Starting phenix.real_space_refine on Sun Sep 13 09:13:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gwf_34311/09_2026/8gwf_34311.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gwf_34311/09_2026/8gwf_34311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gwf_34311/09_2026/8gwf_34311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gwf_34311/09_2026/8gwf_34311.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gwf_34311/09_2026/8gwf_34311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gwf_34311/09_2026/8gwf_34311.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8gwf_34311/09_2026/8gwf_34311.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gwf_34311/09_2026/8gwf_34311.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 55 5.49 5 S 158 5.16 5 C 13735 2.51 5 N 3694 2.21 5 O 4305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21955 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 7492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 931, 7492 Classifications: {'peptide': 931} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 900} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1396 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 600 Classifications: {'peptide': 78} Link IDs: {'TRANS': 77} Chain: "D" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1422 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 545 Classifications: {'RNAv2': 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: {'RNAv2': 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: 4.88, per 1000 atoms: 0.22 Number of scatterers: 21955 At special positions: 0 Unit cell: (154.98, 136.94, 186.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 158 16.00 P 55 15.00 O 4305 8.00 N 3694 7.00 C 13735 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 19 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 16 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 29 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 5 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 26 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 55 " pdb=" ZN F 701 " pdb="ZN ZN F 701 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F 701 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 19 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 16 " pdb=" ZN F 702 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 8 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 26 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 5 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 29 " pdb=" ZN F 703 " pdb="ZN ZN F 703 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 72 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 55 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 50 " Number of angles added : 27 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5094 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 30 sheets defined 39.9% alpha, 10.3% beta 21 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 2.42 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: 3.45 Time building geometry restraints manager: 1.99 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: 12652 33.29 - 66.58: 693 66.58 - 99.87: 23 99.87 - 133.16: 0 133.16 - 166.45: 2 Dihedral angle restraints: 13370 sinusoidal: 5476 harmonic: 7894 Sorted by residual: dihedral pdb=" C4' G I 33 " pdb=" C3' G I 33 " pdb=" C2' G I 33 " pdb=" C1' G I 33 " ideal model delta sinusoidal sigma weight residual 36.35 -35.36 71.70 1 3.10e+00 1.04e-01 6.85e+02 dihedral pdb=" C4' G J 25 " pdb=" C3' G J 25 " pdb=" C2' G J 25 " pdb=" C1' G J 25 " ideal model delta sinusoidal sigma weight residual 36.34 -34.78 71.12 1 3.10e+00 1.04e-01 6.76e+02 dihedral pdb=" O4' G I 33 " pdb=" C4' G I 33 " pdb=" C3' G I 33 " pdb=" C2' G I 33 " ideal model delta sinusoidal sigma weight residual -35.15 23.08 -58.23 1 4.00e+00 6.25e-02 2.84e+02 ... (remaining 13367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.321: 3575 0.321 - 0.642: 2 0.642 - 0.963: 0 0.963 - 1.284: 2 1.284 - 1.605: 2 Chirality restraints: 3581 Sorted by residual: chirality pdb=" CA CYS G 14 " pdb=" N CYS G 14 " pdb=" C CYS G 14 " pdb=" CB CYS G 14 " both_signs ideal model delta sigma weight residual False 2.51 0.91 1.61 2.00e-01 2.50e+01 6.44e+01 chirality pdb=" CA TYR G 32 " pdb=" N TYR G 32 " pdb=" C TYR G 32 " pdb=" CB TYR G 32 " both_signs ideal model delta sigma weight residual False 2.51 1.18 1.33 2.00e-01 2.50e+01 4.42e+01 chirality pdb=" CA GLN G 11 " pdb=" N GLN G 11 " pdb=" C GLN G 11 " pdb=" CB GLN G 11 " both_signs ideal model delta sigma weight residual False 2.51 1.49 1.02 2.00e-01 2.50e+01 2.60e+01 ... (remaining 3578 not shown) Planarity restraints: 3748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 72 " -0.030 2.00e-02 2.50e+03 5.97e-02 3.57e+01 pdb=" C VAL A 72 " 0.103 2.00e-02 2.50e+03 pdb=" O VAL A 72 " -0.039 2.00e-02 2.50e+03 pdb=" N LYS A 73 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 363 " 0.106 5.00e-02 4.00e+02 1.40e-01 3.15e+01 pdb=" N PRO E 364 " -0.241 5.00e-02 4.00e+02 pdb=" CA PRO E 364 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO E 364 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 490 " 0.092 5.00e-02 4.00e+02 1.20e-01 2.31e+01 pdb=" N PRO F 491 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO F 491 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO F 491 " 0.062 5.00e-02 4.00e+02 ... (remaining 3745 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 299 2.62 - 3.19: 18637 3.19 - 3.76: 34097 3.76 - 4.33: 46279 4.33 - 4.90: 74396 Nonbonded interactions: 173708 Sorted by model distance: nonbonded pdb=" O SER D 173 " pdb=" OG SER D 177 " model vdw 2.045 3.040 nonbonded pdb=" OD1 ASN F 381 " pdb=" OG SER F 424 " model vdw 2.140 3.040 nonbonded pdb=" O PRO E 77 " pdb=" OG SER E 80 " model vdw 2.141 