70) cc_final: 0.6599 (t70) REVERT: B 158 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7790 (tt0) REVERT: B 171 GLU cc_start: 0.7521 (pt0) cc_final: 0.7179 (pt0) REVERT: D 65 GLN cc_start: 0.7107 (tm130) cc_final: 0.6593 (mm110) REVERT: D 73 GLN cc_start: 0.7661 (tp40) cc_final: 0.7376 (tt0) REVERT: D 77 GLU cc_start: 0.8389 (tp30) cc_final: 0.7677 (mt-10) REVERT: D 155 GLU cc_start: 0.7916 (pp20) cc_final: 0.7611 (pp20) REVERT: F 68 MET cc_start: 0.5758 (mmm) cc_final: 0.5551 (mmm) REVERT: F 192 LYS cc_start: 0.0334 (OUTLIER) cc_final: -0.0015 (ptmt) REVERT: F 260 ASP cc_start: 0.7383 (p0) cc_final: 0.7116 (m-30) REVERT: F 324 TYR cc_start: 0.4063 (m-10) cc_final: 0.3262 (t80) REVERT: F 343 PHE cc_start: 0.2394 (t80) cc_final: 0.2095 (m-80) REVERT: F 531 GLN cc_start: -0.0032 (OUTLIER) cc_final: -0.0336 (mt0) REVERT: F 545 ILE cc_start: 0.2081 (mm) cc_final: 0.1822 (mt) REVERT: F 554 HIS cc_start: -0.0495 (OUTLIER) cc_final: -0.0951 (m-70) REVERT: E 233 MET cc_start: 0.4495 (OUTLIER) cc_final: 0.3590 (mtt) REVERT: E 579 ARG cc_start: 0.3265 (mmp80) cc_final: 0.2498 (mmp-170) REVERT: G 86 LYS cc_start: 0.1822 (OUTLIER) cc_final: 0.1120 (mptt) outliers start: 62 outliers final: 36 residues processed: 259 average time/residue: 0.1644 time to fit residues: 66.5833 Evaluate side-chains 246 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 202 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 72 VAL 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 434 SER Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 545 LYS 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 128 LEU Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 173 SER 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 493 ILE Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain E residue 233 MET 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 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: 3.9990 chunk 216 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 240 optimal weight: 5.9990 chunk 193 optimal weight: 8.9990 chunk 189 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 297 ASN A 822 GLN B 88 GLN ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN D 43 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN ** E 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.197591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.133838 restraints weight = 69831.308| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 5.16 r_work: 0.2883 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 1.0054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.107 22559 Z= 0.484 Angle : 0.956 24.569 30906 Z= 0.483 Chirality : 0.056 0.395 3581 Planarity : 0.007 0.187 3748 Dihedral : 12.168 74.067 3738 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.87 % Favored : 89.98 % Rotamer: Outliers : 3.64 % Allowed : 29.41 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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 aren not related in a simple way. whole: -2.40 (0.15), residues: 2650 helix: -0.47 (0.16), residues: 1005 sheet: -1.64 (0.32), residues: 258 loop : -2.52 (0.15), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 96 TYR 0.036 0.003 TYR F 396 PHE 0.026 0.003 PHE E 422 TRP 0.018 0.003 TRP A 290 HIS 0.019 0.002 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.01168 (22527) covalent geometry : angle 0.93187 (30879) hydrogen bonds : bond 0.08608 ( 842) hydrogen bonds : angle 5.13234 ( 2324) metal coordination : bond 0.02814 ( 32) metal coordination : angle 7.21884 ( 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 279 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 197 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8635 (mm-40) cc_final: 0.8223 (mt0) REVERT: A 158 ASN cc_start: 0.8848 (m110) cc_final: 0.8618 (m-40) REVERT: A 221 ASP cc_start: 0.8847 (t0) cc_final: 0.8386 (t0) REVERT: A 258 ASP cc_start: 0.8477 (t70) cc_final: 0.8097 (t0) REVERT: A 267 LYS cc_start: 0.8814 (mmmt) cc_final: 0.8590 (mptt) REVERT: A 350 