Starting phenix.real_space_refine on Wed Mar 4 19:26:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6iro_9720/03_2026/6iro_9720_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6iro_9720/03_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_9720/03_2026/6iro_9720_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6iro_9720/03_2026/6iro_9720_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6iro_9720/03_2026/6iro_9720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6iro_9720/03_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-dev-5986/lib/python3.9/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: 3.08, per 1000 atoms: 0.19 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: 1.37 Conformation dependent library (CDL) restraints added in 359.7 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: 2.27 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: 3.52 Time building geometry restraints manager: 1.78 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=" C PHE G 25 " pdb=" N PRO G 26 " ideal model delta sigma weight residual 1.335 1.312 0.023 8.70e-03 1.32e+04 7.00e+00 bond pdb=" C3' DG J 66 " pdb=" O3' DG J 66 " ideal model delta sigma weight residual 1.422 1.489 -0.067 3.00e-02 1.11e+03 4.94e+00 bond pdb=" C3' DG I 99 " pdb=" O3' DG I 99 " ideal model delta sigma weight residual 1.422 1.488 -0.066 3.00e-02 1.11e+03 4.82e+00 bond pdb=" CB GLU C 56 " pdb=" CG GLU C 56 " ideal model delta sigma weight residual 1.520 1.457 0.063 3.00e-02 1.11e+03 4.46e+00 bond pdb=" C3' DA I 113 " pdb=" O3' DA I 113 " ideal model delta sigma weight residual 1.422 1.485 -0.063 3.00e-02 1.11e+03 4.42e+00 ... (remaining 16990 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 23231 2.45 - 4.90: 870 4.90 - 7.34: 94 7.34 - 9.79: 18 9.79 - 12.24: 5 Bond angle restraints: 24218 Sorted by residual: 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=" C THR E 80 " pdb=" N ASP E 81 " pdb=" CA ASP E 81 " ideal model delta sigma weight residual 122.82 129.80 -6.98 1.42e+00 4.96e-01 2.42e+01 angle pdb=" C GLY C 37 " pdb=" N ASN C 38 " pdb=" CA ASN C 38 " ideal model delta sigma weight residual 121.54 130.68 -9.14 1.91e+00 2.74e-01 2.29e+01 angle pdb=" C THR A 80 " pdb=" N ASP A 81 " pdb=" CA ASP A 81 " ideal model delta sigma weight residual 122.82 129.55 -6.73 1.42e+00 4.96e-01 2.25e+01 angle pdb=" C GLY G 37 " pdb=" N ASN G 38 " pdb=" CA ASN G 38 " ideal model delta sigma weight residual 122.82 129.09 -6.27 1.42e+00 4.96e-01 1.95e+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 - 0.059: 2024 0.059 - 0.118: 572 0.118 - 0.177: 125 0.177 - 0.237: 21 0.237 - 0.296: 12 Chirality restraints: 2754 Sorted by residual: 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=" CB ILE B 34 " pdb=" CA ILE B 34 " pdb=" CG1 ILE B 34 " pdb=" CG2 ILE B 34 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA LYS F 31 " pdb=" N LYS F 31 " pdb=" C LYS F 31 " pdb=" CB LYS F 31 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.420 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 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= 0.420 Angle : 1.075 12.238 24218 Z= 0.603 Chirality : 0.060 0.296 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 covalent geometry : bond 0.00967 (16995) covalent geometry : angle 1.07529 (24218) hydrogen bonds : bond 0.17075 ( 809) hydrogen bonds : angle 5.45760 ( 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 : 0.438 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: 0.7906 (tt) REVERT: L 470 MET cc_start: 0.8833 (tpt) cc_final: 0.8295 (tpp) REVERT: L 570 LYS cc_start: 0.8752 (mttt) cc_final: 0.8535 (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: 0.8831 (tt) REVERT: E 42 ARG cc_start: 0.7620 (mmm160) cc_final: 0.7272 (mmm-85) REVERT: E 50 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7350 (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: 0.8033 (tm-30) outliers start: 8 outliers final: 0 residues