3.040 nonbonded pdb=" N2 G I 12 " pdb=" O2 C J 48 " model vdw 2.148 2.496 nonbonded pdb=" O CYS E 471 " pdb=" OG1 THR E 588 " model vdw 2.171 3.040 ... (remaining 173703 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 6 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 192)) selection = (chain 'D' and (resid 6 through 21 or (resid 22 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 42 or (resid 43 and (name N or name CA or name C or na \ me O or name CB )) or resid 44 through 46 or (resid 47 and (name N or name CA or \ name C or name O or name CB )) or resid 48 through 192)) } ncs_group { reference = (chain 'E' and (resid 1 through 473 or resid 475 through 703)) selection = (chain 'F' and (resid 1 through 473 or resid 475 through 703)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.11 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.220 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: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.550 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.055 22559 Z= 0.328 Angle : 0.969 34.266 30906 Z= 0.549 Chirality : 0.069 1.605 3581 Planarity : 0.006 0.140 3748 Dihedral : 18.268 166.450 8276 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.43 % Favored : 91.19 % Rotamer: Outliers : 5.14 % Allowed : 33.58 % Favored : 61.28 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.16), residues: 2650 helix: 0.34 (0.18), residues: 947 sheet: -1.60 (0.35), residues: 218 loop : -2.47 (0.15), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 303 TYR 0.022 0.001 TYR F 299 PHE 0.017 0.001 PHE F 437 TRP 0.037 0.002 TRP G 53 HIS 0.007 0.001 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00856 / 0.33 (22527) covalent geometry : angle 0.95752 / 0.55 (30879) hydrogen bonds : bond 0.18370 / 11.87 ( 842) hydrogen bonds : angle 6.41261 / 4.47 ( 2324) metal coordination : bond 0.01942 / 1.51 ( 32) metal coordination : angle 5.22093 / 2.92 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 296 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.7063 (tptt) cc_final: 0.6792 (tptp) REVERT: A 114 ILE cc_start: 0.5885 (mt) cc_final: 0.5594 (mt) REVERT: A 115 SER cc_start: 0.7645 (OUTLIER) cc_final: 0.7119 (m) REVERT: A 161 ASP cc_start: 0.7922 (m-30) cc_final: 0.7523 (m-30) REVERT: A 258 ASP cc_start: 0.8608 (m-30) cc_final: 0.8172 (t0) REVERT: A 366 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7602 (pp) REVERT: A 499 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.8526 (m-30) REVERT: A 607 SER cc_start: 0.8933 (OUTLIER) cc_final: 0.8723 (t) REVERT: A 665 GLU cc_start: 0.8760 (pm20) cc_final: 0.8497 (pm20) REVERT: B 135 TYR cc_start: 0.8245 (t80) cc_final: 0.8039 (t80) REVERT: C 15 SER cc_start: 0.8832 (t) cc_final: 0.8084 (m) REVERT: F 9 ASN cc_start: 0.7774 (t0) cc_final: 0.7491 (m-40) REVERT: F 68 MET cc_start: 0.7886 (mtm) cc_final: 0.6658 (mmt) REVERT: F 453 SER cc_start: 0.1031 (OUTLIER) cc_final: 0.0655 (t) REVERT: F 544 VAL cc_start: 0.0757 (OUTLIER) cc_final: 0.0246 (t) REVERT: F 576 MET cc_start: -0.0071 (mmt) cc_final: -0.2126 (mtt) REVERT: E 233 MET cc_start: 0.7716 (mpm) cc_final: 0.6808 (tpp) REVERT: E 315 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8439 (p0) REVERT: G 46 SER cc_start: 0.6456 (OUTLIER) cc_final: 0.5763 (t) outliers start: 116 outliers final: 27 residues processed: 398 average time/residue: 0.1565 time to fit residues: 95.0098 Evaluate side-chains 195 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 318 CYS Chi-restraints excluded: chain F residue 453 SER Chi-restraints excluded: chain F residue 544 VAL Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain G residue 2 ASN Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 27 ASN Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 102 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 197 optimal weight: 0.0980 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN A 725 HIS A 790 ASN B 73 GLN D 176 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN F 164 HIS ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 492 GLN F 516 ASN ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 554 HIS G 98 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.125595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.077224 restraints weight = 140855.655| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 7.57 r_work: 0.3178 rms_B_bonded: 6.52 restraints_weight: 2.0000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 22559 Z= 0.255 Angle : 0.842 17.825 30906 Z= 0.417 Chirality : 0.050 0.636 3581 Planarity : 0.006 0.069 3748 Dihedral : 9.950 149.257 3585 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.00 % Favored : 90.73 % Rotamer: Outliers : 5.40 % Allowed : 30.60 % Favored : 64.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.16), residues: 2650 helix: 0.07 (0.17), residues: 957 sheet: -1.29 (0.34), residues: 234 loop : -2.41 (0.15), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 390 TYR 0.020 0.002 TYR A 831 PHE 0.033 0.002 PHE E 422 TRP 0.026 0.002 TRP B 182 HIS 0.008 0.002 HIS A 810 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.25 (22527) covalent geometry : angle 0.82408 / 0.42 (30879) hydrogen bonds : bond 0.05723 / 3.65 ( 842) hydrogen bonds : angle 5.48763 / 3.84 ( 2324) metal coordination : bond 0.01914 / 1.35 ( 32) metal coordination : angle 5.96051 / 3.67 ( 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 291 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 169 time to evaluate : 0.836 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 50 LYS cc_start: 0.7702 (tptt) cc_final: 0.7427 (tptp) REVERT: A 110 MET cc_start: 0.8029 (tpp) cc_final: 0.7681 (tpp) REVERT: A 258 ASP cc_start: 0.9070 (m-30) cc_final: 0.8559 (t0) REVERT: A 665 GLU cc_start: 0.8988 (pm20) cc_final: 0.8776 (pm20) REVERT: A 924 MET cc_start: 0.8837 (mmm) cc_final: 0.8446 (mtt) REVERT: B 62 MET cc_start: 0.8588 (ttt) cc_final: 0.8040 (tpp) REVERT: B 174 MET cc_start: 0.9234 (tpp) cc_final: 0.8912 (tpp) REVERT: C 38 ASP cc_start: 0.9051 (t0) cc_final: 0.8779 (t0) REVERT: C 67 ASP cc_start: 0.8190 (t0) cc_final: 0.7893 (t0) REVERT: D 77 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8233 (tm-30) REVERT: D 189 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8509 (tt) REVERT: F 9 ASN cc_start: 0.8446 (t0) cc_final: 0.8073 (m110) REVERT: F 68 MET cc_start: 0.8200 (mtm) cc_final: 0.6918 (mmt) REVERT: F 460 LYS cc_start: -0.2118 (OUTLIER) cc_final: -0.2924 (tttm) REVERT: F 531 GLN cc_start: 0.2708 (OUTLIER) cc_final: 0.1959 (mm-40) REVERT: F 576 MET cc_start: 0.1620 (mmt) cc_final: 0.0834 (mtt) REVERT: E 274 MET cc_start: 0.8348 (mmm) cc_final: 0.7739 (mmp) REVERT: G 31 TYR cc_start: 0.7875 (m-10) cc_final: 0.7633 (m-80) REVERT: G 35 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8207 (m) outliers start: 122 outliers final: 50 residues processed: 277 average time/residue: 0.1520 time to fit residues: 65.3968 Evaluate side-chains 189 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 135 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 318 CYS Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 436 MET Chi-restraints excluded: chain F residue 460 LYS Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 426 CYS Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain G residue 2 ASN Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 77 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 264 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 255 optimal weight: 30.0000 chunk 136 optimal weight: 9.9990 chunk 56 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 118 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN A 9 ASN A 113 HIS A 168 ASN A 447 ASN A 898 HIS C 34 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.125533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.074460 restraints weight = 133797.279| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 7.28 r_work: 0.3176 rms_B_bonded: 5.13 restraints_weight: 2.0000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 22559 Z= 0.137 Angle : 0.692 15.761 30906 Z= 0.342 Chirality : 0.045 0.329 3581 Planarity : 0.005 0.051 3748 Dihedral : 9.298 137.709 3558 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.02 % Favored : 91.72 % Rotamer: Outliers : 3.78 % Allowed : 30.55 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.16), residues: 2650 helix: 0.33 (0.17), residues: 960 sheet: -1.23 (0.33), residues: 239 loop : -2.27 (0.15), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 555 TYR 0.020 0.001 TYR F 299 PHE 0.021 0.001 PHE F 373 TRP 0.023 0.002 TRP B 182 HIS 0.012 0.001 HIS A 898 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (22527) covalent geometry : angle 0.67656 / 0.34 (30879) hydrogen bonds : bond 0.04885 / 3.11 ( 842) hydrogen bonds : angle 5.07616 / 3.55 ( 2324) metal coordination : bond 0.01575 / 1.21 ( 32) metal coordination : angle 4.93562 / 3.06 ( 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 238 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 153 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.7708 (tptt) cc_final: 0.7435 (tptp) REVERT: A 63 ASP cc_start: 0.9215 (OUTLIER) cc_final: 0.8572 (t0) REVERT: A 110 MET cc_start: 0.8037 (tpp) cc_final: 0.7637 (tpp) REVERT: A 138 ASN cc_start: 0.9103 (OUTLIER) cc_final: 0.8429 (p0) REVERT: A 258 ASP cc_start: 0.9024 (m-30) cc_final: 0.8618 (t0) REVERT: A 380 MET cc_start: 0.7471 (mmt) cc_final: 0.7270 (mmm) REVERT: A 618 ASP cc_start: 0.8594 (t0) cc_final: 0.8344 (t0) REVERT: A 924 MET cc_start: 0.8804 (mmm) cc_final: 0.8251 (mtt) REVERT: B 57 ARG cc_start: 0.7053 (mpt180) cc_final: 0.6545 (mpt180) REVERT: C 19 GLN cc_start: 0.8402 (mp10) cc_final: 0.7634 (mp10) REVERT: C 38 ASP cc_start: 0.9019 (t0) cc_final: 0.8666 (t0) REVERT: D 60 GLU cc_start: 0.8343 (tm-30) cc_final: 0.8017 (pp20) REVERT: D 71 TYR cc_start: 0.7903 (OUTLIER) cc_final: 0.7311 (t80) REVERT: F 9 ASN cc_start: 0.8376 (t0) cc_final: 0.7965 (m110) REVERT: F 68 MET cc_start: 0.8125 (mtm) cc_final: 0.6888 (mmt) REVERT: F 167 TRP cc_start: 0.3837 (p-90) cc_final: 0.3301 (p-90) REVERT: F 460 LYS cc_start: -0.2926 (OUTLIER) cc_final: -0.3437 (tttm) REVERT: F 531 GLN cc_start: 0.1728 (OUTLIER) cc_final: 0.1032 (mm-40) REVERT: F 576 MET cc_start: 0.1350 (mmt) cc_final: -0.0012 (mtt) REVERT: E 274 MET cc_start: 0.8541 (mmm) cc_final: 0.8041 (mmp) REVERT: G 2 ASN cc_start: 0.9038 (OUTLIER) cc_final: 0.8812 (m-40) outliers start: 85 outliers final: 45 residues processed: 227 average time/residue: 0.1479 time to fit residues: 52.8786 Evaluate side-chains 184 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 133 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 318 CYS Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 460 LYS Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain G residue 2 ASN Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 77 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 240 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 chunk 236 optimal weight: 30.0000 chunk 70 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 25 optimal weight: 0.0970 chunk 118 optimal weight: 9.9990 chunk 237 optimal weight: 8.9990 chunk 261 optimal weight: 9.9990 chunk 242 optimal weight: 30.0000 chunk 220 optimal weight: 20.0000 overall best weight: 6.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN A 113 HIS A 447 ASN A 489 ASN ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.118115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.067499 restraints weight = 126992.141| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 6.63 r_work: 0.2974 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.080 22559 Z= 0.467 Angle : 0.957 23.467 30906 Z= 0.473 Chirality : 0.056 0.342 3581 Planarity : 0.006 0.063 3748 Dihedral : 9.779 147.795 3556 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.36 % Favored : 89.37 % Rotamer: Outliers : 5.58 % Allowed : 29.94 % Favored : 64.