Starting phenix.real_space_refine on Sat Sep 12 12:33:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6iro_9720/09_2026/6iro_9720_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6iro_9720/09_2026/6iro_9720.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 { model { file = "/net/cci-nas-00/data/ceres_data/6iro_9720/09_2026/6iro_9720_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6iro_9720/09_2026/6iro_9720_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6iro_9720/09_2026/6iro_9720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6iro_9720/09_2026/6iro_9720.map" } 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: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 25 5.16 5 C 9253 2.51 5 N 2955 2.21 5 O 3581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 16108 Number of models: 1 Model: "" Number of chains: 12 Chain: "L" Number of atoms: 4070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 4070 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 15, 'TRANS': 477} Chain breaks: 3 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: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.17, per 1000 atoms: 0.20 Number of scatterers: 16108 At special positions: 0 Unit cell: (145.52, 131.61, 126.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 25 16.00 P 294 15.00 O 3581 8.00 N 2955 7.00 C 9253 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 483.4 milliseconds 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2388 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 12 sheets defined 62.1% alpha, 3.8% beta 126 base pairs and 255 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'L' and resid 102 through 113 removed outlier: 3.648A pdb=" N LYS L 107 " --> pdb=" O GLU L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 116 through 118 No H-bonds generated for 'chain 'L' and resid 116 through 118' Processing helix chain 'L' and resid 119 through 124 removed outlier: 3.639A pdb=" N ILE L 123 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU L 124 " --> pdb=" O LYS L 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 119 through 124' Processing helix chain 'L' and resid 134 through 142 removed outlier: 3.929A pdb=" N ASP L 138 " --> pdb=" O ARG L 134 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL L 139 " --> pdb=" O GLN L 135 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU L 140 " --> pdb=" O VAL L 136 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLU L 142 " --> pdb=" O ASP L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 213 Processing helix chain 'L' and resid 226 through 241 removed outlier: 3.661A pdb=" N LEU L 238 " --> pdb=" O PHE L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 253 through 255 No H-bonds generated for 'chain 'L' and resid 253 through 255' Processing helix chain 'L' and resid 256 through 268 removed outlier: 3.797A pdb=" N LEU L 261 " --> pdb=" O LEU L 257 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN L 265 " --> pdb=" O LEU L 261 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP L 267 " --> pdb=" O GLU L 263 " (cutoff:3.500A) Processing helix chain 'L' and resid 281 through 289 removed outlier: 3.885A pdb=" N GLU L 285 " --> pdb=" O GLU L 281 " (cutoff:3.500A) Processing helix chain 'L' and resid 304 through 309 removed outlier: 3.592A pdb=" N ARG L 308 " --> pdb=" O GLU L 304 " (cutoff:3.500A) Processing helix chain 'L' and resid 327 through 331 removed outlier: 3.582A pdb=" N LYS L 330 " --> pdb=" O HIS L 327 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN L 331 " --> pdb=" O ARG L 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 327 through 331' Processing helix chain 'L' and resid 334 through 341 Processing helix chain 'L' and resid 360 through 369 removed outlier: 3.802A pdb=" N TRP L 364 " --> pdb=" O LEU L 360 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA L 365 " --> pdb=" O HIS L 361 " (cutoff:3.500A) Processing helix chain 'L' and resid 378 through 390 removed outlier: 3.593A pdb=" N ASP L 382 " --> pdb=" O ALA L 378 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TRP L 384 " --> pdb=" O ASP L 380 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE L 385 " --> pdb=" O PHE L 381 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER L 387 " --> pdb=" O ASP L 383 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N GLU L 388 " --> pdb=" O TRP L 384 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER L 389 " --> pdb=" O PHE L 385 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR L 390 " --> pdb=" O SER L 386 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 405 Processing helix chain 'L' and resid 413 through 417 removed outlier: 3.817A pdb=" N VAL L 417 " --> pdb=" O LYS L 414 " (cutoff:3.500A) Processing helix chain 'L' and resid 434 through 445 removed outlier: 3.587A pdb=" N LYS L 439 " --> pdb=" O SER L 435 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS L 442 " --> pdb=" O LYS L 438 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU L 445 " --> pdb=" O TYR L 441 " (cutoff:3.500A) Processing helix chain 'L' and resid 467 through 478 removed outlier: 3.613A pdb=" N ARG L 473 " --> pdb=" O MET L 469 " (cutoff:3.500A) Processing helix chain 'L' and resid 479 through 483 removed outlier: 3.871A pdb=" N LYS L 483 " --> pdb=" O TYR L 480 " (cutoff:3.500A) Processing helix chain 'L' and resid 495 through 500 removed outlier: 3.511A pdb=" N ASN L 500 " --> pdb=" O HIS L 496 " (cutoff:3.500A) Processing helix chain 'L' and resid 501 through 518 removed outlier: 3.581A pdb=" N LYS L 512 " --> pdb=" O ASP L 508 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU L 516 " --> pdb=" O LYS L 512 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU L 517 " --> pdb=" O