Starting phenix.real_space_refine on Sat Sep 12 00:56:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uo4_26639/09_2026/7uo4_26639_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uo4_26639/09_2026/7uo4_26639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uo4_26639/09_2026/7uo4_26639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uo4_26639/09_2026/7uo4_26639.map" model { file = "/net/cci-nas-00/data/ceres_data/7uo4_26639/09_2026/7uo4_26639_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uo4_26639/09_2026/7uo4_26639_neut.cif" } resolution = 3.38 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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 73 5.49 5 Mg 1 5.21 5 S 82 5.16 5 C 7573 2.51 5 N 2096 2.21 5 O 2643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s 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: 12470 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7467 Classifications: {'peptide': 927} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 896} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1416 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 180} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 559 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain: "D" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1417 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 180} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "P" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 719 Classifications: {'RNA': 34} Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 18} Link IDs: {'rna3p': 33} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 765 Classifications: {'RNA': 36} Modifications used: {'rna3p_pur': 18, 'rna3p_pyr': 18} Link IDs: {'rna3p': 35} Chain: "A" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 104 Unusual residues: {' MG': 1, ' ZN': 2, 'NWX': 1} Classifications: {'undetermined': 4, 'water': 68} Link IDs: {None: 71} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2451 SG CYS A 301 30.506 90.742 110.832 1.00 11.32 S ATOM 2492 SG CYS A 306 31.486 93.156 111.380 1.00 12.03 S ATOM 2524 SG CYS A 310 31.767 90.452 113.656 1.00 8.37 S ATOM 3932 SG CYS A 487 30.903 88.984 90.661 1.00 15.59 S ATOM 5185 SG CYS A 645 30.725 91.687 91.190 1.00 17.94 S ATOM 5191 SG CYS A 646 29.589 89.986 93.116 1.00 10.61 S Time building chain proxies: 2.90, per 1000 atoms: 0.23 Number of scatterers: 12470 At special positions: 0 Unit cell: (90.525, 125.67, 166.14, 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 S 82 16.00 P 73 15.00 Mg 1 11.99 O 2643 8.00 N 2096 7.00 C 7573 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: 1.07 Conformation dependent library (CDL) restraints added in 532.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1003 " pdb="ZN ZN A1003 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 306 " pdb=" ZN A1004 " pdb="ZN ZN A1004 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 645 " Number of angles added : 6 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2644 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 12 sheets defined 53.9% alpha, 12.2% beta 33 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 Processing helix chain 'A' and resid 76 through 89 removed outlier: 3.510A pdb=" N THR A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 86 " --> pdb=" O HIS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.575A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.906A pdb=" N LYS A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE A 145 " --> pdb=" O THR A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 removed outlier: 3.658A pdb=" N LYS A 159 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 178 through 199 Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.504A pdb=" N ASN A 209 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 256 through 260 Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.708A pdb=" N LEU A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.352A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 447 through 455 Processing helix chain 'A' and resid 456 through 459 Processing helix chain 'A' and resid 465 through 479 removed outlier: 4.234A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.522A pdb=" N GLN A 492 " --> pdb=" O ASN A 489 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 489 through 493' Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.564A pdb=" N TRP A 509 " --> pdb=" O PHE A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 518 removed outlier: 3.945A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 removed outlier: 3.754A pdb=" N PHE A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 581 removed outlier: 4.316A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 removed outlier: 3.598A pdb=" N MET A 601 " --> pdb=" O GLY A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 647 through 662 Processing helix chain 'A' and resid 689 through 709 removed outlier: 3.564A pdb=" N PHE A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 733 removed outlier: 3.617A pdb=" N ASN A 722 " --> pdb=" O LYS A 718 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU A 729 " --> pdb=" O HIS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 753 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 790 removed outlier: 3.877A pdb=" N VAL A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 797 No H-bonds generated for 'chain 'A' and resid 795 through 797' Processing helix chain 'A' and resid 804 through 808 Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 847 through 852 Processing helix chain 'A' and resid 855 through 867 removed outlier: 3.968A pdb=" N PHE A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER A 861 " --> pdb=" O GLU A 857 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 903 removed outlier: 3.785A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TYR A 884 " --> pdb=" O VAL A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 923 removed outlier: 4.235A pdb=" N TYR A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 8 through 29 removed outlier: 3.804A pdb=" N TYR B 12 " --> pdb=" O SER B 8 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA B 27 " --> pdb=" O GLU B 23 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN B 28 " --> pdb=" O GLN B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 96 removed outlier: 3.779A pdb=" N LEU B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 109 Processing helix chain 'B' and resid 118 through 125 removed outlier: 3.999A pdb=" N LEU B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'C' and resid 5 through 20 removed outlier: 3.853A pdb=" N VAL C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 41 removed outlier: 3.576A pdb=" N ALA C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 62 removed outlier: 3.905A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 73 removed outlier: 3.792A pdb=" N GLU C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 29 removed outlier: 3.916A pdb=" N ALA D 13 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 82 removed outlier: 3.675A pdb=" N LYS D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 99 removed outlier: 3.873A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 112 removed outlier: 3.774A pdb=" N ASP D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 141 Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 173 through 180 removed outlier: 3.506A pdb=" N SER D 177 " --> pdb=" O MET D 174 " (cutoff:3.500A) Proline residue: D 178 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 21 removed outlier: 4.511A pdb=" N ARG A 18 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N PHE A 45 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE A 37 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LYS A 47 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE A 35 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N LEU A 49 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ARG A 33 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N THR A 51 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N VAL A 31 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N CYS A 53 " --> pdb=" O ASP A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 21 removed outlier: 4.511A pdb=" N ARG A 18 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN A 52 " --> pdb=" O ARG A 74 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASP A 60 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE A 66 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TYR A 69 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 104 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AA4, first strand: chain 'A' and resid 342 through 343 Processing sheet with id=AA5, first strand: chain 'A' and resid 334 through 335 removed outlier: 3.550A pdb=" N VAL A 338 " --> pdb=" O VAL A 335 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 346 through 347 Processing sheet with id=AA7, first strand: chain 'A' and resid 397 through 399 removed outlier: 6.696A pdb=" N LEU A 673 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 414 through 415 removed outlier: 3.548A pdb=" N VAL A 844 " --> pdb=" O ASN A 414 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 755 through 758 removed outlier: 3.862A pdb=" N ALA A 762 " --> pdb=" O TRP A 617 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TRP A 617 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 766 " --> pdb=" O HIS A 613 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 816 through 822 Processing sheet with id=AB2, first strand: chain 'B' and resid 128 through 132 removed outlier: 5.755A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 127 through 132 removed outlier: 3.508A pdb=" N LEU D 189 " --> pdb=" O GLU D 155 " (cutoff:3.500A) 547 hydrogen bonds defined for protein. 