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.15), residues: 2650 helix: -0.50 (0.16), residues: 961 sheet: -1.42 (0.35), residues: 218 loop : -2.42 (0.15), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 116 TYR 0.029 0.003 TYR A 788 PHE 0.030 0.003 PHE A 594 TRP 0.025 0.002 TRP A 916 HIS 0.011 0.002 HIS A 650 Details of bonding type rmsd/Z covalent geometry : bond 0.01056 / 0.47 (22527) covalent geometry : angle 0.92964 / 0.47 (30879) hydrogen bonds : bond 0.06892 / 4.50 ( 842) hydrogen bonds : angle 5.74378 / 4.01 ( 2324) metal coordination : bond 0.02491 / 1.63 ( 32) metal coordination : angle 7.74446 / 4.66 ( 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 258 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 132 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.9308 (OUTLIER) cc_final: 0.8633 (t0) REVERT: A 110 MET cc_start: 0.8139 (tpp) cc_final: 0.7880 (tpp) REVERT: A 138 ASN cc_start: 0.9162 (OUTLIER) cc_final: 0.8516 (p0) REVERT: A 258 ASP cc_start: 0.9258 (OUTLIER) cc_final: 0.8903 (t0) REVERT: A 668 MET cc_start: 0.9175 (ttp) cc_final: 0.8737 (ttt) REVERT: A 798 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8900 (mtmm) REVERT: A 924 MET cc_start: 0.8767 (mmm) cc_final: 0.8418 (mtt) REVERT: B 75 ARG cc_start: 0.8666 (ttp80) cc_final: 0.8443 (ttp80) REVERT: C 38 ASP cc_start: 0.9329 (t0) cc_final: 0.9055 (t0) REVERT: D 48 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8112 (tm-30) REVERT: D 128 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6773 (tp) REVERT: F 68 MET cc_start: 0.8571 (mtm) cc_final: 0.7431 (mmt) REVERT: F 167 TRP cc_start: 0.4279 (p-90) cc_final: 0.3704 (p-90) REVERT: F 289 SER cc_start: 0.5965 (OUTLIER) cc_final: 0.5645 (p) REVERT: F 460 LYS cc_start: -0.2765 (OUTLIER) cc_final: -0.3316 (tttm) REVERT: F 531 GLN cc_start: 0.1772 (OUTLIER) cc_final: 0.1555 (tp40) REVERT: F 576 MET cc_start: 0.0893 (mmt) cc_final: -0.0767 (mtt) REVERT: E 21 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8692 (mmm160) REVERT: E 25 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7279 (mm) REVERT: E 274 MET cc_start: 0.8682 (mmm) cc_final: 0.8202 (mmp) REVERT: E 429 MET cc_start: 0.4724 (ptm) cc_final: 0.4419 (ppp) REVERT: E 475 PHE cc_start: 0.4400 (OUTLIER) cc_final: 0.4086 (p90) outliers start: 126 outliers final: 73 residues processed: 247 average time/residue: 0.1367 time to fit residues: 53.3374 Evaluate side-chains 204 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 120 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 318 CYS Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 460 LYS Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 24 PHE Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 426 CYS Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 475 PHE Chi-restraints excluded: chain E residue 545 ILE Chi-restraints excluded: chain G residue 2 ASN Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 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: 0.8980 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 179 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 chunk 199 optimal weight: 7.9990 chunk 263 optimal weight: 9.9990 chunk 176 optimal weight: 5.9990 chunk 231 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 447 ASN B 118 ASN C 34 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.122307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.071216 restraints weight = 120823.235| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 7.01 r_work: 0.3088 rms_B_bonded: 5.63 restraints_weight: 2.0000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 22559 Z= 0.138 Angle : 0.700 19.429 30906 Z= 0.343 Chirality : 0.045 0.249 3581 Planarity : 0.004 0.060 3748 Dihedral : 9.093 130.662 3554 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.64 % Favored : 92.10 % Rotamer: Outliers : 3.60 % Allowed : 31.30 % Favored : 65.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.16), residues: 2650 helix: 0.11 (0.17), residues: 967 sheet: -1.18 (0.34), residues: 228 loop : -2.22 (0.15), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 442 TYR 0.017 0.001 TYR A 237 PHE 0.019 0.001 PHE F 373 TRP 0.025 0.002 TRP B 182 HIS 0.005 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (22527) covalent geometry : angle 0.68149 / 0.34 (30879) hydrogen bonds : bond 0.04891 / 3.12 ( 842) hydrogen bonds : angle 5.04589 / 3.53 ( 2324) metal coordination : bond 0.01253 / 0.92 ( 32) metal coordination : angle 5.42147 / 3.08 ( 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 215 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 134 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.9331 (OUTLIER) cc_final: 0.8790 (t70) REVERT: A 110 MET cc_start: 0.8110 (tpp) cc_final: 0.7835 (mmm) REVERT: A 138 ASN cc_start: 0.9097 (OUTLIER) cc_final: 0.8402 (p0) REVERT: A 161 ASP cc_start: 0.8197 (m-30) cc_final: 0.7840 (t0) REVERT: A 258 ASP cc_start: 0.9171 (m-30) cc_final: 0.8839 (t0) REVERT: A 365 ARG cc_start: 0.7590 (tpp-160) cc_final: 0.7280 (tpp-160) REVERT: A 380 MET cc_start: 0.7551 (mmt) cc_final: 0.7323 (mmm) REVERT: A 668 MET cc_start: 0.9107 (ttp) cc_final: 0.8641 (ttt) REVERT: A 798 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8922 (mtmm) REVERT: A 924 MET cc_start: 0.8837 (mmm) cc_final: 0.8402 (mtt) REVERT: B 52 ASP cc_start: 0.8095 (m-30) cc_final: 0.7818 (t0) REVERT: B 77 GLU cc_start: 0.8440 (tp30) cc_final: 0.8035 (tp30) REVERT: C 19 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8043 (mt0) REVERT: C 38 ASP cc_start: 0.9204 (t0) cc_final: 0.8827 (t0) REVERT: D 48 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8199 (tm-30) REVERT: D 60 GLU cc_start: 0.8437 (pp20) cc_final: 0.8235 (pp20) REVERT: D 62 MET cc_start: 0.8369 (tmm) cc_final: 0.8097 (tmm) REVERT: D 129 MET cc_start: 0.7684 (mpp) cc_final: 0.7441 (mpp) REVERT: F 9 ASN cc_start: 0.8877 (t0) cc_final: 0.8409 (m110) REVERT: F 68 MET cc_start: 0.8220 (mtm) cc_final: 0.7101 (mmt) REVERT: F 167 TRP cc_start: 0.4237 (p-90) cc_final: 0.3708 (p-90) REVERT: F 289 SER cc_start: 0.5398 (OUTLIER) cc_final: 0.5070 (p) REVERT: F 460 LYS cc_start: -0.2621 (OUTLIER) cc_final: -0.3167 (tttm) REVERT: F 531 GLN cc_start: 0.1770 (OUTLIER) cc_final: 0.1563 (tp40) REVERT: F 576 MET cc_start: 0.0979 (mmt) cc_final: -0.0636 (mtt) REVERT: E 274 MET cc_start: 0.8745 (mmm) cc_final: 0.8402 (mmp) REVERT: E 436 MET cc_start: 0.6951 (mmm) cc_final: 0.6750 (mmm) REVERT: E 475 PHE cc_start: 0.4319 (OUTLIER) cc_final: 0.4051 (p90) REVERT: E 576 MET cc_start: -0.3785 (tmm) cc_final: -0.4069 (ttp) REVERT: G 89 TYR cc_start: 0.7259 (m-80) cc_final: 0.7031 (m-80) outliers start: 81 outliers final: 48 residues processed: 207 average time/residue: 0.1659 time to fit residues: 53.2795 Evaluate side-chains 181 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 125 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 318 CYS Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 460 LYS Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 426 CYS Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 475 PHE Chi-restraints excluded: chain G residue 2 ASN Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 109 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 23 optimal weight: 1.9990 chunk 191 optimal weight: 7.9990 chunk 215 optimal weight: 0.0050 chunk 263 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 157 optimal weight: 7.9990 chunk 196 optimal weight: 50.0000 chunk 64 optimal weight: 4.9990 chunk 225 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 204 optimal weight: 0.8980 overall best weight: 1.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN A 898 HIS ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 GLN ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.121487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.071400 restraints weight = 132612.570| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 6.98 r_work: 0.3039 rms_B_bonded: 5.51 restraints_weight: 2.0000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22559 Z= 0.163 Angle : 0.692 19.056 30906 Z= 0.337 Chirality : 0.045 0.251 3581 Planarity : 0.004 0.063 3748 Dihedral : 8.784 120.407 3552 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.51 % Favored : 91.26 % Rotamer: Outliers : 3.64 % Allowed : 30.64 % Favored : 65.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.16), residues: 2650 helix: 0.22 (0.17), residues: 976 sheet: -1.20 (0.34), residues: 228 loop : -2.13 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 75 TYR 0.027 0.002 TYR F 457 PHE 0.018 0.001 PHE F 373 TRP 0.020 0.001 TRP B 182 HIS 0.004 0.001 HIS F 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (22527) covalent geometry : angle 0.67422 / 0.34 (30879) hydrogen bonds : bond 0.04845 / 3.10 ( 842) hydrogen bonds : angle 4.94149 / 3.46 ( 2324) metal coordination : bond 0.01138 / 0.82 ( 32) metal coordination : angle 5.26028 / 3.02 ( 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 214 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 132 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.9325 (OUTLIER) cc_final: 0.9000 (t70) REVERT: A 110 MET cc_start: 0.8133 (tpp) cc_final: 0.7820 (mmm) REVERT: A 138 ASN cc_start: 0.9136 (OUTLIER) cc_final: 0.8444 (p0) REVERT: A 161 ASP cc_start: 0.8308 (m-30) cc_final: 0.7938 (t0) REVERT: A 258 ASP cc_start: 0.9194 (m-30) cc_final: 0.8826 (t0) REVERT: A 380 MET cc_start: 0.7598 (mmt) cc_final: 0.7327 (mmm) REVERT: A 618 ASP cc_start: 0.8772 (t0) cc_final: 0.8519 (t0) REVERT: A 668 MET cc_start: 0.9114 (ttp) cc_final: 0.8635 (ttt) REVERT: A 924 MET cc_start: 0.8810 (mmm) cc_final: 0.8422 (mtt) REVERT: B 57 ARG cc_start: 0.7209 (mpt180) cc_final: 0.6811 (mpt180) REVERT: B 77 GLU cc_start: 0.8504 (tp30) cc_final: 0.8091 (tp30) REVERT: C 19 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8087 (mt0) REVERT: C 38 ASP cc_start: 0.9262 (t0) cc_final: 0.8901 (t0) REVERT: D 48 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8262 (tm-30) REVERT: D 62 MET cc_start: 0.8346 (tmm) cc_final: 0.8041 (tmm) REVERT: D 129 MET cc_start: 0.7706 (mpp) cc_final: 0.7436 (mpp) REVERT: F 9 ASN cc_start: 0.8618 (t0) cc_final: 0.8195 (m-40) REVERT: F 68 MET cc_start: 0.8342 (mtm) cc_final: 0.7255 (mmt) REVERT: F 167 TRP cc_start: 0.4234 (p-90) cc_final: 0.3687 (p-90) REVERT: F 289 SER cc_start: 0.5769 (OUTLIER) cc_final: 0.5442 (p) REVERT: F 460 LYS cc_start: -0.2394 (OUTLIER) cc_final: -0.3063 (tttm) REVERT: F 576 MET cc_start: 0.1072 (mmt) cc_final: -0.0425 (mtt) REVERT: E 274 MET cc_start: 0.8620 (mmm) cc_final: 0.8119 (mmp) REVERT: E 436 MET cc_start: 0.7180 (mmm) cc_final: 0.6950 (mmm) REVERT: E 576 MET cc_start: -0.3851 (tmm) cc_final: -0.4207 (ttp) outliers start: 82 outliers final: 58 residues processed: 205 average time/residue: 0.1519 time to fit residues: 48.5887 Evaluate side-chains 190 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 127 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 621 LYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 318 CYS Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 460 LYS Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 426 CYS Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain G residue 2 ASN Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 102 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 