LYS L 513 " (cutoff:3.500A) Processing helix chain 'L' and resid 527 through 541 removed outlier: 3.712A pdb=" N LEU L 531 " --> pdb=" O MET L 527 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE L 533 " --> pdb=" O ARG L 529 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP L 536 " --> pdb=" O ASP L 532 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR L 539 " --> pdb=" O GLU L 535 " (cutoff:3.500A) Processing helix chain 'L' and resid 555 through 565 removed outlier: 3.710A pdb=" N GLN L 559 " --> pdb=" O GLU L 555 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE L 561 " --> pdb=" O ARG L 557 " (cutoff:3.500A) Processing helix chain 'L' and resid 601 through 610 removed outlier: 3.521A pdb=" N ASP L 605 " --> pdb=" O ASN L 601 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP L 610 " --> pdb=" O LEU L 606 " (cutoff:3.500A) Processing helix chain 'L' and resid 632 through 652 removed outlier: 3.796A pdb=" N GLU L 638 " --> pdb=" O GLU L 634 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU L 644 " --> pdb=" O ALA L 640 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG L 645 " --> pdb=" O THR L 641 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU L 646 " --> pdb=" O GLN L 642 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP L 647 " --> pdb=" O LYS L 643 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE L 651 " --> pdb=" O ASP L 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.838A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 130 removed outlier: 3.583A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.665A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.121A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.668A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.545A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 16 through 21' Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.711A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.998A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.597A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.872A pdb=" N LEU D 99 " --> pdb=" O VAL D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 121 removed outlier: 4.036A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.924A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 113 removed outlier: 3.793A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.696A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG E 128 " --> pdb=" O ILE E 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.815A pdb=" N GLY F 28 " --> pdb=" O ASN F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.739A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.185A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.895A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.914A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.513A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 34 through 44 removed outlier: 3.797A pdb=" N VAL H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 80 removed outlier: 3.568A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.750A pdb=" N LEU H 99 " --> pdb=" O VAL H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 121 removed outlier: 4.022A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 218 through 219 removed outlier: 7.132A pdb=" N ILE L 218 " --> pdb=" O LEU L 410 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'L' and resid 298 through 301 removed outlier: 6.706A pdb=" N LEU L 249 " --> pdb=" O ILE L 322 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASP L 324 " --> pdb=" O LEU L 249 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE L 251 " --> pdb=" O ASP L 324 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE L 321 " --> pdb=" O LEU L 349 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE L 351 " --> pdb=" O ILE L 321 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE L 323 " --> pdb=" O ILE L 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 427 through 431 removed outlier: 7.519A pdb=" N VAL L 593 " --> pdb=" O PHE L 624 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N LEU L 626 " --> pdb=" O VAL L 593 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LEU L 522 " --> pdb=" O VAL L 594 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU L 576 " --> pdb=" O VAL L 521 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE L 523 " --> pdb=" O LEU L 576 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.957A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA7, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.606A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.018A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.868A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.608A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.077A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 77 through 78 483 hydrogen bonds defined for protein. 