1539 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 160 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1874 1.29 - 1.42: 3779 1.42 - 1.55: 6855 1.55 - 1.68: 143 1.68 - 1.81: 129 Bond restraints: 12780 Sorted by residual: bond pdb=" O24 NWX A1001 " pdb=" P25 NWX A1001 " ideal model delta sigma weight residual 1.758 1.640 0.118 2.00e-02 2.50e+03 3.46e+01 bond pdb=" C03 NWX A1001 " pdb=" N33 NWX A1001 " ideal model delta sigma weight residual 1.329 1.387 -0.058 2.00e-02 2.50e+03 8.41e+00 bond pdb=" O16 NWX A1001 " pdb=" P17 NWX A1001 " ideal model delta sigma weight residual 1.653 1.710 -0.057 2.00e-02 2.50e+03 8.19e+00 bond pdb=" C05 NWX A1001 " pdb=" N06 NWX A1001 " ideal model delta sigma weight residual 1.297 1.351 -0.054 2.00e-02 2.50e+03 7.18e+00 bond pdb=" C02 NWX A1001 " pdb=" N07 NWX A1001 " ideal model delta sigma weight residual 1.378 1.414 -0.036 2.00e-02 2.50e+03 3.29e+00 ... (remaining 12775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 17226 1.65 - 3.31: 398 3.31 - 4.96: 40 4.96 - 6.61: 4 6.61 - 8.27: 3 Bond angle restraints: 17671 Sorted by residual: angle pdb=" O5' C P 25 " pdb=" C5' C P 25 " pdb=" C4' C P 25 " ideal model delta sigma weight residual 109.40 112.94 -3.54 8.00e-01 1.56e+00 1.95e+01 angle pdb=" O5' A T 103 " pdb=" C5' A T 103 " pdb=" C4' A T 103 " ideal model delta sigma weight residual 109.40 112.29 -2.89 8.00e-01 1.56e+00 1.31e+01 angle pdb=" O5' C P 24 " pdb=" C5' C P 24 " pdb=" C4' C P 24 " ideal model delta sigma weight residual 109.40 112.12 -2.72 8.00e-01 1.56e+00 1.16e+01 angle pdb=" O5' G T 122 " pdb=" C5' G T 122 " pdb=" C4' G T 122 " ideal model delta sigma weight residual 109.40 112.12 -2.72 8.00e-01 1.56e+00 1.16e+01 angle pdb=" O5' A P 31 " pdb=" C5' A P 31 " pdb=" C4' A P 31 " ideal model delta sigma weight residual 109.40 112.12 -2.72 8.00e-01 1.56e+00 1.16e+01 ... (remaining 17666 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.02: 7284 23.02 - 46.05: 330 46.05 - 69.07: 115 69.07 - 92.10: 23 92.10 - 115.12: 2 Dihedral angle restraints: 7754 sinusoidal: 3670 harmonic: 4084 Sorted by residual: dihedral pdb=" CA VAL A 609 " pdb=" C VAL A 609 " pdb=" N GLU A 610 " pdb=" CA GLU A 610 " ideal model delta harmonic sigma weight residual -180.00 -161.91 -18.09 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA ASP B 175 " pdb=" CB ASP B 175 " pdb=" CG ASP B 175 " pdb=" OD1 ASP B 175 " ideal model delta sinusoidal sigma weight residual -30.00 -89.60 59.60 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" C4' C P 24 " pdb=" C3' C P 24 " pdb=" O3' C P 24 " pdb=" P C P 25 " ideal model delta sinusoidal sigma weight residual 220.00 108.15 111.85 1 3.50e+01 8.16e-04 1.08e+01 ... (remaining 7751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1704 0.052 - 0.105: 260 0.105 - 0.157: 84 0.157 - 0.210: 1 0.210 - 0.262: 1 Chirality restraints: 2050 Sorted by residual: chirality pdb=" C10 NWX A1001 " pdb=" C08 NWX A1001 " pdb=" C11 NWX A1001 " pdb=" O14 NWX A1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.78 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C11 NWX A1001 " pdb=" C10 NWX A1001 " pdb=" C12 NWX A1001 " pdb=" O30 NWX A1001 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" CA ILE B 185 " pdb=" N ILE B 185 " pdb=" C ILE B 185 " pdb=" CB ILE B 185 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 2047 not shown) Planarity restraints: 1998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP D 182 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO D 183 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO D 183 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 183 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 56 " 0.006 2.00e-02 2.50e+03 1.30e-02 1.68e+00 pdb=" C GLN B 56 " -0.022 2.00e-02 2.50e+03 pdb=" O GLN B 56 " 0.008 2.00e-02 2.50e+03 pdb=" N ARG B 57 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 168 " -0.020 5.00e-02 4.00e+02 3.04e-02 1.47e+00 pdb=" N PRO A 169 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 169 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 169 " -0.017 5.00e-02 4.00e+02 ... (remaining 1995 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 88 2.49 - 3.09: 9454 3.09 - 3.69: 19357 3.69 - 4.30: 28582 4.30 - 4.90: 47362 Nonbonded interactions: 104843 Sorted by model distance: nonbonded pdb="ZN ZN A1003 " pdb=" O HOH A1160 " model vdw 1.885 2.230 nonbonded pdb=" OD1 ASP D 101 " pdb=" OG SER D 151 " model vdw 1.900 3.040 nonbonded pdb=" O ILE B 120 " pdb=" OG1 THR B 124 " model vdw 1.975 3.040 nonbonded pdb=" OG1 THR A 540 " pdb=" OE1 GLU A 