86 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 263 optimal weight: 0.0980 chunk 212 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 241 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 ASN A 292 GLN A 447 ASN ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 537 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.119732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.069419 restraints weight = 129088.613| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 6.44 r_work: 0.3041 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 22559 Z= 0.220 Angle : 0.732 19.525 30906 Z= 0.358 Chirality : 0.047 0.270 3581 Planarity : 0.005 0.065 3748 Dihedral : 8.631 101.871 3552 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.70 % Favored : 91.15 % Rotamer: Outliers : 3.95 % Allowed : 30.42 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.16), residues: 2650 helix: 0.11 (0.17), residues: 976 sheet: -1.35 (0.33), residues: 246 loop : -2.14 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 443 TYR 0.020 0.002 TYR F 457 PHE 0.021 0.002 PHE F 373 TRP 0.019 0.002 TRP D 182 HIS 0.006 0.001 HIS F 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.22 (22527) covalent geometry : angle 0.71442 / 0.36 (30879) hydrogen bonds : bond 0.05168 / 3.32 ( 842) hydrogen bonds : angle 5.00034 / 3.51 ( 2324) metal coordination : bond 0.01300 / 0.89 ( 32) metal coordination : angle 5.48133 / 3.15 ( 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 224 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 135 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.9364 (OUTLIER) cc_final: 0.9010 (t70) REVERT: A 110 MET cc_start: 0.8046 (tpp) cc_final: 0.7737 (mmm) REVERT: A 138 ASN cc_start: 0.9114 (OUTLIER) cc_final: 0.8385 (p0) REVERT: A 161 ASP cc_start: 0.8455 (m-30) cc_final: 0.8085 (t0) REVERT: A 258 ASP cc_start: 0.9187 (m-30) cc_final: 0.8839 (t0) REVERT: A 365 ARG cc_start: 0.7387 (tpp-160) cc_final: 0.7154 (tpp-160) REVERT: A 380 MET cc_start: 0.7637 (mmt) cc_final: 0.7378 (mmm) REVERT: A 396 PHE cc_start: 0.8538 (t80) cc_final: 0.8266 (t80) REVERT: A 618 ASP cc_start: 0.8877 (t0) cc_final: 0.8566 (t0) REVERT: A 668 MET cc_start: 0.9105 (ttp) cc_final: 0.8684 (ttt) REVERT: A 924 MET cc_start: 0.8792 (mmm) cc_final: 0.8499 (mtp) REVERT: B 52 ASP cc_start: 0.8425 (m-30) cc_final: 0.7815 (t0) REVERT: B 57 ARG cc_start: 0.7332 (mpt180) cc_final: 0.6940 (mpt180) REVERT: B 157 GLN cc_start: 0.8338 (mm110) cc_final: 0.8084 (mm110) REVERT: C 19 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8195 (mt0) REVERT: C 38 ASP cc_start: 0.9239 (t0) cc_final: 0.8876 (t0) REVERT: D 48 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8275 (tm-30) REVERT: D 62 MET cc_start: 0.8360 (tmm) cc_final: 0.8090 (tmm) REVERT: D 129 MET cc_start: 0.7671 (mpp) cc_final: 0.7413 (mpp) REVERT: F 68 MET cc_start: 0.8452 (mtm) cc_final: 0.7515 (mmt) REVERT: F 289 SER cc_start: 0.5369 (OUTLIER) cc_final: 0.4999 (p) REVERT: F 460 LYS cc_start: -0.3535 (OUTLIER) cc_final: -0.3920 (tttm) REVERT: F 576 MET cc_start: 0.0616 (mmt) cc_final: -0.1315 (mtt) REVERT: E 274 MET cc_start: 0.8611 (mmm) cc_final: 0.7978 (mmm) REVERT: E 475 PHE cc_start: 0.4532 (OUTLIER) cc_final: 0.4288 (p90) REVERT: E 576 MET cc_start: -0.3876 (tmm) cc_final: -0.4399 (ttp) REVERT: G 2 ASN cc_start: 0.8979 (OUTLIER) cc_final: 0.8710 (m-40) outliers start: 89 outliers final: 62 residues processed: 213 average time/residue: 0.1516 time to fit residues: 50.8169 Evaluate side-chains 193 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 124 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 621 LYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 318 CYS Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 429 MET Chi-restraints excluded: chain F residue 460 LYS Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 426 CYS Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 475 PHE Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain E residue 545 ILE Chi-restraints excluded: chain G residue 2 ASN Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 106 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 252 optimal weight: 8.9990 chunk 204 optimal weight: 5.9990 chunk 216 optimal weight: 6.9990 chunk 190 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 240 optimal weight: 6.9990 chunk 193 optimal weight: 7.9990 chunk 189 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 HIS ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 GLN ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 519 ASN G 11 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.117010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.067286 restraints weight = 137629.254| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 7.79 r_work: 0.2825 rms_B_bonded: 5.71 restraints_weight: 2.0000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 22559 Z= 0.286 Angle : 0.793 21.401 30906 Z= 0.387 Chirality : 0.049 0.289 3581 Planarity : 0.005 0.067 3748 Dihedral : 8.499 88.206 3552 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.30 % Favored : 90.54 % Rotamer: Outliers : 4.08 % Allowed : 30.55 % Favored : 65.