1428 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 326 hydrogen bonds 652 hydrogen bond angles 0 basepair planarities 126 basepair parallelities 255 stacking parallelities Total time for adding SS restraints: 3.15 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3359 1.33 - 1.45: 5183 1.45 - 1.57: 7825 1.57 - 1.70: 585 1.70 - 1.82: 43 Bond restraints: 16995 Sorted by residual: bond pdb=" C3' DA J 60 " pdb=" O3' DA J 60 " ideal model delta sigma weight residual 1.435 1.380 0.055 1.30e-02 5.92e+03 1.81e+01 bond pdb=" C3' DG J 66 " pdb=" O3' DG J 66 " ideal model delta sigma weight residual 1.435 1.489 -0.054 1.30e-02 5.92e+03 1.70e+01 bond pdb=" C3' DG J 53 " pdb=" O3' DG J 53 " ideal model delta sigma weight residual 1.435 1.381 0.054 1.30e-02 5.92e+03 1.70e+01 bond pdb=" C5' DG J 37 " pdb=" C4' DG J 37 " ideal model delta sigma weight residual 1.512 1.541 -0.029 7.00e-03 2.04e+04 1.67e+01 bond pdb=" C3' DG I 99 " pdb=" O3' DG I 99 " ideal model delta sigma weight residual 1.435 1.488 -0.053 1.30e-02 5.92e+03 1.65e+01 ... (remaining 16990 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 23008 2.45 - 4.90: 1077 4.90 - 7.34: 110 7.34 - 9.79: 18 9.79 - 12.24: 5 Bond angle restraints: 24218 Sorted by residual: angle pdb=" O4' DA J 40 " pdb=" C4' DA J 40 " pdb=" C3' DA J 40 " ideal model delta sigma weight residual 106.00 101.83 4.17 6.00e-01 2.78e+00 4.84e+01 angle pdb=" O4' DG J 29 " pdb=" C4' DG J 29 " pdb=" C3' DG J 29 " ideal model delta sigma weight residual 106.00 102.10 3.90 6.00e-01 2.78e+00 4.23e+01 angle pdb=" C VAL L 417 " pdb=" N GLU L 418 " pdb=" CA GLU L 418 " ideal model delta sigma weight residual 121.70 133.30 -11.60 1.80e+00 3.09e-01 4.15e+01 angle pdb=" O4' DC I 109 " pdb=" C4' DC I 109 " pdb=" C3' DC I 109 " ideal model delta sigma weight residual 106.00 102.46 3.54 6.00e-01 2.78e+00 3.48e+01 angle pdb=" O4' DA I 39 " pdb=" C4' DA I 39 " pdb=" C3' DA I 39 " ideal model delta sigma weight residual 106.00 102.61 3.39 6.00e-01 2.78e+00 3.19e+01 ... (remaining 24213 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 7946 35.64 - 71.29: 1487 71.29 - 106.93: 50 106.93 - 142.58: 4 142.58 - 178.22: 7 Dihedral angle restraints: 9494 sinusoidal: 5809 harmonic: 3685 Sorted by residual: dihedral pdb=" CA LEU A 60 " pdb=" C LEU A 60 " pdb=" N LEU A 61 " pdb=" CA LEU A 61 " ideal model delta harmonic sigma weight residual -180.00 -143.09 -36.91 0 5.00e+00 4.00e-02 5.45e+01 dihedral pdb=" CA LEU E 60 " pdb=" C LEU E 60 " pdb=" N LEU E 61 " pdb=" CA LEU E 61 " ideal model delta harmonic sigma weight residual -180.00 -143.40 -36.60 0 5.00e+00 4.00e-02 5.36e+01 dihedral pdb=" CA LEU D 99 " pdb=" C LEU D 99 " pdb=" N PRO D 100 " pdb=" CA PRO D 100 " ideal model delta harmonic sigma weight residual -180.00 -146.67 -33.33 0 5.00e+00 4.00e-02 4.44e+01 ... (remaining 9491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2056 0.065 - 0.129: 558 0.129 - 0.194: 113 0.194 - 0.258: 21 0.258 - 0.323: 6 Chirality restraints: 2754 Sorted by residual: chirality pdb=" C3' DA J 71 " pdb=" C4' DA J 71 " pdb=" O3' DA J 71 " pdb=" C2' DA J 71 " both_signs ideal model delta sigma weight residual False -2.73 -2.41 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CB VAL E 117 " pdb=" CA VAL E 117 " pdb=" CG1 VAL E 117 " pdb=" CG2 VAL E 117 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C3' DG J 66 " pdb=" C4' DG J 66 " pdb=" O3' DG J 66 " pdb=" C2' DG J 66 " both_signs ideal model delta sigma weight residual False -2.73 -2.44 -0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 2751 not shown) Planarity restraints: 2054 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 98 " 0.020 2.00e-02 2.50e+03 2.25e-02 1.01e+01 pdb=" CG TYR F 98 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR F 98 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR F 98 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR F 98 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR F 98 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR F 98 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR F 98 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 39 " -0.042 2.00e-02 2.50e+03 1.76e-02 8.48e+00 pdb=" N9 DA I 39 " 0.034 2.00e-02 2.50e+03 pdb=" C8 DA I 39 " 0.010 2.00e-02 2.50e+03 pdb=" N7 DA I 39 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DA I 39 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 39 " -0.007 2.00e-02 2.50e+03 pdb=" N6 DA I 39 " -0.014 2.00e-02 2.50e+03 pdb=" N1 DA I 39 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DA I 39 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 39 " 0.010 2.00e-02 2.50e+03 pdb=" C4 DA I 39 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 120 " -0.048 5.00e-02 4.00e+02 7.26e-02 8.43e+00 pdb=" N PRO A 121 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 121 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 121 " -0.040 5.00e-02 4.00e+02 ... (remaining 2051 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3645 2.79 - 3.32: 13231 3.32 - 3.84: 29801 3.84 - 4.37: 34354 4.37 - 4.90: 50598 Nonbonded interactions: 131629 Sorted by model distance: nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.262 3.040 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 65 " model vdw 2.264 3.040 nonbonded pdb=" OH TYR L 191 " pdb=" O SER L 233 " model vdw 2.313 3.040 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.332 3.040 nonbonded pdb=" OG SER D 84 " pdb=" OP1 DG J 39 " model vdw 2.344 3.040 ... (remaining 131624 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 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 or (resid 19 through 20 and (name N or name CA or name C or name \ O or name CB )) or resid 21 through 22 or (resid 23 and (name N or name CA or na \ me C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 17 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } 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: 0.980 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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.790 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 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 : 0.010 0.085 16995 Z= 0.753 Angle : 1.161 12.238 24218 Z= 0.872 Chirality : 0.063 0.323 2754 Planarity : 0.007 0.073 2054 Dihedral : 26.535 178.220 7106 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.74 % Allowed : 2.04 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.08 % Twisted Proline : 5.00 % Twisted General : 0.25 % 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: -4.09 (0.18), residues: 1238 helix: -2.45 (0.14), residues: 708 sheet: -2.33 (0.66), residues: 66 loop : -2.97 (0.23), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 39 TYR 0.054 0.004 TYR F 98 PHE 0.038 0.004 PHE L 540 TRP 0.014 0.002 TRP L 600 HIS 0.007 0.002 HIS L 478 Details of bonding type rmsd/Z covalent geometry : bond 0.01012 / 0.75 (16995) covalent geometry : angle 1.16119 / 0.87 (24218) hydrogen bonds : bond 0.17075 / 11.02 ( 809) hydrogen bonds : angle 5.45760 / 3.75 ( 2080) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 231 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 193 ASN cc_start: 0.8862 (t0) cc_final: 0.8461 (m110) REVERT: L 323 ILE cc_start: 0.8831 (mt) cc_final: 0.8608 (mp) REVERT: L 325 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7757 (tm-30) REVERT: L 327 HIS cc_start: 0.8378 (m90) cc_final: 0.7910 (m170) REVERT: L 351 ILE cc_start: 0.8221 (mt) cc_final: 0.7907 (tt) REVERT: L 470 MET cc_start: 0.8833 (tpt) cc_final: 0.8296 (tpp) REVERT: L 570 LYS cc_start: 0.8752 (mttt) cc_final: 0.8536 (tptt) REVERT: C 95 LYS cc_start: 0.9102 (tptm) cc_final: 0.8831 (tppt) REVERT: C 102 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8830 (tt) REVERT: E 42 ARG cc_start: 0.7620 (mmm160) cc_final: 0.7310 (mmm-85) REVERT: E 50 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7351 (mm-30) REVERT: F 25 ASN cc_start: 0.5234 (m-40) cc_final: 0.4827 (m110) REVERT: H 73 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8034 (tm-30) outliers start: 8 outliers final: 0 residues processed: 235 average time/residue: 0.1550 time to fit residues: 50.5719 Evaluate side-chains 139 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 30.0000 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 111 HIS L 230 GLN L 437 GLN L 526 GLN L 542 ASN L 613 HIS A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN D 46 HIS D 81 ASN D 106 HIS E 68 GLN H 60 ASN H 81 ASN H 92 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.087883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.060185 restraints weight = 59132.752| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.54 r_work: 0.2899 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16995 Z= 0.173 Angle : 0.781 10.944 24218 Z= 0.447 Chirality : 0.054 0.407 2754 Planarity : 0.005 0.058 2054 Dihedral : 31.135 176.051 4592 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.49 % Allowed : 8.83 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.08 % 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: -2.11 (0.22), residues: 1238 helix: -0.60 (0.18), residues: 725 sheet: -1.78 (0.68), residues: 66 loop : -2.61 (0.25), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 30 TYR 0.023 0.002 TYR F 98 PHE 0.015 0.002 PHE L 540 TRP 0.009 0.001 TRP L 260 HIS 0.005 0.001 HIS L 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.17 (16995) covalent geometry : angle 0.78118 / 0.45 (24218) hydrogen bonds : bond 0.06465 / 4.13 ( 809) hydrogen bonds : angle 3.77682 / 2.65 ( 2080) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: L 193 ASN cc_start: 0.8908 (t0) cc_final: 0.8633 (m110) REVERT: L 267 TRP cc_start: 0.7210 (m100) cc_final: 0.6576 (m100) REVERT: L 323 ILE cc_start: 0.8747 (mt) cc_final: 0.8532 (mp) REVERT: L 351 ILE cc_start: 0.7961 (mt) cc_final: 0.7615 (tt) REVERT: L 470 MET cc_start: 0.9056 (tpt) cc_final: 0.8617 (tpp) REVERT: L 570 LYS cc_start: 0.8835 (mttt) cc_final: 0.8505 (tptt) REVERT: B 63 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8621 (mt-10) REVERT: C 61 GLU cc_start: 0.8389 (tp30) cc_final: 0.8177 (tt0) REVERT: C 95 LYS cc_start: 0.9380 (tptm) cc_final: 0.9064 (tppt) REVERT: C 111 ILE cc_start: 0.8537 (mp) cc_final: 0.8182 (mp) REVERT: D 58 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.8897 (mt) REVERT: D 65 ASP cc_start: 0.9076 (t0) cc_final: 0.8873 (t0) REVERT: E 42 ARG cc_start: 0.7634 (mmm160) cc_final: 0.7333 (mmm-85) REVERT: F 80 THR cc_start: 0.9389 (m) cc_final: 0.9091 (p) REVERT: G 92 GLU cc_start: 0.8576 (pm20) cc_final: 0.8240 (pm20) outliers start: 16 outliers final: 5 residues processed: 170 average time/residue: 0.1312 time to fit residues: 32.8291 Evaluate side-chains 145 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 367 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain H residue 31 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 63 optimal weight: 0.7980 chunk 131 optimal weight: 30.0000 chunk 90 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 122 optimal weight: 30.0000 chunk 18 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 144 optimal weight: 30.0000 chunk 19 optimal weight: 7.9990 chunk 116 optimal weight: 0.5980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 542 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.087995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.059848 restraints weight = 59477.443| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.50 r_work: 0.2897 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16995 Z= 0.152 Angle : 0.708 11.193 24218 Z= 0.408 Chirality : 0.051 0.434 2754 Planarity : 0.005 0.053 2054 Dihedral : 30.684 176.806 4590 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.23 % Allowed : 9.76 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.08 % 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: -1.07 (0.23), residues: 1238 helix: 0.37 (0.19), residues: 730 sheet: -1.68 (0.64), residues: 67 loop : -2.38 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 42 TYR 0.026 0.002 TYR L 320 PHE 0.011 0.001 PHE L 540 TRP 0.005 0.001 TRP L 267 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.15 (16995) covalent geometry : angle 0.70815 / 0.41 (24218) hydrogen bonds : bond 0.05640 / 3.60 ( 809) hydrogen bonds : angle 3.44620 / 2.41 ( 