Starting phenix.real_space_refine on Sun Sep 13 00:00:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6oet_20037/09_2026/6oet_20037.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oet_20037/09_2026/6oet_20037.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6oet_20037/09_2026/6oet_20037.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oet_20037/09_2026/6oet_20037.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6oet_20037/09_2026/6oet_20037.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6oet_20037/09_2026/6oet_20037.cif" model { file = "/net/cci-nas-00/data/ceres_data/6oet_20037/09_2026/6oet_20037.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oet_20037/09_2026/6oet_20037.cif" } resolution = 3.4 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 2 6.06 5 P 205 5.49 5 S 105 5.16 5 C 11728 2.51 5 N 3482 2.21 5 O 4080 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: 19604 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4969 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 618, 4963 Classifications: {'peptide': 618} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 591} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 618, 4963 Classifications: {'peptide': 618} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 591} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 5059 Chain: "B" Number of atoms: 2691 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 342, 2670 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 322} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 342, 2670 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 322} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 2713 Chain: "C" Number of atoms: 5010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5010 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 596} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2673 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 343, 2663 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 19, 'TRANS': 323} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 343, 2663 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 19, 'TRANS': 323} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 2718 Chain: "F" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1030 Classifications: {'DNA': 50} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 49} Chain: "I" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 303 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "J" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 303 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "G" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1205 Classifications: {'DNA': 59} Link IDs: {'rna3p': 58} Chain: "L" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 611 Classifications: {'DNA': 30} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 29} Chain: "M" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 805 Classifications: {'DNA': 39} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 38} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2632 SG CYS A 727 26.378 99.796 107.700 1.00 58.29 S ATOM 2653 SG CYS A 730 23.465 100.415 109.872 1.00 56.60 S ATOM 10347 SG CYS C 727 84.020 63.935 96.316 1.00 52.70 S ATOM 10368 SG CYS C 730 86.625 61.891 97.877 1.00 55.44 S Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ACYS A 907 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 907 " occ=0.50 residue: pdb=" N AHIS B 47 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 47 " occ=0.50 residue: pdb=" N AARG B 237 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 237 " occ=0.50 residue: pdb=" N AHIS D 47 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS D 47 " occ=0.50 residue: pdb=" P DT I 15 " occ=0.85 ... (18 atoms not shown) pdb=" C6 DT I 15 " occ=0.85 residue: pdb=" P DT J 15 " occ=0.85 ... (18 atoms not shown) pdb=" C6 DT J 15 " occ=0.85 Time building chain proxies: 6.22, per 1000 atoms: 0.32 Number of scatterers: 19604 At special positions: 0 Unit cell: (109.14, 156.22, 162.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Ca 2 19.99 S 105 16.00 P 205 15.00 O 4080 8.00 N 3482 7.00 C 11728 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: 1.65 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1102 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 727 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 730 " pdb=" ZN C1102 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 730 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 727 " Number of angles added : 4 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3612 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 16 sheets defined 36.7% alpha, 22.4% beta 102 base pairs and 166 stacking pairs defined. Time for finding SS restraints: 2.70 Creating SS restraints... Processing helix chain 'A' and resid 404 through 422 removed outlier: 3.680A pdb=" N LEU A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLU A 410 " --> pdb=" O HIS A 406 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU A 411 " --> pdb=" O ARG A 407 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN A 414 " --> pdb=" O GLU A 410 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 418 " --> pdb=" O GLN A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 442 removed outlier: 3.763A pdb=" N LEU A 434 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 456 Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 477 through 493 Processing helix chain 'A' and resid 499 through 506 removed outlier: 3.584A pdb=" N LEU A 503 " --> pdb=" O PRO A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'A' and resid 664 through 683 removed outlier: 3.744A pdb=" N LEU A 668 " --> pdb=" O ASP A 664 " (cutoff:3.500A) Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'A' and resid 735 through 739 Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'A' and resid 768 through 777 Processing helix chain 'A' and resid 792 through 812 Processing helix chain 'A' and resid 822 through 842 removed outlier: 3.972A pdb=" N ARG A 826 " --> pdb=" O SER A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 858 Processing