processed: 235 average time/residue: 0.1630 time to fit residues: 52.6695 Evaluate side-chains 138 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 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... Flipped N/Q/H residues before XYZ refinement: L 111 HIS L 437 GLN L 526 GLN L 542 ASN L 613 HIS ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 68 GLN H 81 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.088665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.061054 restraints weight = 58932.908| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.54 r_work: 0.2924 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16995 Z= 0.162 Angle : 0.664 10.983 24218 Z= 0.385 Chirality : 0.040 0.177 2754 Planarity : 0.005 0.051 2054 Dihedral : 30.380 176.438 4592 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.21 % Allowed : 8.64 % Favored : 90.15 % 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: -1.93 (0.22), residues: 1238 helix: -0.42 (0.18), residues: 732 sheet: -1.82 (0.66), residues: 66 loop : -2.59 (0.25), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 92 TYR 0.018 0.001 TYR F 98 PHE 0.013 0.001 PHE L 274 TRP 0.006 0.001 TRP L 364 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00349 (16995) covalent geometry : angle 0.66449 (24218) hydrogen bonds : bond 0.04838 ( 809) hydrogen bonds : angle 3.50190 ( 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 193 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 267 TRP cc_start: 0.7554 (m100) cc_final: 0.6967 (m100) REVERT: L 277 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.8092 (mp10) REVERT: L 323 ILE cc_start: 0.8603 (mt) cc_final: 0.8372 (mp) REVERT: L 325 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8255 (mp0) REVERT: L 351 ILE cc_start: 0.7831 (mt) cc_final: 0.7447 (tt) REVERT: L 433 MET cc_start: 0.8251 (ttm) cc_final: 0.7842 (ttt) REVERT: L 470 MET cc_start: 0.9117 (tpt) cc_final: 0.8662 (tpp) REVERT: L 570 LYS cc_start: 0.8822 (mttt) cc_final: 0.8481 (tptt) REVERT: B 63 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8546 (mt-10) REVERT: C 95 LYS cc_start: 0.9417 (tptm) cc_final: 0.9092 (tppt) REVERT: D 58 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9017 (mt) REVERT: D 65 ASP cc_start: 0.9085 (t0) cc_final: 0.8847 (t0) REVERT: E 42 ARG cc_start: 0.7639 (mmm160) cc_final: 0.7380 (mmm-85) REVERT: E 51 ILE cc_start: 0.8817 (mt) cc_final: 0.8565 (mt) REVERT: F 80 THR cc_start: 0.9419 (m) cc_final: 0.9182 (p) REVERT: F 91 LYS cc_start: 0.9235 (tppt) cc_final: 0.8905 (tttp) REVERT: H 32 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8174 (mm-30) REVERT: H 44 GLN cc_start: 0.9127 (tm-30) cc_final: 0.8834 (tm-30) REVERT: H 102 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7976 (tm-30) outliers start: 13 outliers final: 3 residues processed: 191 average time/residue: 0.1373 time to fit residues: 37.8709 Evaluate side-chains 143 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 138 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 277 GLN Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 66 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 63 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 116 optimal weight: 0.5980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 542 ASN L 620 GLN A 93 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN D 46 HIS E 68 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.088399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.060625 restraints weight = 59206.769| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.64 r_work: 0.2900 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16995 Z= 0.160 Angle : 0.619 7.387 24218 Z= 0.360 Chirality : 0.039 0.172 2754 Planarity : 0.004 0.049 2054 Dihedral : 30.052 176.102 4590 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.14 % Allowed : 10.59 % Favored : 87.27 % 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: -0.88 (0.24), residues: 1238 helix: 0.48 (0.19), residues: 740 sheet: -1.42 (0.65), residues: 67 loop : -2.34 (0.26), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 92 TYR 0.013 0.001 TYR F 98 PHE 0.012 0.001 PHE E 67 TRP 0.007 0.001 TRP L 600 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00349 (16995) covalent geometry : angle 0.61887 (24218) hydrogen bonds : bond 0.04585 ( 809) hydrogen bonds : angle 3.29021 ( 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 174 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: L 323 ILE cc_start: 0.8490 (mt) cc_final: 0.8236 (mp) REVERT: L 325 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8262 (mp0) REVERT: L 351 ILE cc_start: 0.7878 (mt) cc_final: 0.7453 (tt) REVERT: L 433 MET cc_start: 0.8238 (ttm) cc_final: 0.7872 (ttt) REVERT: L 469 MET cc_start: 0.8676 (mmt) cc_final: 0.8460 (mmp) REVERT: L 470 MET cc_start: 0.9147 (tpt) cc_final: 0.8688 (tpp) REVERT: L 570 LYS cc_start: 0.8878 (mttt) cc_final: 0.8553 (tptt) REVERT: B 63 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8582 (mt-10) REVERT: C 84 GLN cc_start: 0.9461 (tp40) cc_final: 0.9193 (tp40) REVERT: C 95 LYS cc_start: 0.9447 (tptm) cc_final: 0.9158 (tppt) REVERT: D 65 ASP cc_start: 0.9106 (t0) cc_final: 0.8842 (t0) REVERT: E 42 ARG cc_start: 0.7646 (mmm160) cc_final: 0.7430 (mmm-85) REVERT: E 51 ILE cc_start: 0.8811 (mt) cc_final: 0.8515 (mt) REVERT: F 80 THR cc_start: 0.9430 (m) cc_final: 0.9161 (p) REVERT: H 32 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8180 (mm-30) REVERT: H 44 GLN cc_start: 0.9100 (tm-30) cc_final: 0.8858 (tm-30) REVERT: H 102 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8143 (tm-30) outliers start: 23 outliers final: 9 residues processed: 166 average time/residue: 0.1365 time to fit residues: 33.0902 Evaluate side-chains 142 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 476 CYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain H residue 86 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 103 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 100 optimal weight: 0.0370 chunk 43 optimal weight: 10.0000 chunk 28 optimal weight: 30.0000 chunk 23 optimal weight: 20.0000 chunk 58 optimal weight: 0.0040 chunk 25 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 overall best weight: 0.9674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN 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 = 0.3822 r_free = 0.3822 target = 0.088962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.061154 restraints weight = 59002.725| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.58 r_work: 0.2913 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16995 Z= 0.150 Angle : 0.602 7.751 24218 Z= 0.350 Chirality : 0.038 0.166 2754 Planarity : 0.004 0.050 2054 Dihedral : 29.867 176.174 4590 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.86 % Allowed : 12.08 % Favored : 86.06 % 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: -0.30 (0.24), residues: 1238 helix: 0.99 (0.20), residues: 741 sheet: -1.07 (0.66), residues: 67 loop : -2.19 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 63 TYR 0.010 0.001 TYR L 191 PHE 0.012 0.001 PHE E 67 TRP 0.007 0.001 TRP L 267 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00325 (16995) covalent geometry : angle 0.60168 (24218) hydrogen bonds : bond 0.04260 ( 809) hydrogen bonds : angle 3.14674 ( 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 172 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: L 323 ILE cc_start: 0.8439 (mt) cc_final: 0.8103 (mp) REVERT: L 325 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8280 (mp0) REVERT: L 351 ILE cc_start: 0.7902 (mt) cc_final: 0.7500 (tt) REVERT: L 433 MET cc_start: 0.8269 (ttm) cc_final: 0.7938 (ttt) REVERT: L 470 MET cc_start: 0.9125 (tpt) cc_final: 0.8698 (tpp) REVERT: L 570 LYS cc_start: 0.8855 (mttt) cc_final: 0.8550 (tptt) REVERT: B 63 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8431 (mt-10) REVERT: C 84 GLN cc_start: 0.9459 (tp40) cc_final: 0.9068 (tp-100) REVERT: C 95 LYS cc_start: 0.9428 (tptm) cc_final: 0.9186 (tppt) REVERT: E 42 ARG cc_start: 0.7680 (mmm160) cc_final: 0.7407 (mmm-85) REVERT: E 51 ILE cc_start: 0.8873 (mt) cc_final: 0.8557 (mt) REVERT: E 97 GLU cc_start: 0.8735 (tt0) cc_final: 0.8467 (mt-10) REVERT: F 80 THR cc_start: 0.9433 (m) cc_final: 0.9168 (p) REVERT: G 89 ASN cc_start: 0.9053 (m-40) cc_final: 0.8842 (m-40) REVERT: G 92 GLU cc_start: 0.8500 (pm20) cc_final: 0.7998 (pm20) REVERT: H 32 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8132 (mm-30) REVERT: H 44 GLN cc_start: 0.9005 (tm-30) cc_final: 0.8761 (tm-30) REVERT: H 102 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7996 (tm-30) outliers start: 20 outliers final: 10 residues processed: 165 average time/residue: 0.1340 time to fit residues: 32.4685 Evaluate side-chains 148 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 18 SER Chi-restraints excluded: chain D residue 29 THR 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 99 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 55 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.088508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.060495 restraints weight = 58707.146| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.60 r_work: 0.2889 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16995 Z= 0.164 Angle : 0.611 7.381 24218 Z= 0.352 Chirality : 0.038 0.167 2754 Planarity : 0.004 0.048 2054 Dihedral : 29.823 176.022 4590 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.04 % Allowed : 13.57 % Favored : 84.39 % 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: 0.02 (0.24), residues: 1238 helix: 1.20 (0.20), residues: 741 sheet: -0.91 (0.66), residues: 67 loop : -1.99 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 30 TYR 0.013 0.001 TYR F 98 PHE 0.011 0.001 PHE E 67 TRP 0.006 0.001 TRP L 600 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00362 (16995) covalent geometry : angle 0.61140 (24218) hydrogen bonds : bond 0.04418 ( 809) hydrogen bonds : angle 3.12616 ( 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 162 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: L 323 ILE cc_start: 0.8373 (mt) cc_final: 0.8017 (mp) REVERT: L 325 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8131 (mp0) REVERT: L 351 ILE cc_start: 0.7902 (mt) cc_final: 0.7504 (tt) REVERT: L 433 MET cc_start: 0.8280 (ttm) cc_final: 0.7802 (ttt) REVERT: L 470 MET cc_start: 0.9150 (tpt) cc_final: 0.8683 (tpp) REVERT: L 570 LYS cc_start: 0.8883 (mttt) cc_final: 0.8569 (tptt) REVERT: A 120 MET cc_start: 0.8596 (mmm) cc_final: 0.8144 (mtp) REVERT: B 63 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8527 (mt-10) REVERT: B 93 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.7514 (mp-120) REVERT: C 84 GLN cc_start: 0.9474 (tp40) cc_final: 0.9052 (tp-100) REVERT: C 95 LYS cc_start: 0.9450 (tptm) cc_final: 0.9209 (tppt) REVERT: E 42 ARG cc_start: 0.7679 (mmm160) cc_final: 0.7398 (mmm-85) REVERT: E 51 ILE cc_start: 0.8867 (mt) cc_final: 0.8568 (mt) REVERT: E 97 GLU cc_start: 0.8730 (tt0) cc_final: 0.8472 (mt-10) REVERT: F 80 THR cc_start: 0.9460 (m) cc_final: 0.9172 (p) REVERT: G 92 GLU cc_start: 0.8540 (pm20) cc_final: 0.8078 (pm20) REVERT: H 32 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8132 (mm-30) REVERT: H 44 GLN cc_start: 0.9034 (tm-30) cc_final: 0.8782 (tm-30) REVERT: H 68 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8510 (tp30) REVERT: H 102 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7812 (tm-30) outliers start: 22 outliers final: 13 residues processed: 156 average time/residue: 0.1335 time to fit residues: 31.0635 Evaluate side-chains 147 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain H residue 86 ILE 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: 0.9980 chunk 142 optimal weight: 7.9990 chunk 79 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 