2080) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: L 193 ASN cc_start: 0.8950 (t0) cc_final: 0.8707 (m110) REVERT: L 267 TRP cc_start: 0.7434 (m100) cc_final: 0.6815 (m100) REVERT: L 277 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7914 (mp10) REVERT: L 329 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8552 (mm) REVERT: L 433 MET cc_start: 0.8148 (ttm) cc_final: 0.7656 (ttt) REVERT: L 470 MET cc_start: 0.9096 (tpt) cc_final: 0.8640 (tpp) REVERT: L 570 LYS cc_start: 0.8861 (mttt) cc_final: 0.8522 (tptt) REVERT: A 120 MET cc_start: 0.8493 (mmm) cc_final: 0.8065 (mtp) REVERT: B 63 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8535 (mt-10) REVERT: C 61 GLU cc_start: 0.8418 (tp30) cc_final: 0.8208 (tt0) REVERT: C 95 LYS cc_start: 0.9399 (tptm) cc_final: 0.9110 (tppt) REVERT: D 58 ILE cc_start: 0.9381 (OUTLIER) cc_final: 0.9075 (mt) REVERT: D 65 ASP cc_start: 0.9070 (t0) cc_final: 0.8859 (t0) REVERT: E 42 ARG cc_start: 0.7642 (mmm160) cc_final: 0.7332 (mmm-85) REVERT: E 51 ILE cc_start: 0.8849 (mt) cc_final: 0.8617 (mt) REVERT: F 80 THR cc_start: 0.9422 (m) cc_final: 0.9138 (p) REVERT: G 61 GLU cc_start: 0.8556 (tp30) cc_final: 0.8339 (tp30) REVERT: G 91 GLU cc_start: 0.7894 (pm20) cc_final: 0.7681 (pm20) REVERT: G 92 GLU cc_start: 0.8583 (pm20) cc_final: 0.8253 (pm20) REVERT: H 32 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7999 (mm-30) REVERT: H 102 GLU cc_start: 0.8343 (tm-30) cc_final: 0.8008 (tm-30) outliers start: 24 outliers final: 10 residues processed: 169 average time/residue: 0.1442 time to fit residues: 35.2806 Evaluate side-chains 146 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 277 GLN Chi-restraints excluded: chain L residue 329 ILE Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 99 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 103 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 97 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 30.0000 chunk 23 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.088026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.059842 restraints weight = 59022.369| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.39 r_work: 0.2899 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16995 Z= 0.145 Angle : 0.673 9.026 24218 Z= 0.388 Chirality : 0.049 0.420 2754 Planarity : 0.004 0.052 2054 Dihedral : 30.567 177.604 4590 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.86 % Allowed : 12.64 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.08 % 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: -0.57 (0.24), residues: 1238 helix: 0.77 (0.20), residues: 738 sheet: -1.33 (0.66), residues: 67 loop : -2.25 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 92 TYR 0.012 0.001 TYR F 98 PHE 0.009 0.001 PHE L 274 TRP 0.006 0.001 TRP L 600 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 (16995) covalent geometry : angle 0.67349 / 0.39 (24218) hydrogen bonds : bond 0.05161 / 3.28 ( 809) hydrogen bonds : angle 3.32696 / 2.32 ( 2080) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: L 267 TRP cc_start: 0.7422 (m100) cc_final: 0.6830 (m100) REVERT: L 433 MET cc_start: 0.8074 (ttm) cc_final: 0.7708 (ttt) REVERT: L 470 MET cc_start: 0.9116 (tpt) cc_final: 0.8691 (tpp) REVERT: L 570 LYS cc_start: 0.8834 (mttt) cc_final: 0.8527 (tptt) REVERT: A 120 MET cc_start: 0.8529 (mmm) cc_final: 0.8022 (mtp) REVERT: B 63 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8545 (mt-10) REVERT: C 95 LYS cc_start: 0.9367 (tptm) cc_final: 0.9068 (tppt) REVERT: D 58 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.9113 (mt) REVERT: E 42 ARG cc_start: 0.7698 (mmm160) cc_final: 0.7391 (mmm-85) REVERT: E 51 ILE cc_start: 0.8861 (mt) cc_final: 0.8598 (mt) REVERT: F 80 THR cc_start: 0.9423 (m) cc_final: 0.9136 (p) REVERT: G 91 GLU cc_start: 0.7969 (pm20) cc_final: 0.7661 (pm20) REVERT: G 92 GLU cc_start: 0.8582 (pm20) cc_final: 0.8127 (pm20) REVERT: H 32 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7968 (mm-30) REVERT: H 98 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8741 (tp) REVERT: H 102 GLU cc_start: 0.8348 (tm-30) cc_final: 0.8144 (tm-30) outliers start: 20 outliers final: 11 residues processed: 152 average time/residue: 0.1313 time to fit residues: 30.0044 Evaluate side-chains 142 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 99 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 55 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 134 optimal weight: 50.0000 chunk 20 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 81 optimal weight: 0.0980 chunk 61 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 117 optimal weight: 0.4980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.088083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.059569 restraints weight = 58525.365| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.32 r_work: 0.2906 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16995 Z= 0.147 Angle : 0.661 8.212 24218 Z= 0.380 Chirality : 0.048 0.419 2754 Planarity : 0.004 0.051 2054 Dihedral : 30.411 178.058 4590 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.23 % Allowed : 12.36 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.08 % 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: 1238 helix: 1.06 (0.20), residues: 740 sheet: -0.98 (0.66), residues: 67 loop : -2.08 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 30 TYR 0.012 0.001 TYR F 98 PHE 0.009 0.001 PHE L 274 TRP 0.006 0.001 TRP L 600 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.15 (16995) covalent geometry : angle 0.66123 / 0.38 (24218) hydrogen bonds : bond 0.05099 / 3.25 ( 809) hydrogen bonds : angle 3.24755 / 2.26 ( 2080) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: L 433 MET cc_start: 0.8104 (ttm) cc_final: 