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.16), residues: 2650 helix: -0.05 (0.17), residues: 967 sheet: -1.30 (0.34), residues: 236 loop : -2.18 (0.16), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 443 TYR 0.024 0.002 TYR G 89 PHE 0.020 0.002 PHE A 321 TRP 0.020 0.002 TRP A 916 HIS 0.007 0.001 HIS F 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00654 / 0.29 (22527) covalent geometry : angle 0.77257 / 0.39 (30879) hydrogen bonds : bond 0.05588 / 3.60 ( 842) hydrogen bonds : angle 5.16985 / 3.64 ( 2324) metal coordination : bond 0.01613 / 1.07 ( 32) metal coordination : angle 6.10411 / 3.45 ( 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 220 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 128 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.9387 (OUTLIER) cc_final: 0.9084 (t70) REVERT: A 110 MET cc_start: 0.8221 (tpp) cc_final: 0.7850 (mmm) REVERT: A 138 ASN cc_start: 0.9147 (OUTLIER) cc_final: 0.8391 (p0) REVERT: A 161 ASP cc_start: 0.8512 (m-30) cc_final: 0.8097 (t0) REVERT: A 258 ASP cc_start: 0.9223 (m-30) cc_final: 0.8876 (t0) REVERT: A 380 MET cc_start: 0.7704 (mmt) cc_final: 0.7416 (mmm) REVERT: A 396 PHE cc_start: 0.8522 (t80) cc_final: 0.8256 (t80) REVERT: A 665 GLU cc_start: 0.8789 (pm20) cc_final: 0.8587 (mp0) REVERT: A 668 MET cc_start: 0.9017 (ttp) cc_final: 0.8605 (ttt) REVERT: A 924 MET cc_start: 0.8657 (mmm) cc_final: 0.8370 (mtp) REVERT: B 77 GLU cc_start: 0.8536 (tp30) cc_final: 0.8082 (tp30) REVERT: C 19 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8276 (mt0) REVERT: C 38 ASP cc_start: 0.9322 (t0) cc_final: 0.9000 (t0) REVERT: D 48 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8313 (tm-30) REVERT: D 62 MET cc_start: 0.8433 (tmm) cc_final: 0.8137 (tmm) REVERT: F 68 MET cc_start: 0.8705 (mtm) cc_final: 0.7499 (mmt) REVERT: F 289 SER cc_start: 0.6352 (OUTLIER) cc_final: 0.6058 (p) REVERT: F 378 MET cc_start: 0.5257 (OUTLIER) cc_final: 0.5036 (mmm) REVERT: F 443 ARG cc_start: -0.2493 (OUTLIER) cc_final: -0.2725 (ptt180) REVERT: F 460 LYS cc_start: -0.2048 (OUTLIER) cc_final: -0.2815 (ttpp) REVERT: F 576 MET cc_start: 0.0761 (mmt) cc_final: -0.0738 (mtt) REVERT: E 576 MET cc_start: -0.4108 (OUTLIER) cc_final: -0.4429 (ttp) REVERT: G 74 ARG cc_start: 0.8348 (ptm-80) cc_final: 0.7713 (ptm-80) outliers start: 92 outliers final: 68 residues processed: 210 average time/residue: 0.1550 time to fit residues: 50.9411 Evaluate side-chains 201 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 125 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 63 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 318 CYS Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 378 MET Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 443 ARG Chi-restraints excluded: chain F residue 460 LYS Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 426 CYS Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain E residue 576 MET Chi-restraints excluded: chain G residue 2 ASN Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 106 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 131 optimal weight: 0.9980 chunk 117 optimal weight: 0.0010 chunk 256 optimal weight: 4.9990 chunk 152 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 chunk 166 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 245 optimal weight: 8.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 381 HIS ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.120009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.069755 restraints weight = 114141.826| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 6.07 r_work: 0.3065 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.5972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22559 Z= 0.123 Angle : 0.681 17.769 30906 Z= 0.331 Chirality : 0.045 0.222 3581 Planarity : 0.004 0.069 3748 Dihedral : 7.989 78.904 3550 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.26 % Favored : 92.59 % Rotamer: Outliers : 2.94 % Allowed : 31.47 % Favored : 65.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.16), residues: 2650 helix: 0.29 (0.17), residues: 970 sheet: -1.19 (0.35), residues: 229 loop : -1.95 (0.16), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 75 TYR 0.020 0.001 TYR E 421 PHE 0.015 0.001 PHE A 102 TRP 0.028 0.002 TRP B 182 HIS 0.007 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (22527) covalent geometry : angle 0.66534 / 0.33 (30879) hydrogen bonds : bond 0.04543 / 2.90 ( 842) hydrogen bonds : angle 4.72484 / 3.33 ( 2324) metal coordination : bond 0.01165 / 0.90 ( 32) metal coordination : angle 4.90176 / 2.73 ( 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 192 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 126 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8906 (OUTLIER) cc_final: 0.8622 (p0) REVERT: A 63 ASP cc_start: 0.9354 (OUTLIER) cc_final: 0.9102 (t70) REVERT: A 110 MET cc_start: 0.8111 (tpp) cc_final: 0.7776 (mmm) REVERT: A 138 ASN cc_start: 0.9063 (OUTLIER) cc_final: 0.8364 (p0) REVERT: A 161 ASP cc_start: 0.8322 (m-30) cc_final: 0.7992 (t0) REVERT: A 258 ASP cc_start: 0.9196 (m-30) cc_final: 0.8858 (t0) REVERT: A 380 MET cc_start: 0.7565 (mmt) cc_final: 0.7292 (mmm) REVERT: A 668 MET cc_start: 0.8978 (ttp) cc_final: 0.8487 (ttt) REVERT: A 906 MET cc_start: 0.8000 (pmm) cc_final: 0.7735 (pmm) REVERT: A 924 MET cc_start: 0.8757 (mmm) cc_final: 0.8353 (mtp) REVERT: B 77 GLU cc_start: 0.8435 (tp30) cc_final: 0.7995 (tp30) REVERT: C 38 ASP cc_start: 0.9246 (t0) cc_final: 0.8850 (t0) REVERT: D 62 MET cc_start: 0.8385 (tmm) cc_final: 0.8107 (tmm) REVERT: D 129 MET cc_start: 0.7594 (mpp) cc_final: 0.7320 (mpp) REVERT: F 68 MET cc_start: 0.8519 (mtm) cc_final: 0.7372 (mmt) REVERT: F 289 SER cc_start: 0.5968 (OUTLIER) cc_final: 0.5677 (p) REVERT: F 378 MET cc_start: 0.5065 (OUTLIER) cc_final: 0.4839 (mmm) REVERT: F 436 MET cc_start: 0.6041 (mpt) cc_final: 0.5835 (mpt) REVERT: F 576 MET cc_start: 0.0974 (mmt) cc_final: -0.0817 (mtt) REVERT: E 68 MET cc_start: 0.8956 (pmm) cc_final: 0.8425 (mmm) REVERT: E 274 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8149 (tpp) REVERT: E 576 MET cc_start: -0.4033 (OUTLIER) cc_final: -0.4492 (ttp) REVERT: G 50 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7743 (t0) REVERT: G 68 GLU cc_start: 0.6911 (tm-30) cc_final: 0.6706 (tm-30) REVERT: G 76 VAL cc_start: 0.8159 (OUTLIER) cc_final: 0.7728 (p) outliers start: 66 outliers final: 45 residues processed: 180 average time/residue: 