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7808 (mt-10) REVERT: A 477 ASP cc_start: 0.8580 (t70) cc_final: 0.8202 (t0) REVERT: A 545 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8550 (mtmt) REVERT: A 898 HIS cc_start: 0.7026 (t70) cc_final: 0.6687 (t-90) REVERT: B 158 GLN cc_start: 0.8560 (tp40) cc_final: 0.8249 (tt0) REVERT: B 171 GLU cc_start: 0.7568 (pt0) cc_final: 0.7283 (pt0) REVERT: D 65 GLN cc_start: 0.7129 (tm130) cc_final: 0.6807 (mm110) REVERT: D 77 GLU cc_start: 0.8688 (tp30) cc_final: 0.8132 (mt-10) REVERT: D 155 GLU cc_start: 0.7870 (pp20) cc_final: 0.7528 (pp20) REVERT: F 49 VAL cc_start: 0.7102 (p) cc_final: 0.6869 (m) REVERT: F 68 MET cc_start: 0.6045 (mmm) cc_final: 0.5715 (mmt) REVERT: F 192 LYS cc_start: 0.0060 (OUTLIER) cc_final: -0.0266 (ptpt) REVERT: F 324 TYR cc_start: 0.4060 (m-10) cc_final: 0.3406 (t80) REVERT: F 531 GLN cc_start: 0.0148 (OUTLIER) cc_final: -0.0174 (mt0) REVERT: E 233 MET cc_start: 0.5136 (OUTLIER) cc_final: 0.4416 (mtt) REVERT: E 579 ARG cc_start: 0.3629 (mmp80) cc_final: 0.2821 (mmp-170) REVERT: G 33 ASN cc_start: 0.4901 (t0) cc_final: 0.4608 (t0) outliers start: 82 outliers final: 66 residues processed: 263 average time/residue: 0.1603 time to fit residues: 66.3567 Evaluate side-chains 255 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 184 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 51 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 262 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 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 772 SER 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 926 THR Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 145 PHE Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 396 TYR 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 495 VAL Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain E residue 29 CYS 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 131 optimal weight: 0.9980 chunk 117 optimal weight: 0.0670 chunk 256 optimal weight: 0.5980 chunk 152 optimal weight: 0.0070 chunk 19 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 166 optimal weight: 7.9990 chunk 135 optimal weight: 0.0070 chunk 172 optimal weight: 30.0000 chunk 245 optimal weight: 2.9990 overall best weight: 0.2754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN ** E 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 537 GLN E 586 GLN G 33 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.204741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.140583 restraints weight = 56642.628| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 4.34 r_work: 0.3050 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 1.0097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 22559 Z= 0.128 Angle : 0.672 17.832 30906 Z= 0.336 Chirality : 0.042 0.215 3581 Planarity : 0.005 0.134 3748 Dihedral : 11.763 73.617 3738 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.07 % Favored : 92.78 % Rotamer: Outliers : 2.59 % Allowed : 30.29 % Favored : 67.12 % 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 aren not related in a simple way. whole: -1.81 (0.16), residues: 2650 helix: 0.14 (0.17), residues: 994 sheet: -1.40 (0.33), residues: 244 loop : -2.24 (0.15), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 96 TYR 0.032 0.001 TYR F 396 PHE 0.025 0.001 PHE D 15 TRP 0.030 0.002 TRP E 114 HIS 0.006 0.001 HIS E 245 Details of bonding type rmsd covalent geometry : bond 0.00260 (22527) covalent geometry : angle 0.65277 (30879) hydrogen bonds : bond 0.05024 ( 842) hydrogen bonds : angle 4.59183 ( 2324) metal coordination : bond 0.01492 ( 32) metal coordination : angle 5.49984 ( 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 249 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 191 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: 0.7575 (OUTLIER) cc_final: 0.7222 (p) REVERT: A 81 GLN cc_start: 0.8510 (mm-40) cc_final: 0.8126 (mt0) REVERT: A 221 ASP cc_start: 0.8497 (t0) cc_final: 0.8063 (t0) REVERT: A 258 ASP cc_start: 0.8319 (t70) cc_final: 