665 " model vdw 2.075 3.040 nonbonded pdb=" O GLY A 25 " pdb=" OG1 THR A 26 " model vdw 2.086 3.040 ... (remaining 104838 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 6 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N \ or name CA or name C or name O or name CB )) or resid 29 through 39 or (resid 4 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 41 or (resid \ 42 through 43 and (name N or name CA or name C or name O or name CB )) or resid \ 44 through 192)) selection = (chain 'D' and (resid 6 through 25 or (resid 26 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 and (name N or name CA or name C or name O or name CB )) or resid 36 throug \ h 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 192)) } 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=1.00 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: 4.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.560 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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 : 0.005 0.154 12788 Z= 0.212 Angle : 0.836 42.512 17677 Z= 0.411 Chirality : 0.042 0.262 2050 Planarity : 0.003 0.035 1998 Dihedral : 14.906 115.121 5110 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 1.27 % Allowed : 7.35 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.06 (0.23), residues: 1366 helix: 0.57 (0.21), residues: 658 sheet: -2.50 (0.40), residues: 154 loop : -1.67 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 836 TYR 0.013 0.001 TYR A 788 PHE 0.011 0.001 PHE A 694 TRP 0.011 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.21 (12780) covalent geometry : angle 0.56952 / 0.38 (17671) hydrogen bonds : bond 0.14710 / 9.16 ( 624) hydrogen bonds : angle 5.81171 / 4.04 ( 1699) metal coordination : bond 0.06202 / 3.71 ( 8) metal coordination : angle 33.21999 / 17.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 903 TYR cc_start: 0.6943 (OUTLIER) cc_final: 0.6591 (m-80) outliers start: 15 outliers final: 4 residues processed: 111 average time/residue: 0.1249 time to fit residues: 20.2471 Evaluate side-chains 76 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 903 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.0470 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0370 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN A 403 ASN A 572 HIS C 19 GLN C 36 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.052576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.036491 restraints weight = 57253.024| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 3.07 r_work: 0.2716 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12788 Z= 0.143 Angle : 0.603 13.871 17677 Z= 0.313 Chirality : 0.040 0.232 2050 Planarity : 0.004 0.041 1998 Dihedral : 14.945 121.651 2602 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.86 % Allowed : 9.97 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.60 (0.23), residues: 1366 helix: 0.95 (0.21), residues: 650 sheet: -2.10 (0.42), residues: 140 loop : -1.51 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 57 TYR 0.025 0.001 TYR D 12 PHE 0.016 0.001 PHE D 92 TRP 0.010 0.001 TRP A 916 HIS 0.008 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (12780) covalent geometry : angle 0.58491 / 0.31 (17671) hydrogen bonds : bond 0.04739 / 3.10 ( 624) hydrogen bonds : angle 4.47180 / 3.13 ( 1699) metal coordination : bond 0.03221 / 2.16 ( 8) metal coordination : angle 8.02379 / 4.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.9480 (mm-40) cc_final: 0.9149 (tp-100) REVERT: A 212 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9034 (mt) REVERT: A 403 ASN cc_start: 0.9302 (OUTLIER) cc_final: 0.8866 (t0) REVERT: B 70 MET cc_start: 0.8646 (tmm) cc_final: 0.8327 (tmm) REVERT: D 60 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8696 (pp20) REVERT: D 67 MET cc_start: 0.9239 (mmp) cc_final: 0.8761 (tpp) REVERT: D 158 GLN cc_start: 0.8682 (pm20) cc_final: 0.8433 (pm20) outliers start: 22 outliers final: 10 residues processed: 94 average time/residue: 0.1096 time to fit residues: 15.8203 Evaluate side-chains 83 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 903 TYR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 44 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 19 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 790 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 = 0.3404 r_free = 0.3404 target = 0.051646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.035900 restraints weight = 57843.247| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 3.06 r_work: 0.2705 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12788 Z= 0.139 Angle : 0.529 8.426 17677 Z= 0.278 Chirality : 0.038 0.241 2050 Planarity : 0.003 0.036 1998 Dihedral : 14.767 120.788 2595 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.03 % Allowed : 10.47 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.39 (0.23), residues: 1366 helix: 1.15 (0.21), residues: 659 sheet: -2.16 (0.40), residues: 152 loop : -1.40 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 285 TYR 0.019 0.001 TYR D 12 PHE 0.014 0.001 PHE D 92 TRP 0.010 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (12780) covalent geometry : angle 0.52018 / 0.28 (17671) hydrogen bonds : bond 0.04073 / 2.67 ( 624) hydrogen bonds : angle 4.21755 / 2.96 ( 1699) metal coordination : bond 0.01713 / 0.96 ( 8) metal coordination : angle 5.24149 / 2.76 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: A 5 GLN cc_start: 0.9563 (mm-40) cc_final: 0.9239 (tp-100) REVERT: A 212 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9042 (mt) REVERT: B 67 MET cc_start: 0.9111 (tpp) cc_final: 0.8451 (tpp) REVERT: B 70 MET cc_start: 0.8623 (tmm) cc_final: 0.8105 (tmm) REVERT: C 47 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8927 (mm-30) REVERT: C 50 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8654 (mm-30) REVERT: D 67 MET cc_start: 0.9241 (mmp) cc_final: 0.8750 (tpp) REVERT: D 158 GLN cc_start: 0.8638 (pm20) cc_final: 0.8273 (pm20) outliers start: 24 outliers final: 14 residues processed: 94 average time/residue: 0.1079 time to fit residues: 15.6419 Evaluate side-chains 84 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 903 TYR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain D residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 76 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 107 optimal weight: 0.0970 chunk 118 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 140 optimal weight: 20.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 403 ASN C 19 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.051379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.035090 restraints weight = 57565.672| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.11 r_work: 0.2693 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12788 Z= 0.148 Angle : 0.529 8.057 17677 Z= 0.278 Chirality : 0.038 0.244 2050 Planarity : 0.003 0.035 1998 Dihedral : 14.789 120.095 2595 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.03 % Allowed : 11.15 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.26 (0.23), residues: 1366 helix: 1.17 (0.21), residues: 665 sheet: -2.00 (0.41), residues: 152 loop : -1.28 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 51 TYR 0.014 0.001 TYR B 135 PHE 0.012 0.001 PHE D 92 TRP 0.009 0.001 TRP A 916 HIS 0.004 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (12780) covalent geometry : angle 0.52424 / 0.28 (17671) hydrogen bonds : bond 0.03843 / 2.55 ( 624) hydrogen bonds : angle 4.16345 / 2.92 ( 1699) metal coordination : bond 0.01189 / 0.69 ( 8) metal coordination : angle 4.05003 / 2.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.573 Fit side-chains REVERT: A 5 GLN cc_start: 0.9555 (mm-40) cc_final: 0.9190 (tp-100) REVERT: A 212 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9060 (mt) REVERT: A 403 ASN cc_start: 0.9382 (OUTLIER) cc_final: 0.9122 (t0) REVERT: B 67 MET cc_start: 0.9077 (tpp) cc_final: 0.8264 (tpp) REVERT: B 70 MET cc_start: 0.8748 (tmm) cc_final: 0.8114 (ppp) REVERT: B 94 MET cc_start: 0.8589 (mtp) cc_final: 0.8196 (ttm) REVERT: C 47 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8856 (mm-30) REVERT: C 50 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8646 (mm-30) REVERT: D 51 ARG cc_start: 0.9338 (ttm-80) cc_final: 0.8938 (ttm110) REVERT: D 60 GLU cc_start: 0.9120 (tm-30) cc_final: 0.8716 (pp20) REVERT: D 67 MET cc_start: 0.9266 (mmp) cc_final: 0.8886 (tpp) REVERT: D 158 GLN cc_start: 0.8643 (pm20) cc_final: 0.8380 (pm20) outliers start: 24 outliers final: 15 residues processed: 90 average time/residue: 0.1114 time to fit residues: 15.4637 Evaluate side-chains 86 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 903 TYR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain D residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 118 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.050135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.034066 restraints weight = 57703.669| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 3.09 r_work: 0.2678 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12788 Z= 0.182 Angle : 0.540 8.378 17677 Z= 0.283 Chirality : 0.039 0.248 2050 Planarity : 0.003 0.034 1998 Dihedral : 14.828 119.612 2595 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.36 % Allowed : 10.98 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.16 (0.24), residues: 1366 helix: 1.25 (0.21), residues: 666 sheet: -2.05 (0.40), residues: 154 loop : -1.19 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 75 TYR 0.013 0.001 TYR A 788 PHE 0.012 0.001 PHE D 92 TRP 0.008 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (12780) covalent geometry : angle 0.53637 / 0.28 (17671) hydrogen bonds : bond 0.03808 / 2.54 ( 624) hydrogen bonds : angle 4.16145 / 2.90 ( 1699) metal coordination : bond 0.00988 / 0.61 ( 8) metal coordination : angle 3.60146 / 1.