0.7652 (ttt) REVERT: L 437 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7794 (pt0) REVERT: L 470 MET cc_start: 0.9106 (tpt) cc_final: 0.8692 (tpp) REVERT: L 570 LYS cc_start: 0.8899 (mttt) cc_final: 0.8581 (tptt) REVERT: A 120 MET cc_start: 0.8517 (mmm) cc_final: 0.7983 (mtp) REVERT: B 63 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8507 (mt-10) REVERT: C 95 LYS cc_start: 0.9390 (tptm) cc_final: 0.9143 (tppt) REVERT: D 58 ILE cc_start: 0.9419 (OUTLIER) cc_final: 0.9203 (mt) REVERT: E 42 ARG cc_start: 0.7602 (mmm160) cc_final: 0.7312 (tpp-160) REVERT: E 51 ILE cc_start: 0.8854 (mt) cc_final: 0.8558 (mt) REVERT: E 97 GLU cc_start: 0.8659 (tt0) cc_final: 0.8403 (mt-10) REVERT: F 80 THR cc_start: 0.9417 (m) cc_final: 0.9128 (p) REVERT: H 32 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8064 (mm-30) REVERT: H 68 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8480 (tp30) REVERT: H 98 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8779 (tp) REVERT: H 102 GLU cc_start: 0.8283 (tm-30) cc_final: 0.8034 (tm-30) outliers start: 24 outliers final: 15 residues processed: 158 average time/residue: 0.1270 time to fit residues: 30.3359 Evaluate side-chains 146 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 221 ASP Chi-restraints excluded: chain L residue 437 GLN Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 99 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 93 optimal weight: 1.9990 chunk 142 optimal weight: 20.0000 chunk 79 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 38 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 620 GLN B 25 ASN B 93 GLN H 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.088067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.060010 restraints weight = 58799.237| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.65 r_work: 0.2885 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16995 Z= 0.142 Angle : 0.654 8.086 24218 Z= 0.375 Chirality : 0.047 0.416 2754 Planarity : 0.004 0.051 2054 Dihedral : 30.334 177.822 4590 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.70 % Allowed : 12.83 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.08 % 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 (0.25), residues: 1238 helix: 1.25 (0.20), residues: 740 sheet: -0.79 (0.68), residues: 67 loop : -1.97 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 266 TYR 0.015 0.001 TYR F 98 PHE 0.017 0.001 PHE L 274 TRP 0.008 0.001 TRP L 267 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (16995) covalent geometry : angle 0.65425 / 0.38 (24218) hydrogen bonds : bond 0.04963 / 3.15 ( 809) hydrogen bonds : angle 3.17214 / 2.21 ( 2080) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: L 433 MET cc_start: 0.8091 (ttm) cc_final: 0.7628 (ttt) REVERT: L 437 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7826 (pt0) REVERT: L 470 MET cc_start: 0.9140 (tpt) cc_final: 0.8736 (tpp) REVERT: L 570 LYS cc_start: 0.8952 (mttt) cc_final: 0.8593 (tptt) REVERT: A 120 MET cc_start: 0.8577 (mmm) cc_final: 0.8078 (mtp) REVERT: B 63 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8526 (mt-10) REVERT: B 93 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.7494 (mp-120) REVERT: C 41 GLU cc_start: 0.8218 (mp0) cc_final: 0.8005 (mp0) REVERT: C 95 LYS cc_start: 0.9436 (tptm) cc_final: 0.9187 (tppt) REVERT: D 96 ARG cc_start: 0.8883 (ttp80) cc_final: 0.8615 (ttp80) REVERT: D 99 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9183 (pp) REVERT: E 51 ILE cc_start: 0.8885 (mt) cc_final: 0.8598 (mt) REVERT: E 97 GLU cc_start: 0.8762 (tt0) cc_final: 0.8511 (mt-10) REVERT: F 80 THR cc_start: 0.9423 (m) cc_final: 0.9132 (p) REVERT: H 32 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8112 (mm-30) REVERT: H 68 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8513 (tp30) REVERT: H 98 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8758 (tp) outliers start: 29 outliers final: 16 residues processed: 154 average time/residue: 0.1267 time to fit residues: 29.2818 Evaluate side-chains 142 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 221 ASP Chi-restraints excluded: chain L residue 437 GLN Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 99 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 7 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 109 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 620 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.088217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.060246 restraints weight = 58409.894| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.71 r_work: 0.2884 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16995 Z= 0.142 Angle : 0.646 9.270 24218 Z= 0.370 Chirality : 0.047 0.417 2754 Planarity : 0.004 0.051 2054 Dihedral : 30.297 177.848 4590 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.32 % Allowed : 13.38 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.08 % 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: 0.23 (0.25), residues: 1238 helix: 1.36 (0.20), residues: 740 sheet: -0.69 (0.68), residues: 67 loop : -1.91 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 92 TYR 0.010 0.001 TYR L 191 PHE 0.012 0.001 PHE E 67 TRP 0.005 0.001 TRP L 600 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (16995) covalent geometry : angle 0.64605 / 0.37 (24218) hydrogen bonds : bond 0.04906 / 3.12 ( 809) hydrogen bonds : angle 3.15150 / 2.19 ( 2080) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: L 277 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7974 (mp10) REVERT: L 433 MET cc_start: 0.8113 (ttm) cc_final: 0.7659 (ttt) REVERT: L 437 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7845 (pt0) REVERT: L 470 MET cc_start: 0.9153 (tpt) cc_final: 0.8772 (tpp) REVERT: L 570 LYS cc_start: 0.8934 (mttt) cc_final: 0.8575 (tptt) REVERT: A 120 MET cc_start: 0.8588 (mmm) cc_final: 0.8102 (mtp) REVERT: B 63 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8515 (mt-10) REVERT: C 95 LYS cc_start: 0.9438 (tptm) cc_final: 0.9185 (tppt) REVERT: D 96 ARG cc_start: 0.8897 (ttp80) cc_final: 0.8637 (ttp80) REVERT: D 99 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9184 (pp) REVERT: E 51 ILE cc_start: 0.8880 (mt) cc_final: 0.8594 (mt) REVERT: E 97 GLU cc_start: 0.8750 (tt0) cc_final: 0.8496 (mt-10) REVERT: F 80 THR cc_start: 0.9423 (m) cc_final: 0.9115 (p) REVERT: H 32 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8078 (mm-30) REVERT: H 44 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8752 (tm-30) REVERT: H 68 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8495 (tp30) REVERT: H 98 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8773 (tp) outliers start: 25 outliers final: 15 residues processed: 146 average time/residue: 0.1216 time to fit residues: 27.0080 Evaluate side-chains 140 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 221 ASP Chi-restraints excluded: chain L residue 277 GLN Chi-restraints excluded: chain L residue 437 GLN Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 99 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 132 optimal weight: 20.0000 chunk 148 optimal weight: 40.0000 chunk 69 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 144 optimal weight: 30.0000 chunk 57 optimal weight: 0.9980 chunk 145 optimal weight: 20.0000 chunk 114 optimal weight: 4.9990 chunk 4 optimal weight: 0.0970 chunk 88 optimal weight: 3.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 620 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.087805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.059519 restraints weight = 58471.780| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.66 r_work: 0.2869 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16995 Z= 0.158 Angle : 0.668 9.440 24218 Z= 0.378 Chirality : 0.047 0.423 2754 Planarity : 0.004 0.048 2054 Dihedral : 30.293 177.996 4590 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.04 % Allowed : 13.85 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.08 % 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 (0.25), residues: 1238 helix: 1.36 (0.20), residues: 742 sheet: -0.97 (0.61), residues: 78 loop : -1.82 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 30 TYR 0.014 0.001 TYR F 98 PHE 0.012 0.001 PHE E 67 TRP 0.006 0.001 TRP L 600 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.16 (16995) covalent geometry : angle 0.66796 / 0.38 (24218) hydrogen bonds : bond 0.05103 / 3.25 ( 809) hydrogen bonds : angle 3.18373 / 2.21 ( 2080) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: L 277 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8127 (mt0) REVERT: L 433 MET cc_start: 0.8131 (ttm) cc_final: 0.7682 (ttt) REVERT: L 437 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7866 (pt0) REVERT: L 470 MET cc_start: 0.9138 (tpt) cc_final: 0.8771 (tpp) REVERT: L 570 LYS cc_start: 0.8946 (mttt) cc_final: 0.8579 (tptt) REVERT: A 120 MET cc_start: 0.8631 (mmm) cc_final: 0.8192 (mtp) REVERT: B 63 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8613 (mt-10) REVERT: C 95 LYS cc_start: 0.9490 (tptm) cc_final: 0.9236 (tppt) REVERT: D 99 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9225 (pp) REVERT: E 51 ILE cc_start: 0.8891 (mt) cc_final: 0.8610 (mt) REVERT: E 97 GLU cc_start: 0.8775 (tt0) cc_final: 0.8510 (mt-10) REVERT: F 80 THR cc_start: 0.9406 (m) cc_final: 0.9087 (p) REVERT: G 36 LYS cc_start: 0.9113 (tppp) cc_final: 0.8911 (ttmm) REVERT: H 32 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8095 (mm-30) REVERT: H 44 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8744 (tm-30) REVERT: H 68 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8444 (tp30) REVERT: H 98 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8788 (tp) outliers start: 22 outliers final: 16 residues processed: 140 average time/residue: 0.1166 time to fit residues: 24.9201 Evaluate side-chains 140 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 221 ASP Chi-restraints excluded: chain L residue 277 GLN Chi-restraints excluded: chain L residue 437 GLN Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 99 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 8 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 123 optimal weight: 30.0000 chunk 78 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 141 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 620 GLN A 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.087212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.058134 restraints weight = 58326.326| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.41 r_work: 0.2852 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16995 Z= 0.183 Angle : 0.676 9.996 24218 Z= 0.380 Chirality : 0.048 0.433 2754 Planarity : 0.004 0.049 2054 Dihedral : 30.339 177.694 4590 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.14 % Allowed : 13.85 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.08 % 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: 0.24 (0.25), residues: 1238 helix: 1.27 (0.20), residues: 748 sheet: -0.89 (0.62), residues: 78 loop : -1.71 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 30 TYR 0.014 0.001 TYR C 50 PHE 0.014 0.001 PHE E 67 TRP 0.008 0.001 TRP L 600 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.18 (16995) covalent geometry : angle 0.67577 / 0.38 (24218) hydrogen bonds : bond 0.05450 / 3.46 ( 809) hydrogen bonds : angle 3.26114 / 2.26 ( 2080) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: L 306 ILE cc_start: 0.9427 (tp) cc_final: 