helix chain 'A' and resid 860 through 868 Processing helix chain 'A' and resid 873 through 890 Processing helix chain 'A' and resid 891 through 893 No H-bonds generated for 'chain 'A' and resid 891 through 893' Processing helix chain 'A' and resid 902 through 908 Processing helix chain 'A' and resid 908 through 924 Processing helix chain 'A' and resid 933 through 942 Processing helix chain 'A' and resid 942 through 951 Processing helix chain 'A' and resid 958 through 975 removed outlier: 3.569A pdb=" N ARG A 969 " --> pdb=" O ASN A 965 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG A 970 " --> pdb=" O LYS A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.688A pdb=" N THR A 995 " --> pdb=" O HIS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1000 Processing helix chain 'A' and resid 1004 through 1008 Processing helix chain 'B' and resid 11 through 13 No H-bonds generated for 'chain 'B' and resid 11 through 13' Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.820A pdb=" N TRP B 172 " --> pdb=" O THR B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'C' and resid 395 through 399 Processing helix chain 'C' and resid 400 through 408 Processing helix chain 'C' and resid 410 through 420 removed outlier: 3.713A pdb=" N ASP C 420 " --> pdb=" O LYS C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 442 removed outlier: 3.710A pdb=" N VAL C 430 " --> pdb=" O ASP C 426 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS C 431 " --> pdb=" O VAL C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 456 removed outlier: 3.848A pdb=" N ALA C 448 " --> pdb=" O GLU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 474 removed outlier: 3.687A pdb=" N CYS C 467 " --> pdb=" O GLN C 463 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR C 474 " --> pdb=" O ILE C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 493 Processing helix chain 'C' and resid 499 through 508 removed outlier: 3.697A pdb=" N LYS C 508 " --> pdb=" O ARG C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 570 removed outlier: 4.150A pdb=" N MET C 570 " --> pdb=" O ALA C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 580 Processing helix chain 'C' and resid 665 through 683 Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 733 through 740 Processing helix chain 'C' and resid 750 through 763 Processing helix chain 'C' and resid 768 through 777 Processing helix chain 'C' and resid 792 through 813 removed outlier: 3.518A pdb=" N CYS C 796 " --> pdb=" O ASP C 792 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY C 813 " --> pdb=" O GLN C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 842 removed outlier: 3.640A pdb=" N ASN C 842 " --> pdb=" O ARG C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 858 Processing helix chain 'C' and resid 859 through 867 removed outlier: 3.669A pdb=" N VAL C 863 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 895 Proline residue: C 891 - end of helix removed outlier: 3.526A pdb=" N SER C 895 " --> pdb=" O PRO C 891 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 907 Processing helix chain 'C' and resid 908 through 923 Processing helix chain 'C' and resid 933 through 942 Processing helix chain 'C' and resid 942 through 950 removed outlier: 3.549A pdb=" N ILE C 946 " --> pdb=" O HIS C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 974 removed outlier: 4.173A pdb=" N LYS C 973 " --> pdb=" O ARG C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 995 removed outlier: 3.892A pdb=" N THR C 995 " --> pdb=" O HIS C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1001 Processing helix chain 'C' and resid 1002 through 1004 No H-bonds generated for 'chain 'C' and resid 1002 through 1004' Processing helix chain 'D' and resid 11 through 13 No H-bonds generated for 'chain 'D' and resid 11 through 13' Processing helix chain 'D' and resid 168 through 172 removed outlier: 3.820A pdb=" N TRP D 172 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 313 Processing sheet with id=AA1, first strand: chain 'A' and resid 517 through 519 removed outlier: 3.584A pdb=" N THR A 705 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N CYS A 599 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 621 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL A 620 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU A 657 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHE A 622 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 517 through 519 removed outlier: 3.584A pdb=" N THR A 705 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N CYS A 599 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 621 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE A 631 " --> pdb=" O LYS A 639 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N LYS A 639 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N HIS A 633 " --> pdb=" O ASN A 637 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ASN A 637 " --> pdb=" O HIS A 633 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 15 through 24 removed outlier: 8.565A pdb=" N GLY B 18 " --> pdb=" O GLN B 33 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLN B 33 " --> pdb=" O GLY B 18 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL B 28 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS B 58 " --> pdb=" O AHIS B 47 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N LEU B 55 " --> pdb=" O MET B 5 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE B 345 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL B 8 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N PHE B 343 " --> pdb=" O VAL B 8 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 61 through 62 removed outlier: 7.031A pdb=" N ILE B 61 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N CYS B 124 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LYS B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LYS B 115 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR B 121 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE B 107 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.188A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N SER B 