0.8109 (t70) REVERT: A 477 ASP cc_start: 0.8071 (t70) cc_final: 0.7630 (t0) REVERT: A 497 ASN cc_start: 0.8553 (t0) cc_final: 0.8292 (t0) REVERT: A 545 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8459 (mtmt) REVERT: A 854 LEU cc_start: 0.8298 (tt) cc_final: 0.8010 (mm) REVERT: B 158 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: B 171 GLU cc_start: 0.7417 (pt0) cc_final: 0.7138 (pt0) REVERT: D 65 GLN cc_start: 0.7089 (tm130) cc_final: 0.6456 (mm110) REVERT: D 73 GLN cc_start: 0.7862 (tp40) cc_final: 0.7535 (tt0) REVERT: D 77 GLU cc_start: 0.8481 (tp30) cc_final: 0.7859 (mt-10) REVERT: D 155 GLU cc_start: 0.7828 (pp20) cc_final: 0.7467 (pp20) REVERT: F 68 MET cc_start: 0.6028 (mmm) cc_final: 0.4100 (mtm) REVERT: F 192 LYS cc_start: -0.0153 (OUTLIER) cc_final: -0.0441 (ptpt) REVERT: F 270 GLN cc_start: 0.5235 (tp-100) cc_final: 0.4913 (mm110) REVERT: F 324 TYR cc_start: 0.4027 (m-10) cc_final: 0.3381 (t80) REVERT: F 531 GLN cc_start: 0.0033 (OUTLIER) cc_final: -0.0266 (mt0) REVERT: F 554 HIS cc_start: -0.0340 (OUTLIER) cc_final: -0.0650 (m90) REVERT: E 164 HIS cc_start: 0.6036 (m-70) cc_final: 0.5430 (p-80) REVERT: E 233 MET cc_start: 0.4961 (OUTLIER) cc_final: 0.4317 (mtt) REVERT: E 274 MET cc_start: 0.2994 (mmm) cc_final: 0.2010 (mtt) REVERT: E 576 MET cc_start: 0.3007 (ppp) cc_final: 0.2286 (pmm) REVERT: E 579 ARG cc_start: 0.3539 (mmp80) cc_final: 0.2734 (mmp-170) REVERT: G 86 LYS cc_start: 0.2868 (OUTLIER) cc_final: 0.1864 (mptt) outliers start: 58 outliers final: 43 residues processed: 238 average time/residue: 0.1681 time to fit residues: 62.1180 Evaluate side-chains 228 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 177 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 72 VAL Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 173 SER 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 495 VAL Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain E residue 29 CYS 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 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 86 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 89 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 chunk 265 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 130 optimal weight: 0.4980 chunk 140 optimal weight: 9.9990 chunk 173 optimal weight: 9.9990 chunk 197 optimal weight: 8.9990 chunk 260 optimal weight: 9.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.202666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.139431 restraints weight = 68164.177| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 5.13 r_work: 0.2975 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- 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 = 0.47 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 = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 1.0219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 22559 Z= 0.163 Angle : 0.694 17.555 30906 Z= 0.346 Chirality : 0.043 0.255 3581 Planarity : 0.005 0.132 3748 Dihedral : 11.717 73.754 3738 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.87 % Favored : 92.02 % Rotamer: Outliers : 2.77 % Allowed : 30.16 % Favored : 67.08 % 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 aren not related in a simple way. whole: -1.71 (0.16), residues: 2650 helix: 0.26 (0.17), residues: 984 sheet: -1.41 (0.33), residues: 250 loop : -2.19 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 96 TYR 0.057 0.002 TYR E 421 PHE 0.021 0.002 PHE D 15 TRP 0.020 0.002 TRP B 182 HIS 0.009 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00380 (22527) covalent geometry : angle 0.67464 (30879) hydrogen bonds : bond 0.05491 ( 842) hydrogen bonds : angle 4.58718 ( 2324) metal coordination : bond 0.01625 ( 32) metal coordination : angle 5.54472 ( 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 247 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 185 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: 0.7657 (OUTLIER) cc_final: 0.7276 (p) REVERT: A 81 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8171 (mt0) REVERT: A 221 ASP cc_start: 0.8618 (t0) cc_final: 0.8173 (t0) REVERT: A 267 LYS cc_start: 0.8812 (mmmt) cc_final: 0.8482 (mmtm) REVERT: A 477 ASP cc_start: 0.8324 (t70) cc_final: 0.7893 (t0) REVERT: A 497 ASN cc_start: 0.8710 (t0) cc_final: 0.8421 (t0) REVERT: A 545 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8487 (mtmt) REVERT: A 796 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8169 (mp0) REVERT: B 158 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7776 (tt0) REVERT: B 171 GLU cc_start: 0.7423 (pt0) cc_final: 0.7169 (pt0) REVERT: D 65 GLN cc_start: 0.7123 (tm130) cc_final: 0.6531 (mm110) REVERT: D 73 GLN cc_start: 0.7925 (tp40) cc_final: 0.7576 (tt0) REVERT: D 77 GLU cc_start: 0.8559 (tp30) cc_final: 0.7929 (mt-10) REVERT: D 155 GLU cc_start: 0.7883 (pp20) cc_final: 0.7534 (pp20) REVERT: F 68 MET cc_start: 0.6009 (mmm) cc_final: 0.4066 (mtm) REVERT: F 192 LYS cc_start: -0.0208 (OUTLIER) cc_final: -0.0527 (ptpt) REVERT: F 260 ASP cc_start: 0.7360 (p0) cc_final: 0.7152 (m-30) REVERT: F 270 GLN cc_start: 0.5144 (tp-100) cc_final: 0.4808 (mm110) REVERT: F 324 TYR cc_start: 0.4047 (m-10) cc_final: 0.3427 (t80) REVERT: F 343 PHE cc_start: 0.2433 (t80) cc_final: 0.2100 (m-80) REVERT: F 531 GLN cc_start: 0.0182 (OUTLIER) cc_final: -0.0124 (mt0) REVERT: F 554 HIS cc_start: -0.0231 (OUTLIER) cc_final: -0.0448 (m90) REVERT: E 164 HIS cc_start: 0.6087 (m-70) cc_final: 0.5485 (p-80) REVERT: E 233 MET cc_start: 0.4981 (OUTLIER) cc_final: 0.4350 (mtt) REVERT: E 576 MET cc_start: 0.3009 (ppp) cc_final: 0.2301 (pmm) REVERT: E 579 ARG cc_start: 0.3643 (mmp80) cc_final: 0.2841 (mmp-170) REVERT: G 52 LYS cc_start: 0.7971 (mppt) cc_final: 0.7482 (mmtt) outliers start: 62 outliers final: 47 residues processed: 237 average time/residue: 0.1697 time to fit residues: 61.9608 Evaluate side-chains 231 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 177 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 20 THR 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 138 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 648 LEU 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 7 SER Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 158 GLN 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 D residue 173 SER 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 495 VAL Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 233 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 130 optimal weight: 7.9990 chunk 157 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 163 optimal weight: 0.0970 chunk 250 optimal weight: 8.9990 chunk 3 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 152 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.204876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.157839 restraints weight = 54276.515| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 3.66 r_work: 0.3169 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 1.0337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 22559 Z= 0.144 Angle : 0.669 17.130 30906 Z= 0.334 Chirality : 0.043 0.245 3581 Planarity : 0.005 0.115 3748 Dihedral : 11.660 73.760 3738 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.64 % Favored : 92.25 % Rotamer: Outliers : 2.85 % Allowed : 29.81 % Favored : 67.34 % 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 aren not related in a simple way. whole: -1.62 (0.16), residues: 2650 helix: 0.35 (0.17), residues: 983 sheet: -1.35 (0.33), residues: 250 loop : -2.14 (0.15), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 96 TYR 0.032 0.001 TYR F 396 PHE 0.022 0.001 PHE D 15 TRP 0.020 0.002 TRP B 182 HIS 0.007 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00329 (22527) covalent geometry : angle 0.65200 (30879) hydrogen bonds : bond 0.05161 ( 842) hydrogen bonds : angle 4.53406 ( 2324) metal coordination : bond 0.01506 ( 32) metal coordination : angle 5.13293 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7968.53 seconds wall clock time: 137 minutes 4.21 seconds (8224.21 seconds total)