0.9123 (tp) REVERT: L 433 MET cc_start: 0.8200 (ttm) cc_final: 0.7741 (ttt) REVERT: L 437 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7845 (pt0) REVERT: L 470 MET cc_start: 0.9132 (tpt) cc_final: 0.8800 (tpp) REVERT: L 570 LYS cc_start: 0.8909 (mttt) cc_final: 0.8565 (tptt) REVERT: A 120 MET cc_start: 0.8677 (mmm) cc_final: 0.8300 (mtp) REVERT: B 63 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8682 (mt-10) REVERT: B 79 LYS cc_start: 0.9378 (OUTLIER) cc_final: 0.9024 (mtpt) REVERT: B 88 TYR cc_start: 0.8878 (m-10) cc_final: 0.8436 (m-80) REVERT: C 95 LYS cc_start: 0.9472 (tptm) cc_final: 0.9206 (tppt) REVERT: D 99 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9272 (pp) REVERT: E 51 ILE cc_start: 0.8888 (mt) cc_final: 0.8615 (mt) REVERT: E 97 GLU cc_start: 0.8752 (tt0) cc_final: 0.8503 (mt-10) REVERT: F 80 THR cc_start: 0.9374 (m) cc_final: 0.9029 (p) REVERT: G 36 LYS cc_start: 0.9101 (tppp) cc_final: 0.8898 (ttmm) REVERT: H 32 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8064 (mm-30) REVERT: H 44 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8696 (tm-30) REVERT: H 68 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8339 (tp30) outliers start: 23 outliers final: 16 residues processed: 140 average time/residue: 0.1321 time to fit residues: 27.7310 Evaluate side-chains 135 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 221 ASP Chi-restraints excluded: chain L residue 437 GLN Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 99 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 20 optimal weight: 20.0000 chunk 28 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 133 optimal weight: 30.0000 chunk 45 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 277 GLN L 620 GLN H 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.087360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.058383 restraints weight = 58197.965| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.48 r_work: 0.2858 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16995 Z= 0.167 Angle : 0.669 10.313 24218 Z= 0.377 Chirality : 0.047 0.430 2754 Planarity : 0.004 0.048 2054 Dihedral : 30.302 177.601 4590 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.67 % Allowed : 14.50 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.08 % 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 (0.25), residues: 1238 helix: 1.33 (0.20), residues: 748 sheet: -0.84 (0.62), residues: 78 loop : -1.71 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 30 TYR 0.012 0.001 TYR C 50 PHE 0.014 0.001 PHE E 67 TRP 0.007 0.001 TRP L 600 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.17 (16995) covalent geometry : angle 0.66905 / 0.38 (24218) hydrogen bonds : bond 0.05257 / 3.33 ( 809) hydrogen bonds : angle 3.21337 / 2.22 ( 2080) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: L 433 MET cc_start: 0.8181 (ttm) cc_final: 0.7717 (ttt) REVERT: L 437 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7835 (pt0) REVERT: L 470 MET cc_start: 0.9137 (tpt) cc_final: 0.8793 (tpp) REVERT: L 570 LYS cc_start: 0.8942 (mttt) cc_final: 0.8581 (tptt) REVERT: A 120 MET cc_start: 0.8673 (mmm) cc_final: 0.8287 (mtp) REVERT: B 63 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8666 (mt-10) REVERT: B 88 TYR cc_start: 0.8867 (m-10) cc_final: 0.8433 (m-80) REVERT: C 95 LYS cc_start: 0.9483 (tptm) cc_final: 0.9217 (tppt) REVERT: D 99 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9279 (pp) REVERT: E 51 ILE cc_start: 0.8889 (mt) cc_final: 0.8607 (mt) REVERT: E 97 GLU cc_start: 0.8733 (tt0) cc_final: 0.8486 (mt-10) REVERT: F 80 THR cc_start: 0.9373 (m) cc_final: 0.9061 (p) REVERT: H 32 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8095 (mm-30) REVERT: H 44 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8697 (tm-30) REVERT: H 68 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8331 (tp30) outliers start: 18 outliers final: 14 residues processed: 132 average time/residue: 0.1225 time to fit residues: 24.3310 Evaluate side-chains 129 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 221 ASP Chi-restraints excluded: chain L residue 437 GLN Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 99 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 41 optimal weight: 20.0000 chunk 119 optimal weight: 0.8980 chunk 100 optimal weight: 0.0970 chunk 51 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 20.0000 chunk 69 optimal weight: 0.9980 chunk 30 optimal weight: 0.0670 chunk 2 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 overall best weight: 0.8118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.088080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.058738 restraints weight = 57691.210| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.32 r_work: 0.2900 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16995 Z= 0.135 Angle : 0.633 10.057 24218 Z= 0.361 Chirality : 0.045 0.416 2754 Planarity : 0.004 0.050 2054 Dihedral : 30.143 177.799 4590 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.58 % Allowed : 14.78 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.08 % 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: 0.56 (0.25), residues: 1238 helix: 1.57 (0.20), residues: 740 sheet: -0.82 (0.62), residues: 79 loop : -1.60 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 30 TYR 0.010 0.001 TYR L 191 PHE 0.010 0.001 PHE E 67 TRP 0.005 0.001 TRP L 364 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.13 (16995) covalent geometry : angle 0.63346 / 0.36 (24218) hydrogen bonds : bond 0.04679 / 2.95 ( 809) hydrogen bonds : angle 3.06844 / 2.12 ( 2080) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3583.02 seconds wall clock time: 62 minutes 12.71 seconds (3732.71 seconds total)