0.1578 time to fit residues: 44.7801 Evaluate side-chains 172 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 118 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 378 MET Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 460 LYS Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 426 CYS Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 576 MET Chi-restraints excluded: chain G residue 2 ASN Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 76 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 89 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 265 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 173 optimal weight: 0.5980 chunk 197 optimal weight: 2.9990 chunk 260 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.119477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.068857 restraints weight = 140048.960| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 7.22 r_work: 0.3007 rms_B_bonded: 5.06 restraints_weight: 2.0000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.6106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 22559 Z= 0.183 Angle : 0.705 18.075 30906 Z= 0.343 Chirality : 0.046 0.253 3581 Planarity : 0.005 0.073 3748 Dihedral : 7.968 80.843 3548 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.36 % Favored : 91.49 % Rotamer: Outliers : 2.46 % Allowed : 31.96 % Favored : 65.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.16), residues: 2650 helix: 0.21 (0.17), residues: 973 sheet: -1.28 (0.34), residues: 239 loop : -1.95 (0.16), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 75 TYR 0.017 0.002 TYR E 421 PHE 0.017 0.002 PHE A 753 TRP 0.018 0.001 TRP B 182 HIS 0.005 0.001 HIS F 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (22527) covalent geometry : angle 0.68942 / 0.34 (30879) hydrogen bonds : bond 0.04830 / 3.12 ( 842) hydrogen bonds : angle 4.80000 / 3.38 ( 2324) metal coordination : bond 0.01140 / 0.82 ( 32) metal coordination : angle 5.03220 / 2.85 ( 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 175 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 120 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8985 (OUTLIER) cc_final: 0.8711 (p0) REVERT: A 63 ASP cc_start: 0.9370 (OUTLIER) cc_final: 0.9118 (t70) REVERT: A 110 MET cc_start: 0.8148 (tpp) cc_final: 0.7817 (mmm) REVERT: A 138 ASN cc_start: 0.9091 (OUTLIER) cc_final: 0.8383 (p0) REVERT: A 161 ASP cc_start: 0.8430 (m-30) cc_final: 0.8068 (t0) REVERT: A 258 ASP cc_start: 0.9221 (m-30) cc_final: 0.8861 (t0) REVERT: A 380 MET cc_start: 0.7536 (mmt) cc_final: 0.7244 (mmm) REVERT: A 668 MET cc_start: 0.9081 (ttp) cc_final: 0.8609 (ttt) REVERT: A 906 MET cc_start: 0.8079 (pmm) cc_final: 0.7837 (pmm) REVERT: A 924 MET cc_start: 0.8767 (mmm) cc_final: 0.8439 (mtp) REVERT: B 77 GLU cc_start: 0.8404 (tp30) cc_final: 0.7983 (tp30) REVERT: C 38 ASP cc_start: 0.9313 (t0) cc_final: 0.8943 (t0) REVERT: D 62 MET cc_start: 0.8315 (tmm) cc_final: 0.8001 (tmm) REVERT: D 129 MET cc_start: 0.7691 (mpp) cc_final: 0.7389 (mpp) REVERT: F 68 MET cc_start: 0.8600 (mtm) cc_final: 0.7430 (mmt) REVERT: F 289 SER cc_start: 0.5857 (OUTLIER) cc_final: 0.5542 (p) REVERT: F 436 MET cc_start: 0.6026 (mpt) cc_final: 0.5774 (mpt) REVERT: F 576 MET cc_start: 0.0825 (mmt) cc_final: -0.1077 (mtt) REVERT: E 68 MET cc_start: 0.9069 (pmm) cc_final: 0.8556 (mmm) REVERT: E 274 MET cc_start: 0.8610 (mmm) cc_final: 0.8222 (tpp) REVERT: E 576 MET cc_start: -0.4171 (OUTLIER) cc_final: -0.4615 (ttp) REVERT: G 74 ARG cc_start: 0.7985 (ptm-80) cc_final: 0.7606 (ptm-80) outliers start: 55 outliers final: 48 residues processed: 169 average time/residue: 0.1532 time to fit residues: 41.0121 Evaluate side-chains 171 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 118 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 40 ASP Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 460 LYS Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 426 CYS Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 576 MET Chi-restraints excluded: chain G residue 2 ASN Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 34 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 130 optimal weight: 2.9990 chunk 157 optimal weight: 10.0000 chunk 39 optimal weight: 0.4980 chunk 163 optimal weight: 9.9990 chunk 250 optimal weight: 30.0000 chunk 3 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 194 optimal weight: 9.9990 chunk 152 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 GLN ** G 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.118719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.067842 restraints weight = 109117.865| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 5.98 r_work: 0.2902 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.6334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 22559 Z= 0.218 Angle : 0.734 18.720 30906 Z= 0.358 Chirality : 0.047 0.265 3581 Planarity : 0.005 0.071 3748 Dihedral : 8.052 77.906 3548 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.70 % Favored : 91.15 % Rotamer: Outliers : 2.90 % Allowed : 31.39 % Favored : 65.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.16), residues: 2650 helix: 0.09 (0.17), residues: 980 sheet: -1.13 (0.36), residues: 216 loop : -1.98 (0.16), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 75 TYR 0.017 0.002 TYR A 831 PHE 0.019 0.002 PHE A 753 TRP 0.017 0.001 TRP A 916 HIS 0.006 0.001 HIS F 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.22 (22527) covalent geometry : angle 0.71701 / 0.36 (30879) hydrogen bonds : bond 0.05077 / 3.27 ( 842) hydrogen bonds : angle 4.89547 / 3.44 ( 2324) metal coordination : bond 0.01286 / 0.90 ( 32) metal coordination : angle 5.31834 / 3.00 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9626.85 seconds wall clock time: 164 minutes 25.50 seconds (9865.50 seconds total)