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.471 Fit side-chains REVERT: A 5 GLN cc_start: 0.9567 (mm-40) cc_final: 0.9210 (tp-100) REVERT: A 212 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9099 (mt) REVERT: B 67 MET cc_start: 0.9107 (tpp) cc_final: 0.8542 (tpp) REVERT: B 70 MET cc_start: 0.8777 (tmm) cc_final: 0.8336 (tmm) REVERT: C 50 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8747 (mm-30) REVERT: D 51 ARG cc_start: 0.9321 (ttm-80) cc_final: 0.8999 (ttm110) REVERT: D 60 GLU cc_start: 0.9153 (tm-30) cc_final: 0.8726 (pp20) REVERT: D 67 MET cc_start: 0.9234 (mmp) cc_final: 0.8903 (tpp) REVERT: D 158 GLN cc_start: 0.8700 (pm20) cc_final: 0.8420 (pm20) outliers start: 28 outliers final: 19 residues processed: 93 average time/residue: 0.1122 time to fit residues: 15.8475 Evaluate side-chains 89 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 HIS Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 903 TYR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain D residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 19 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 32 optimal weight: 0.0980 chunk 122 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.050508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.034471 restraints weight = 57195.879| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.08 r_work: 0.2700 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12788 Z= 0.128 Angle : 0.526 11.680 17677 Z= 0.274 Chirality : 0.038 0.248 2050 Planarity : 0.003 0.032 1998 Dihedral : 14.882 118.607 2595 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.36 % Allowed : 11.82 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.03 (0.24), residues: 1366 helix: 1.32 (0.21), residues: 672 sheet: -1.99 (0.40), residues: 154 loop : -1.08 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 51 TYR 0.022 0.001 TYR D 135 PHE 0.011 0.001 PHE D 92 TRP 0.010 0.001 TRP A 916 HIS 0.003 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (12780) covalent geometry : angle 0.52322 / 0.27 (17671) hydrogen bonds : bond 0.03552 / 2.39 ( 624) hydrogen bonds : angle 4.08980 / 2.85 ( 1699) metal coordination : bond 0.00968 / 0.56 ( 8) metal coordination : angle 3.01444 / 1.60 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.513 Fit side-chains REVERT: A 5 GLN cc_start: 0.9582 (mm-40) cc_final: 0.9290 (tp-100) REVERT: A 212 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9083 (mt) REVERT: B 67 MET cc_start: 0.9094 (tpp) cc_final: 0.8542 (tpp) REVERT: B 70 MET cc_start: 0.8807 (tmm) cc_final: 0.8359 (tmm) REVERT: B 94 MET cc_start: 0.8562 (mtp) cc_final: 0.8319 (ttm) REVERT: C 50 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8833 (mm-30) REVERT: D 51 ARG cc_start: 0.9293 (ttm-80) cc_final: 0.9044 (ttm110) REVERT: D 67 MET cc_start: 0.9266 (mmp) cc_final: 0.9031 (tpp) REVERT: D 158 GLN cc_start: 0.8607 (pm20) cc_final: 0.8325 (pm20) outliers start: 28 outliers final: 20 residues processed: 95 average time/residue: 0.1109 time to fit residues: 16.0848 Evaluate side-chains 90 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 HIS Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 903 TYR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain D residue 101 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 64 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 13 optimal weight: 0.0980 chunk 22 optimal weight: 0.5980 chunk 111 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 116 optimal weight: 0.3980 chunk 57 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 790 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 = 0.3406 r_free = 0.3406 target = 0.050770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.034971 restraints weight = 56929.202| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.07 r_work: 0.2709 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12788 Z= 0.110 Angle : 0.526 10.084 17677 Z= 0.276 Chirality : 0.038 0.244 2050 Planarity : 0.003 0.035 1998 Dihedral : 14.860 117.671 2595 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.77 % Allowed : 12.75 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.02 (0.24), residues: 1366 helix: 1.29 (0.21), residues: 673 sheet: -1.95 (0.41), residues: 154 loop : -1.03 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 57 TYR 0.014 0.001 TYR D 12 PHE 0.010 0.001 PHE D 92 TRP 0.011 0.001 TRP A 916 HIS 0.003 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (12780) covalent geometry : angle 0.52330 / 0.28 (17671) hydrogen bonds : bond 0.03441 / 2.32 ( 624) hydrogen bonds : angle 4.08995 / 2.85 ( 1699) metal coordination : bond 0.00869 / 0.49 ( 8) metal coordination : angle 2.70947 / 1.45 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.403 Fit side-chains REVERT: A 5 GLN cc_start: 0.9564 (mm-40) cc_final: 0.9294 (tp-100) REVERT: A 212 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9060 (mt) REVERT: B 67 MET cc_start: 0.9117 (tpp) cc_final: 0.8354 (tpp) REVERT: B 70 MET cc_start: 0.8850 (tmm) cc_final: 0.8310 (ppp) REVERT: B 94 MET cc_start: 0.8557 (mtp) cc_final: 0.8306 (ttm) REVERT: C 50 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8827 (mm-30) REVERT: D 51 ARG cc_start: 0.9310 (ttm-80) cc_final: 0.9055 (ttm110) REVERT: D 60 GLU cc_start: 0.9180 (tm-30) cc_final: 0.8840 (pp20) REVERT: D 67 MET cc_start: 0.9277 (mmp) cc_final: 0.9068 (tpp) REVERT: D 155 GLU cc_start: 0.8422 (pm20) cc_final: 0.8148 (pm20) REVERT: D 158 GLN cc_start: 0.8543 (pm20) cc_final: 0.8239 (pm20) outliers start: 21 outliers final: 17 residues processed: 87 average time/residue: 0.1165 time to fit residues: 15.3968 Evaluate side-chains 87 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 903 TYR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain D residue 101 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 129 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 41 optimal weight: 0.0370 chunk 14 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 111 optimal weight: 0.5980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN ** A 790 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 = 0.3405 r_free = 0.3405 target = 0.051353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.035492 restraints weight = 57611.941| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 3.10 r_work: 0.2705 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12788 Z= 0.120 Angle : 0.528 9.744 17677 Z= 0.274 Chirality : 0.038 0.243 2050 Planarity : 0.003 0.035 1998 Dihedral : 14.836 117.024 2595 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.77 % Allowed : 13.26 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.14 (0.24), residues: 1366 helix: 1.43 (0.21), residues: 672 sheet: -1.70 (0.42), residues: 142 loop : -1.06 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 75 TYR 0.011 0.001 TYR D 12 PHE 0.009 0.001 PHE A 741 TRP 0.010 0.001 TRP A 916 HIS 0.003 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (12780) covalent geometry : angle 0.52573 / 0.27 (17671) hydrogen bonds : bond 0.03405 / 2.29 ( 624) hydrogen bonds : angle 4.05140 / 2.83 ( 1699) metal coordination : bond 0.00673 / 0.40 ( 8) metal coordination : angle 2.47706 / 1.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.471 Fit side-chains REVERT: A 5 GLN cc_start: 0.9569 (mm-40) cc_final: 0.9289 (tp-100) REVERT: A 212 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9049 (mt) REVERT: B 67 MET cc_start: 0.9120 (tpp) cc_final: 0.8364 (tpp) REVERT: B 70 MET cc_start: 0.8806 (tmm) cc_final: 0.8294 (ppp) REVERT: B 94 MET cc_start: 0.8452 (mtp) cc_final: 0.8224 (ttm) REVERT: C 50 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8873 (mm-30) REVERT: D 51 ARG cc_start: 0.9306 (ttm-80) cc_final: 0.8971 (ttm110) REVERT: D 60 GLU cc_start: 0.9233 (tm-30) cc_final: 0.8892 (pp20) REVERT: D 155 GLU cc_start: 0.8460 (pm20) cc_final: 0.8163 (pm20) REVERT: D 157 GLN cc_start: 0.9015 (mt0) cc_final: 0.8782 (mp10) REVERT: D 158 GLN cc_start: 0.8506 (pm20) cc_final: 0.8242 (pm20) outliers start: 21 outliers final: 17 residues processed: 86 average time/residue: 0.1126 time to fit residues: 14.8104 Evaluate side-chains 88 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain D residue 101 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 83 optimal weight: 0.5980 chunk 125 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 790 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 = 0.3399 r_free = 0.3399 target = 0.050486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.034633 restraints weight = 57218.049| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 3.09 r_work: 0.2701 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12788 Z= 0.131 Angle : 0.547 11.261 17677 Z= 0.282 Chirality : 0.038 0.244 2050 Planarity : 0.003 0.033 1998 Dihedral : 14.829 117.365 2593 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.86 % Allowed : 13.43 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.24), residues: 1366 helix: 1.46 (0.21), residues: 672 sheet: -1.68 (0.42), residues: 142 loop : -1.06 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 57 TYR 0.019 0.001 TYR D 135 PHE 0.009 0.001 PHE A 741 TRP 0.009 0.001 TRP A 916 HIS 0.003 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (12780) covalent geometry : angle 0.54563 / 0.28 (17671) hydrogen bonds : bond 0.03446 / 2.33 ( 624) hydrogen bonds : angle 4.06914 / 2.85 ( 1699) metal coordination : bond 0.00673 / 0.42 ( 8) metal coordination : angle 2.39977 / 1.