194 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER B 141 " --> pdb=" O PHE B 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA7, first strand: chain 'B' and resid 205 through 210 removed outlier: 5.634A pdb=" N HIS B 207 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLY B 220 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER B 209 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE B 218 " --> pdb=" O SER B 209 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP B 239 " --> pdb=" O ALA B 246 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 262 through 265 Processing sheet with id=AA9, first strand: chain 'C' and resid 517 through 519 removed outlier: 5.398A pdb=" N ILE C 631 " --> pdb=" O PRO C 590 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG C 621 " --> pdb=" O ASP C 600 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA C 619 " --> pdb=" O MET C 602 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N MET C 627 " --> pdb=" O GLU C 642 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLU C 642 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE C 629 " --> pdb=" O VAL C 640 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 534 through 536 removed outlier: 7.078A pdb=" N LEU C 655 " --> pdb=" O PHE C 557 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE C 624 " --> pdb=" O PRO C 654 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA C 619 " --> pdb=" O MET C 602 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG C 621 " --> pdb=" O ASP C 600 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE C 631 " --> pdb=" O PRO C 590 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N CYS C 599 " --> pdb=" O THR C 705 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 15 through 24 removed outlier: 8.565A pdb=" N GLY D 18 " --> pdb=" O GLN D 33 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLN D 33 " --> pdb=" O GLY D 18 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL D 28 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS D 58 " --> pdb=" O AHIS D 47 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N LEU D 55 " --> pdb=" O MET D 5 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE D 345 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL D 8 " --> pdb=" O PHE D 343 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N PHE D 343 " --> pdb=" O VAL D 8 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 61 through 62 removed outlier: 7.031A pdb=" N ILE D 61 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N CYS D 124 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LYS D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LYS D 115 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR D 121 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE D 107 " --> pdb=" O LYS D 127 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.188A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N SER D 194 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER D 141 " --> pdb=" O PHE D 156 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AB6, first strand: chain 'D' and resid 205 through 210 removed outlier: 5.633A pdb=" N HIS D 207 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N GLY D 220 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER D 209 " --> pdb=" O ILE D 218 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE D 218 " --> pdb=" O SER D 209 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP D 239 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 262 through 265 688 hydrogen bonds defined for protein. 1932 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 257 hydrogen bonds 510 hydrogen bond angles 0 basepair planarities 102 basepair parallelities 166 stacking parallelities Total time for adding SS restraints: 5.47 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3324 1.32 - 1.44: 6148 1.44 - 1.56: 10423 1.56 - 1.68: 407 1.68 - 1.80: 159 Bond restraints: 20461 Sorted by residual: bond pdb=" C3' DG M 21 " pdb=" O3' DG M 21 " ideal model delta sigma weight residual 1.435 1.371 0.064 1.30e-02 5.92e+03 2.43e+01 bond pdb=" C3' DG F 39 " pdb=" O3' DG F 39 " ideal model delta sigma weight residual 1.435 1.374 0.061 1.30e-02 5.92e+03 2.17e+01 bond pdb=" C3' DG G 50 " pdb=" O3' DG G 50 " ideal model delta sigma weight residual 1.435 1.377 0.058 1.30e-02 5.92e+03 2.02e+01 bond pdb=" C4' DA M 18 " pdb=" C3' DA M 18 " ideal model delta sigma weight residual 1.529 1.485 0.044 1.00e-02 1.00e+04 1.96e+01 bond pdb=" C3' DC L 17 " pdb=" O3' DC L 17 " ideal model delta sigma weight residual 1.435 1.378 0.057 1.30e-02 5.92e+03 1.94e+01 ... (remaining 20456 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 26884 1.96 - 3.91: 1498 3.91 - 5.87: 129 5.87 - 7.82: 21 7.82 - 9.78: 13 Bond angle restraints: 28545 Sorted by residual: angle pdb=" O4' DC I 14 " pdb=" C4' DC I 14 " pdb=" C3' DC I 14 " ideal model delta sigma weight residual 106.00 102.50 3.50 6.00e-01 2.78e+00 3.40e+01 angle pdb=" O4' DA L 18 " pdb=" C4' DA L 18 " pdb=" C3' DA L 18 " ideal model delta sigma weight residual 106.00 102.52 3.48 6.00e-01 2.78e+00 3.37e+01 angle pdb=" O4' DT F 29 " pdb=" C4' DT F 29 " pdb=" C3' DT F 29 " ideal model delta sigma weight residual 106.00 102.62 3.38 6.00e-01 2.78e+00 3.17e+01 angle pdb=" O4' DA M 18 " pdb=" C4' DA M 18 " pdb=" C3' DA M 18 " ideal model delta sigma weight residual 106.00 102.69 3.31 6.00e-01 2.78e+00 3.04e+01 angle pdb=" N LYS D 336 " pdb=" CA LYS D 336 " pdb=" C LYS D 336 " ideal model delta sigma weight residual 111.28 117.09 -5.81 1.09e+00 8.42e-01 2.84e+01 ... (remaining 28540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.92: 10070 26.92 - 53.84: 1469 53.84 - 80.77: 207 80.77 - 107.69: 7 107.69 - 134.61: 1 Dihedral angle restraints: 11754 sinusoidal: 6148 harmonic: 5606 Sorted by residual: dihedral pdb=" CA GLN A 520 " pdb=" C GLN A 520 " pdb=" N PRO A 521 " pdb=" CA PRO A 521 " ideal model delta harmonic sigma weight residual 180.00 149.25 30.75 0 5.00e+00 4.00e-02 3.78e+01 dihedral pdb=" CA GLN C 463 " pdb=" C GLN C 463 " pdb=" N PRO C 464 " pdb=" CA PRO C 464 " ideal model delta harmonic sigma weight residual 180.00 -154.25 -25.75 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA ILE D 316 " pdb=" C ILE D 316 " pdb=" N TRP D 317 " pdb=" CA TRP D 317 " ideal model delta harmonic sigma weight residual 180.00 155.07 24.93 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 11751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2197 0.058 - 0.116: 754 0.116 - 0.174: 157 0.174 - 0.232: 17 0.232 - 0.290: 3 Chirality restraints: 3128 Sorted by residual: chirality pdb=" CB VAL C 943 " pdb=" CA VAL C 943 " pdb=" CG1 VAL C 943 " pdb=" CG2 VAL C 943 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CB VAL C 545 " pdb=" CA VAL C 545 " pdb=" CG1 VAL C 545 " pdb=" CG2 VAL C 545 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB VAL C 776 " pdb=" CA VAL C 776 " pdb=" CG1 VAL C 776 " pdb=" CG2 VAL C 776 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 3125 not shown) Planarity restraints: 2955 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 98 " 0.050 5.00e-02 4.00e+02 7.53e-02 9.07e+00 pdb=" N PRO B 99 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 788 " 0.050 5.00e-02 4.00e+02 7.53e-02 9.06e+00 pdb=" N PRO C 789 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO C 789 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 789 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 98 " -0.050 5.00e-02 4.00e+02 7.49e-02 8.98e+00 pdb=" N PRO D 99 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO D 99 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 99 " -0.042 5.00e-02 4.00e+02 ... (remaining 2952 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 4845 2.78 - 3.31: 16128 3.31 - 3.84: 35670 3.84 - 4.37: 40821 4.37 - 4.90: 65751 Nonbonded interactions: 163215 Sorted by model distance: nonbonded pdb=" OD2 ASP A 546 " pdb=" OG SER B 259 " model vdw 2.256 3.040 nonbonded pdb=" OE2 GLU A 803 " pdb=" OH TYR A 928 " model vdw 2.260 3.040 nonbonded pdb=" O TYR A 935 " pdb=" OG1 THR A 939 " model vdw 2.272 3.040 nonbonded pdb=" O SER C 543 " pdb=" OG SER C 543 " model vdw 2.292 3.040 nonbonded pdb=" OH TYR C 805 " pdb=" OD1 ASP C 834 " model vdw 2.295 3.040 ... (remaining 163210 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 'A' and (resid 391 through 906 or resid 908 through 1006 or (resid 1007 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1101 through 11 \ 02)) selection = (chain 'C' and (resid 391 through 392 or (resid 393 and (name N or name CA or na \ me C or name O or name CB )) or resid 394 through 457 or (resid 458 and (name N \ or name CA or name C or name O or name CB )) or resid 459 through 906 or resid 9 \ 08 through 1102)) } ncs_group { reference = (chain 'B' and (resid 1 through 46 or resid 48 through 117 or (resid 118 and (na \ me N or name CA or name C or name O or name CB )) or resid 119 through 236 or re \ sid 238 through 335 or (resid 336 and (name N or name CA or name C or name O or \ name CB )) or resid 337 through 340 or (resid 341 through 342 and (name N or nam \ e CA or name C or name O or name CB )) or resid 343 through 350)) selection = (chain 'D' and (resid 1 through 46 or resid 48 through 236 or resid 238 through \ 350)) } ncs_group { reference = chain 'I' selection = chain 'J' } 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=0.50 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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 27.140 Find NCS groups from input model: 0.340 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: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 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 : 0.011 0.126 20469 Z= 0.659 Angle : 0.998 24.606 28549 Z= 0.686 Chirality : 0.059 0.290 3128 Planarity : 0.007 0.075 2955 Dihedral : 22.107 134.610 8142 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.81 % Favored : 94.08 % Rotamer: Outliers : 3.50 % Allowed : 7.66 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 1.11 % 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: -3.55 (0.15), residues: 1922 helix: -2.49 (0.14), residues: 647 sheet: -1.46 (0.27), residues: 340 loop : -2.57 (0.17), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 442 TYR 0.019 0.002 TYR A 757 PHE 0.024 0.003 PHE A 916 TRP 0.018 0.003 TRP C 893 HIS 0.014 0.002 HIS A 991 Details of bonding type rmsd/Z covalent geometry : bond 0.01045 / 0.66 (20461) covalent geometry : angle 0.97569 / 0.68 (28545) hydrogen bonds : bond 0.16514 / 11.12 ( 917) hydrogen bonds : angle 6.96896 / 5.01 ( 2442) metal coordination : bond 0.10143 / 5.46 ( 8) metal coordination : angle 17.83511 / 9.24 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 172 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 568 MET cc_start: 0.7425 (mmm) cc_final: 0.7204 (mmp) REVERT: A 847 MET cc_start: 0.7936 (ptt) cc_final: 0.7577 (ptm) REVERT: B 52 GLN cc_start: 0.8172 (mp10) cc_final: 0.7903 (mm110) REVERT: B 110 MET cc_start: 0.8742 (mmt) cc_final: 0.8417 (mmt) REVERT: C 456 GLN cc_start: 0.7652 (mt0) cc_final: 0.7165 (mt0) REVERT: C 458 ARG cc_start: 0.6880 (ttp80) cc_final: 0.6471 (mmt180) REVERT: C 857 LEU cc_start: 0.9292 (tp) cc_final: 0.9058 (tp) REVERT: C 1003 MET cc_start: 0.8971 (mmt) cc_final: 0.8375 (mmt) REVERT: D 120 VAL cc_start: 0.7752 (OUTLIER) cc_final: 0.7297 (t) REVERT: D 152 MET cc_start: 0.7463 (tpp) cc_final: 0.7240 (tpp) REVERT: D 162 MET cc_start: 0.8699 (mmt) cc_final: 0.8449 (mmp) REVERT: D 209 SER cc_start: 0.8097 (OUTLIER) cc_final: 0.7896 (p) REVERT: D 259 SER cc_start: 0.8629 (OUTLIER) cc_final: 0.8337 (p) REVERT: D 326 THR cc_start: 0.8865 (OUTLIER) cc_final: 0.8466 (p) outliers start: 57 outliers final: 9 residues processed: 219 average time/residue: 0.1493 time to fit residues: 50.4480 Evaluate side-chains 121 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 326 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 445 HIS ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 HIS A 830 GLN A 978 GLN A 990 HIS A1000 GLN ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN B 53 ASN B 90 GLN B 101 ASN B 337 GLN C 443 ASN C 965 ASN C1004 ASN D 33 GLN D 53 ASN D 181 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.117835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.082115 