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 5 GLN cc_start: 0.9575 (mm-40) cc_final: 0.9293 (tp-100) REVERT: A 212 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9038 (mt) REVERT: B 67 MET cc_start: 0.9136 (tpp) cc_final: 0.8376 (tpp) REVERT: B 70 MET cc_start: 0.8808 (tmm) cc_final: 0.8260 (ppp) REVERT: B 94 MET cc_start: 0.8451 (mtp) cc_final: 0.8213 (ttm) REVERT: D 51 ARG cc_start: 0.9265 (ttm-80) cc_final: 0.9035 (ttm110) REVERT: D 60 GLU cc_start: 0.9256 (tm-30) cc_final: 0.8861 (pp20) REVERT: D 67 MET cc_start: 0.9319 (mmp) cc_final: 0.8953 (tpp) REVERT: D 155 GLU cc_start: 0.8419 (pm20) cc_final: 0.8154 (pm20) REVERT: D 158 GLN cc_start: 0.8527 (pm20) cc_final: 0.8260 (pm20) outliers start: 22 outliers final: 19 residues processed: 87 average time/residue: 0.1125 time to fit residues: 15.0251 Evaluate side-chains 88 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 101 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 82 optimal weight: 0.1980 chunk 89 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 119 optimal weight: 30.0000 chunk 52 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 136 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 790 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 = 0.3405 r_free = 0.3405 target = 0.052878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.036946 restraints weight = 61684.846| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.14 r_work: 0.2701 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12788 Z= 0.128 Angle : 0.548 10.794 17677 Z= 0.283 Chirality : 0.038 0.245 2050 Planarity : 0.003 0.032 1998 Dihedral : 14.839 117.776 2593 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.94 % Allowed : 13.68 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.21 (0.24), residues: 1366 helix: 1.50 (0.21), residues: 671 sheet: -1.63 (0.42), residues: 142 loop : -1.04 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 75 TYR 0.017 0.001 TYR A 903 PHE 0.009 0.001 PHE A 741 TRP 0.009 0.001 TRP A 916 HIS 0.003 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (12780) covalent geometry : angle 0.54668 / 0.28 (17671) hydrogen bonds : bond 0.03425 / 2.32 ( 624) hydrogen bonds : angle 4.06419 / 2.86 ( 1699) metal coordination : bond 0.00664 / 0.41 ( 8) metal coordination : angle 2.35681 / 1.26 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 5 GLN cc_start: 0.9582 (mm-40) cc_final: 0.9296 (tp-100) REVERT: A 212 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9029 (mt) REVERT: B 67 MET cc_start: 0.9124 (tpp) cc_final: 0.8360 (tpp) REVERT: B 70 MET cc_start: 0.8806 (tmm) cc_final: 0.8260 (ppp) REVERT: B 94 MET cc_start: 0.8456 (mtp) cc_final: 0.8183 (ttm) REVERT: C 47 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8808 (mm-30) REVERT: C 62 MET cc_start: 0.9002 (mtt) cc_final: 0.8614 (mtt) REVERT: D 51 ARG cc_start: 0.9258 (ttm-80) cc_final: 0.9031 (ttm110) REVERT: D 60 GLU cc_start: 0.9277 (tm-30) cc_final: 0.8969 (pp20) REVERT: D 67 MET cc_start: 0.9316 (mmp) cc_final: 0.8962 (tpp) REVERT: D 158 GLN cc_start: 0.8612 (pm20) cc_final: 0.8300 (pm20) outliers start: 23 outliers final: 20 residues processed: 85 average time/residue: 0.1082 time to fit residues: 14.0876 Evaluate side-chains 88 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 101 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 123 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 790 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 = 0.3402 r_free = 0.3402 target = 0.052678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.036057 restraints weight = 61670.707| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 3.20 r_work: 0.2691 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12788 Z= 0.137 Angle : 0.557 11.097 17677 Z= 0.289 Chirality : 0.038 0.247 2050 Planarity : 0.003 0.032 1998 Dihedral : 14.847 118.215 2593 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.77 % Allowed : 13.85 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.25 (0.24), residues: 1366 helix: 1.55 (0.21), residues: 671 sheet: -1.80 (0.40), residues: 156 loop : -0.97 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 57 TYR 0.017 0.001 TYR A 903 PHE 0.009 0.001 PHE A 741 TRP 0.008 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (12780) covalent geometry : angle 0.55496 / 0.29 (17671) hydrogen bonds : bond 0.03444 / 2.32 ( 624) hydrogen bonds : angle 4.09496 / 2.90 ( 1699) metal coordination : bond 0.00657 / 0.42 ( 8) metal coordination : angle 2.39020 / 1.27 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2955.54 seconds wall clock time: 51 minutes 46.34 seconds (3106.34 seconds total)