restraints weight = 108080.679| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 3.61 r_work: 0.3000 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 14 (22 function evaluations) r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20469 Z= 0.181 Angle : 0.675 10.331 28549 Z= 0.381 Chirality : 0.047 0.240 3128 Planarity : 0.005 0.059 2955 Dihedral : 24.151 127.523 4376 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.84 % Allowed : 11.40 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.18), residues: 1922 helix: -0.58 (0.19), residues: 651 sheet: -0.89 (0.29), residues: 328 loop : -2.04 (0.18), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 696 TYR 0.014 0.001 TYR A 757 PHE 0.018 0.002 PHE B 48 TRP 0.019 0.002 TRP D 317 HIS 0.008 0.001 HIS A 937 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (20461) covalent geometry : angle 0.67201 / 0.38 (28545) hydrogen bonds : bond 0.05382 / 3.64 ( 917) hydrogen bonds : angle 4.95662 / 3.59 ( 2442) metal coordination : bond 0.01401 / 0.77 ( 8) metal coordination : angle 5.81624 / 2.98 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 GLU cc_start: 0.8651 (pt0) cc_final: 0.8429 (pp20) REVERT: A 442 ARG cc_start: 0.6123 (mmm-85) cc_final: 0.5889 (tpp-160) REVERT: A 473 ASN cc_start: 0.9155 (t0) cc_final: 0.8871 (t0) REVERT: A 568 MET cc_start: 0.7828 (mmm) cc_final: 0.7573 (mmp) REVERT: A 847 MET cc_start: 0.8296 (ptt) cc_final: 0.8073 (ptm) REVERT: B 52 GLN cc_start: 0.8437 (mp10) cc_final: 0.7956 (mm110) REVERT: C 456 GLN cc_start: 0.7705 (mt0) cc_final: 0.7117 (mt0) REVERT: C 458 ARG cc_start: 0.7027 (ttp80) cc_final: 0.6408 (mmt180) REVERT: C 617 GLU cc_start: 0.8654 (pt0) cc_final: 0.8366 (pt0) REVERT: C 857 LEU cc_start: 0.9277 (tp) cc_final: 0.9060 (tt) REVERT: C 1003 MET cc_start: 0.8833 (mmt) cc_final: 0.8472 (mmt) REVERT: D 285 MET cc_start: 0.8636 (mmm) cc_final: 0.8049 (mmm) outliers start: 29 outliers final: 20 residues processed: 153 average time/residue: 0.1243 time to fit residues: 30.8629 Evaluate side-chains 141 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 78 CYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 327 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 157 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 HIS ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.117871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.081478 restraints weight = 104483.700| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 3.31 r_work: 0.3015 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20469 Z= 0.168 Angle : 0.622 11.992 28549 Z= 0.351 Chirality : 0.044 0.236 3128 Planarity : 0.004 0.052 2955 Dihedral : 23.992 122.595 4368 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.43 % Allowed : 13.72 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.19), residues: 1922 helix: 0.22 (0.20), residues: 655 sheet: -0.64 (0.29), residues: 345 loop : -1.72 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 284 TYR 0.018 0.001 TYR B 234 PHE 0.016 0.001 PHE B 48 TRP 0.021 0.002 TRP D 317 HIS 0.005 0.001 HIS A 937 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 (20461) covalent geometry : angle 0.61737 / 0.35 (28545) hydrogen bonds : bond 0.04844 / 3.34 ( 917) hydrogen bonds : angle 4.56568 / 3.32 ( 2442) metal coordination : bond 0.01379 / 0.69 ( 8) metal coordination : angle 6.60755 / 3.42 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 GLU cc_start: 0.8644 (pt0) cc_final: 0.8383 (pp20) REVERT: A 442 ARG cc_start: 0.6472 (mmm-85) cc_final: 0.6075 (ttm-80) REVERT: A 568 MET cc_start: 0.7756 (mmm) cc_final: 0.7554 (mmp) REVERT: A 847 MET cc_start: 0.8292 (ptt) cc_final: 0.8064 (ptm) REVERT: B 52 GLN cc_start: 0.8452 (mp10) cc_final: 0.8002 (tp40) REVERT: C 456 GLN cc_start: 0.7566 (mt0) cc_final: 0.7026 (mt0) REVERT: C 458 ARG cc_start: 0.6881 (ttp80) cc_final: 0.6277 (mmt180) REVERT: C 841 MET cc_start: 0.8981 (mmm) cc_final: 0.8613 (mtp) REVERT: C 1003 MET cc_start: 0.8787 (mmt) cc_final: 0.8451 (mmt) REVERT: D 152 MET cc_start: 0.8173 (tpp) cc_final: 0.7691 (ttm) REVERT: D 285 MET cc_start: 0.8679 (mmm) cc_final: 0.8130 (mmm) outliers start: 22 outliers final: 20 residues processed: 149 average time/residue: 0.1429 time to fit residues: 33.8280 Evaluate side-chains 142 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 78 CYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 327 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 42 optimal weight: 0.0170 chunk 24 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 181 optimal weight: 0.7980 chunk 152 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN C1000 GLN ** D 23 ASN ** 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 = 0.3832 r_free = 0.3832 target = 0.118492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.082175 restraints weight = 107342.150| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.32 r_work: 0.3017 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20469 Z= 0.157 Angle : 0.603 9.602 28549 Z= 0.339 Chirality : 0.043 0.213 3128 Planarity : 0.004 0.049 2955 Dihedral : 23.921 120.657 4368 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.14 % Allowed : 15.02 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.19), residues: 1922 helix: 0.61 (0.21), residues: 660 sheet: -0.58 (0.29), residues: 351 loop : -1.49 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 440 TYR 0.021 0.001 TYR B 234 PHE 0.013 0.001 PHE A 916 TRP 0.037 0.002 TRP B 317 HIS 0.004 0.001 HIS C 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (20461) covalent geometry : angle 0.60019 / 0.34 (28545) hydrogen bonds : bond 0.04500 / 3.11 ( 917) hydrogen bonds : angle 4.39126 / 3.21 ( 2442) metal coordination : bond 0.01149 / 0.59 ( 8) metal coordination : angle 5.17916 / 2.70 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 414 GLN cc_start: 0.8044 (pm20) cc_final: 0.7813 (pm20) REVERT: A 417 GLU cc_start: 0.8667 (pt0) cc_final: 0.8399 (pp20) REVERT: A 442 ARG cc_start: 0.6554 (mmm-85) cc_final: 0.6137 (ttm-80) REVERT: A 847 MET cc_start: 0.8304 (ptt) cc_final: 0.8048 (ptm) REVERT: A 936 PHE cc_start: 0.9018 (OUTLIER) cc_final: 0.8351 (m-10) REVERT: B 52 GLN cc_start: 0.8395 (mp10) cc_final: 0.7987 (tp40) REVERT: C 455 MET cc_start: 0.6404 (mmt) cc_final: 0.5871 (tpp) REVERT: C 456 GLN cc_start: 0.7585 (mt0) cc_final: 0.6953 (mt0) REVERT: C 458 ARG cc_start: 0.6843 (ttp80) cc_final: 0.6219 (mmt180) REVERT: C 1003 MET cc_start: 0.8782 (mmt) cc_final: 0.8465 (mmt) REVERT: D 152 MET cc_start: 0.8206 (tpp) cc_final: 0.7715 (ttm) REVERT: D 162 MET cc_start: 0.9075 (mmt) cc_final: 0.8752 (mmp) REVERT: D 285 MET cc_start: 0.8700 (mmm) cc_final: 0.8193 (mmm) outliers start: 34 outliers final: 26 residues processed: 155 average time/residue: 0.1361 time to fit residues: 33.9535 Evaluate side-chains 147 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 78 CYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 327 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 193 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 185 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 111 optimal weight: 0.0030 chunk 158 optimal weight: 0.9990 chunk 172 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 196 optimal weight: 20.0000 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 473 ASN A 740 ASN ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.119172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.083086 restraints weight = 93251.806| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 3.12 r_work: 0.3044 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20469 Z= 0.137 Angle : 0.583 11.430 28549 Z= 0.328 Chirality : 0.042 0.221 3128 Planarity : 0.004 0.047 2955 Dihedral : 23.835 119.643 4368 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.02 % Allowed : 15.86 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.19), residues: 1922 helix: 0.87 (0.21), residues: 659 sheet: -0.50 (0.29), residues: 346 loop : -1.37 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 927 TYR 0.018 0.001 TYR B 234 PHE 0.012 0.001 PHE B 48 TRP 0.023 0.001 TRP B 317 HIS 0.003 0.001 HIS A 937 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (20461) covalent geometry : angle 0.58063 / 0.33 (28545) hydrogen bonds : bond 0.04273 / 2.97 ( 917) hydrogen bonds : angle 4.26876 / 3.13 ( 2442) metal coordination : bond 0.01034 / 0.53 ( 8) metal coordination : angle 4.83107 / 2.52 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 GLU cc_start: 0.8669 (pt0) cc_final: 0.8400 (pp20) REVERT: A 442 ARG cc_start: 0.6661 (mmm-85) cc_final: 0.6222 (ttm-80) REVERT: A 529 ARG cc_start: 0.7483 (ttp-110) cc_final: 0.7198 (ttp-110) REVERT: A 847 MET cc_start: 0.8266 (ptt) cc_final: 0.7996 (ptm) REVERT: A 936 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.8422 (m-10) REVERT: B 52 GLN cc_start: 0.8335 (mp10) cc_final: 0.7992 (tp40) REVERT: C 455 MET cc_start: 0.6377 (mmt) cc_final: 0.5899 (tpp) REVERT: C 456 GLN cc_start: 0.7571 (mt0) cc_final: 0.7331 (mt0) REVERT: C 806 LYS cc_start: 0.8467 (tttt) cc_final: 0.8082 (tttt) REVERT: C 883 MET cc_start: 0.8799 (tpt) cc_final: 0.8417 (tpt) REVERT: C 1003 MET cc_start: 0.8752 (mmt) cc_final: 0.8417 (mmt) REVERT: D 152 MET cc_start: 0.8131 (tpp) cc_final: 0.7630 (ttm) REVERT: D 162 MET cc_start: 0.9025 (mmt) cc_final: 0.8719 (mmp) REVERT: D 285 MET cc_start: 0.8706 (mmm) cc_final: 0.8200 (mmm) outliers start: 32 outliers final: 25 residues processed: 149 average time/residue: 0.1382 time to fit residues: 33.1149 Evaluate side-chains 145 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 602 MET Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 78 CYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 327 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 103 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 chunk 189 optimal weight: 0.5980 chunk 75 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 197 optimal weight: 30.0000 chunk 109 optimal weight: 0.8980 chunk 194 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** 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 = 0.3835 r_free = 0.3835 target = 0.118756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.083136 restraints weight = 85587.166| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.95 r_work: 0.3047 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20469 Z= 0.152 Angle : 0.588 10.442 28549 Z= 0.328 Chirality : 0.043 0.209 3128 Planarity : 0.004 0.047 2955 Dihedral : 23.826 118.732 4367 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.02 % Allowed : 16.39 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.19), residues: 1922 helix: 1.02 (0.21), residues: 658 sheet: -0.37 (0.28), residues: 344 loop : -1.27 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 855 TYR 0.014 0.001 TYR A 757 PHE 0.013 0.001 PHE A 916 TRP 0.035 0.002 TRP B 317 HIS 0.004 0.001 HIS C 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (20461) covalent geometry : angle 0.58552 / 0.33 (28545) hydrogen bonds : bond 0.04289 / 2.99 ( 917) hydrogen bonds : angle 4.19637 / 3.07 ( 2442) metal coordination : bond 0.01180 / 0.61 ( 8) metal coordination : angle 4.73362 / 2.46 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 GLU cc_start: 0.8645 (pt0) cc_final: 0.8373 (pp20) REVERT: A 682 MET cc_start: 0.9032 (ptp) cc_final: 0.8651 (ptm) REVERT: A 883 MET cc_start: 0.9206 (tpp) cc_final: 0.8947 (tpp) REVERT: A 936 PHE cc_start: 0.9030 (OUTLIER) cc_final: 0.8379 (m-10) REVERT: B 52 GLN cc_start: 0.8324 (mp10) cc_final: 0.7985 (tp40) REVERT: C 455 MET cc_start: 0.6328 (mmt) cc_final: 0.5871 (tpp) REVERT: C 456 GLN cc_start: 0.7615 (mt0) cc_final: 0.7376 (mt0) REVERT: C 529 ARG cc_start: 0.8346 (mmm-85) cc_final: 0.7985 (mmm-85) REVERT: C 849 MET cc_start: 0.8252 (ttm) cc_final: 0.8042 (ttm) REVERT: C 1003 MET cc_start: 0.8749 (mmt) cc_final: 0.8381 (mmt) REVERT: D 152 MET cc_start: 0.8129 (tpp) cc_final: 0.7609 (ttm) REVERT: D 162 MET cc_start: 0.9002 (mmt) cc_final: 0.8692 (mmp) REVERT: D 285 MET cc_start: 0.8697 (mmm) cc_final: 0.8165 (mmm) outliers start: 32 outliers final: 26 residues processed: 145 average time/residue: 0.1404 time to fit residues: 33.0004 Evaluate side-chains 144 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 78 CYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 327 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 20 optimal weight: 0.4980 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 162 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** 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 = 0.3846 r_free = 0.3846 target = 0.119300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.082249 restraints weight = 118272.637| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 3.59 r_work: 0.3025 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20469 Z= 0.135 Angle : 0.568 11.523 28549 Z= 0.318 Chirality : 0.042 0.205 3128 Planarity : 0.004 0.046 2955 Dihedral : 23.776 118.461 4367 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.26 % Allowed : 16.15 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.19), residues: 1922 helix: 1.12 (0.21), residues: 659 sheet: -0.25 (0.29), residues: 344 loop : -1.19 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 529 TYR 0.013 0.001 TYR A 757 PHE 0.011 0.001 PHE B 48 TRP 0.035 0.001 TRP B 317 HIS 0.004 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.14 (20461) covalent geometry : angle 0.56576 / 0.32 (28545) hydrogen bonds : bond 0.04107 / 2.88 ( 917) hydrogen bonds : angle 4.09553 / 3.01 ( 2442) metal coordination : bond 0.01055 / 0.54 ( 8) metal coordination : angle 4.41372 / 2.30 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 ARG cc_start: 0.6646 (mmm-85) cc_final: 0.5777 (mtp-110) REVERT: A 682 MET cc_start: 0.9132 (ptp) cc_final: 0.8770 (ptm) REVERT: A 936 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.8398 (m-10) REVERT: B 52 GLN cc_start: 0.8324 (mp10) cc_final: 0.7975 (tp40) REVERT: C 455 MET cc_start: 0.6281 (mmt) cc_final: 0.5684 (tpp) REVERT: C 456 GLN cc_start: 0.7619 (mt0) cc_final: 0.7390 (mt0) REVERT: C 529 ARG cc_start: 0.8386 (mmm-85) cc_final: 0.7990 (mmm-85) REVERT: C 576 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8671 (tp30) REVERT: C 806 LYS cc_start: 0.8490 (tttt) cc_final: 0.8195 (tttt) REVERT: C 1003 MET cc_start: 0.8754 (mmt) cc_final: 0.8412 (mmt) REVERT: D 162 MET cc_start: 0.9019 (mmt) cc_final: 0.8687 (mmp) REVERT: D 285 MET cc_start: 0.8763 (mmm) cc_final: 0.8227 (mmm) outliers start: 36 outliers final: 29 residues processed: 144 average time/residue: 0.1299 time to fit residues: 30.7815 Evaluate side-chains 140 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 602 MET Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 78 CYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 327 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 80 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 191 optimal weight: 50.0000 chunk 11 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 201 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 148 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 473 ASN ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.118797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.082743 restraints weight = 116027.907| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.86 r_work: 0.2998 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20469 Z= 0.162 Angle : 0.590 10.626 28549 Z= 0.328 Chirality : 0.043 0.231 3128 Planarity : 0.004 0.047 2955 Dihedral : 23.788 118.291 4367 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.14 % Allowed : 16.75 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.19), residues: 1922 helix: 1.13 (0.21), residues: 659 sheet: -0.28 (0.28), residues: 349 loop : -1.16 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 529 TYR 0.014 0.001 TYR A 757 PHE 0.014 0.001 PHE A 916 TRP 0.039 0.002 TRP B 317 HIS 0.005 0.001 HIS C 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (20461) covalent geometry : angle 0.58780 / 0.33 (28545) hydrogen bonds : bond 0.04283 / 2.99 ( 917) hydrogen bonds : angle 4.10237 / 3.01 ( 2442) metal coordination : bond 0.01296 / 0.68 ( 8) metal coordination : angle 4.76627 / 2.48 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 682 MET cc_start: 0.9132 (ptp) cc_final: 0.8812 (ptm) REVERT: A 936 PHE cc_start: 0.9058 (OUTLIER) cc_final: 0.8439 (m-10) REVERT: B 52 GLN cc_start: 0.8332 (mp10) cc_final: 0.8007 (tp40) REVERT: C 455 MET cc_start: 0.6386 (mmt) cc_final: 0.5798 (tpp) REVERT: C 456 GLN cc_start: 0.7659 (mt0) cc_final: 0.7431 (mt0) REVERT: C 806 LYS cc_start: 0.8508 (tttt) cc_final: 0.8171 (tttt) REVERT: C 1003 MET cc_start: 0.8761 (mmt) cc_final: 0.8440 (mmt) REVERT: D 152 MET cc_start: 0.8101 (ttm) cc_final: 0.7863 (ttm) REVERT: D 162 MET cc_start: 0.9035 (mmt) cc_final: 0.8714 (mmp) REVERT: D 285 MET cc_start: 0.8770 (mmm) cc_final: 0.8208 (mmm) outliers start: 34 outliers final: 31 residues processed: 138 average time/residue: 0.1239 time to fit residues: 28.1511 Evaluate side-chains 146 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain C residue 961 ASN Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 78 CYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 327 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 85 optimal weight: 0.9980 chunk 153 optimal weight: 0.7980 chunk 160 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 199 optimal weight: 50.0000 chunk 3 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** 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 = 0.3857 r_free = 0.3857 target = 0.120121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.084098 restraints weight = 115493.336| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 3.80 r_work: 0.3026 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20469 Z= 0.125 Angle : 0.563 10.551 28549 Z= 0.315 Chirality : 0.041 0.240 3128 Planarity : 0.004 0.046 2955 Dihedral : 23.680 118.925 4367 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.96 % Allowed : 16.92 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.19), residues: 1922 helix: 1.23 (0.21), residues: 657 sheet: -0.08 (0.29), residues: 344 loop : -1.12 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 440 TYR 0.013 0.001 TYR A 757 PHE 0.011 0.001 PHE B 48 TRP 0.033 0.001 TRP B 317 HIS 0.003 0.001 HIS A 795 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.13 (20461) covalent geometry : angle 0.56102 / 0.31 (28545) hydrogen bonds : bond 0.03943 / 2.77 ( 917) hydrogen bonds : angle 4.03425 / 2.96 ( 2442) metal coordination : bond 0.00954 / 0.49 ( 8) metal coordination : angle 4.09866 / 2.13 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 442 ARG cc_start: 0.6486 (mmm-85) cc_final: 0.5724 (mtp-110) REVERT: A 682 MET cc_start: 0.9114 (ptp) cc_final: 0.8758 (ptm) REVERT: A 797 ASP cc_start: 0.8409 (m-30) cc_final: 0.8033 (m-30) REVERT: A 936 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.8404 (m-10) REVERT: B 52 GLN cc_start: 0.8297 (mp10) cc_final: 0.7968 (tp40) REVERT: C 455 MET cc_start: 0.6450 (mmt) cc_final: 0.6110 (tpp) REVERT: C 456 GLN cc_start: 0.7637 (mt0) cc_final: 0.7401 (mt0) REVERT: C 529 ARG cc_start: 0.8438 (mmm-85) cc_final: 0.7999 (mmm-85) REVERT: C 714 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8384 (tt0) REVERT: C 806 LYS cc_start: 0.8463 (tttt) cc_final: 0.8140 (tttt) REVERT: C 1003 MET cc_start: 0.8823 (mmt) cc_final: 0.8445 (mmt) REVERT: D 162 MET cc_start: 0.9026 (mmt) cc_final: 0.8693 (mmp) REVERT: D 218 ILE cc_start: 0.8319 (pt) cc_final: 0.8031 (mt) REVERT: D 285 MET cc_start: 0.8747 (mmm) cc_final: 0.8183 (mmm) outliers start: 31 outliers final: 25 residues processed: 142 average time/residue: 0.1391 time to fit residues: 32.3912 Evaluate side-chains 141 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 714 GLU Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain C residue 961 ASN Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 78 CYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 327 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 168 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 117 optimal weight: 0.7980 chunk 170 optimal weight: 0.5980 chunk 184 optimal weight: 3.9990 chunk 45 optimal weight: 0.3980 chunk 194 optimal weight: 9.9990 chunk 158 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 182 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 GLN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.120482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.084241 restraints weight = 94550.740| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 3.17 r_work: 0.3069 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20469 Z= 0.121 Angle : 0.553 10.473 28549 Z= 0.310 Chirality : 0.041 0.252 3128 Planarity : 0.004 0.046 2955 Dihedral : 23.630 119.738 4366 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.78 % Allowed : 17.10 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.20), residues: 1922 helix: 1.28 (0.21), residues: 658 sheet: -0.03 (0.29), residues: 339 loop : -1.06 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 440 TYR 0.014 0.001 TYR A 757 PHE 0.011 0.001 PHE B 318 TRP 0.033 0.002 TRP B 317 HIS 0.003 0.001 HIS A 937 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.12 (20461) covalent geometry : angle 0.55138 / 0.31 (28545) hydrogen bonds : bond 0.03894 / 2.74 ( 917) hydrogen bonds : angle 3.98658 / 2.93 ( 2442) metal coordination : bond 0.00906 / 0.46 ( 8) metal coordination : angle 3.82794 / 2.00 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 442 ARG cc_start: 0.6601 (mmm-85) cc_final: 0.5846 (mtp-110) REVERT: A 682 MET cc_start: 0.9102 (ptp) cc_final: 0.8738 (ptm) REVERT: A 797 ASP cc_start: 0.8311 (m-30) cc_final: 0.8017 (m-30) REVERT: A 936 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.8402 (m-10) REVERT: A 983 GLU cc_start: 0.8044 (pt0) cc_final: 0.7755 (tt0) REVERT: B 52 GLN cc_start: 0.8263 (mp10) cc_final: 0.7981 (tp40) REVERT: C 455 MET cc_start: 0.6425 (mmt) cc_final: 0.6087 (tpp) REVERT: C 456 GLN cc_start: 0.7591 (mt0) cc_final: 0.7359 (mt0) REVERT: C 529 ARG cc_start: 0.8359 (mmm-85) cc_final: 0.7953 (mmm-85) REVERT: C 574 ILE cc_start: 0.9133 (mt) cc_final: 0.8763 (mm) REVERT: C 578 MET cc_start: 0.7403 (ptp) cc_final: 0.7059 (ptm) REVERT: C 806 LYS cc_start: 0.8380 (tttt) cc_final: 0.8146 (tttt) REVERT: C 1003 MET cc_start: 0.8801 (mmt) cc_final: 0.8438 (mmt) REVERT: D 162 MET cc_start: 0.8982 (mmt) cc_final: 0.8639 (mmp) REVERT: D 218 ILE cc_start: 0.8293 (pt) cc_final: 0.8031 (mt) REVERT: D 285 MET cc_start: 0.8731 (mmm) cc_final: 0.8185 (mmm) outliers start: 28 outliers final: 23 residues processed: 140 average time/residue: 0.1326 time to fit residues: 30.8255 Evaluate side-chains 139 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain C residue 961 ASN Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 78 CYS Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 327 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 165 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 26 optimal weight: 0.0980 chunk 63 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 155 optimal weight: 0.0980 chunk 100 optimal weight: 0.3980 chunk 83 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** 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 = 0.3877 r_free = 0.3877 target = 0.121366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.085344 restraints weight = 85070.434| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.03 r_work: 0.3096 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20469 Z= 0.113 Angle : 0.542 10.353 28549 Z= 0.304 Chirality : 0.040 0.257 3128 Planarity : 0.004 0.045 2955 Dihedral : 23.574 121.198 4365 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.43 % Allowed : 17.52 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.20), residues: 1922 helix: 1.35 (0.21), residues: 657 sheet: 0.12 (0.29), residues: 335 loop : -1.02 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 440 TYR 0.013 0.001 TYR A 757 PHE 0.010 0.001 PHE B 48 TRP 0.028 0.001 TRP B 317 HIS 0.003 0.001 HIS A 942 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.11 (20461) covalent geometry : angle 0.54033 / 0.30 (28545) hydrogen bonds : bond 0.03736 / 2.64 ( 917) hydrogen bonds : angle 3.92392 / 2.89 ( 2442) metal coordination : bond 0.00814 / 0.41 ( 8) metal coordination : angle 3.49930 / 1.82 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4848.83 seconds wall clock time: 83 minutes 42.73 seconds (5022.73 seconds total)