110 optimal weight: 0.0770 chunk 52 optimal weight: 0.7980 chunk 6 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.089350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.061813 restraints weight = 59096.172| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.77 r_work: 0.2903 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16995 Z= 0.144 Angle : 0.594 8.021 24218 Z= 0.343 Chirality : 0.037 0.163 2754 Planarity : 0.004 0.057 2054 Dihedral : 29.713 176.159 4590 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.67 % Allowed : 14.68 % 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: 0.25 (0.25), residues: 1238 helix: 1.36 (0.20), residues: 743 sheet: -0.66 (0.66), residues: 67 loop : -1.87 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 42 TYR 0.010 0.001 TYR L 191 PHE 0.011 0.001 PHE E 67 TRP 0.004 0.001 TRP L 364 HIS 0.006 0.001 HIS L 111 Details of bonding type rmsd covalent geometry : bond 0.00311 (16995) covalent geometry : angle 0.59449 (24218) hydrogen bonds : bond 0.04073 ( 809) hydrogen bonds : angle 3.04443 ( 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 159 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: L 277 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7907 (mp10) REVERT: L 323 ILE cc_start: 0.8324 (mt) cc_final: 0.7967 (mp) REVERT: L 325 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8142 (mp0) REVERT: L 351 ILE cc_start: 0.7831 (mt) cc_final: 0.7435 (tt) REVERT: L 433 MET cc_start: 0.8266 (ttm) cc_final: 0.7766 (ttt) REVERT: L 437 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7665 (pt0) REVERT: L 470 MET cc_start: 0.9149 (tpt) cc_final: 0.8689 (tpp) REVERT: L 570 LYS cc_start: 0.8885 (mttt) cc_final: 0.8541 (tptt) REVERT: L 609 MET cc_start: 0.8774 (tpt) cc_final: 0.8500 (tpt) REVERT: A 59 GLU cc_start: 0.8643 (pm20) cc_final: 0.8341 (pm20) REVERT: A 120 MET cc_start: 0.8557 (mmm) cc_final: 0.8113 (mtp) REVERT: B 63 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8503 (mt-10) REVERT: B 93 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8420 (mm110) REVERT: C 84 GLN cc_start: 0.9457 (tp40) cc_final: 0.9048 (tp-100) REVERT: C 95 LYS cc_start: 0.9456 (tptm) cc_final: 0.9213 (tppt) REVERT: E 42 ARG cc_start: 0.7629 (mmm160) cc_final: 0.7348 (mmm-85) REVERT: E 51 ILE cc_start: 0.8863 (mt) cc_final: 0.8522 (mt) REVERT: E 97 GLU cc_start: 0.8761 (tt0) cc_final: 0.8517 (mt-10) REVERT: F 80 THR cc_start: 0.9465 (m) cc_final: 0.9187 (p) REVERT: G 92 GLU cc_start: 0.8592 (pm20) cc_final: 0.8165 (pm20) REVERT: H 32 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8133 (mm-30) REVERT: H 44 GLN cc_start: 0.9084 (tm-30) cc_final: 0.8839 (tm-30) REVERT: H 68 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8553 (tp30) outliers start: 18 outliers final: 11 residues processed: 154 average time/residue: 0.1276 time to fit residues: 29.3828 Evaluate side-chains 148 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 82 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain H residue 86 ILE 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: 6.9990 chunk 26 optimal weight: 0.0870 chunk 109 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 83 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 117 optimal weight: 0.5980 overall best weight: 1.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.088723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.060876 restraints weight = 58625.682| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.70 r_work: 0.2882 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16995 Z= 0.165 Angle : 0.607 8.773 24218 Z= 0.347 Chirality : 0.037 0.169 2754 Planarity : 0.004 0.047 2054 Dihedral : 29.681 176.113 4590 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.77 % Allowed : 14.96 % Favored : 83.27 % 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: 0.37 (0.25), residues: 1238 helix: 1.42 (0.20), residues: 743 sheet: -0.49 (0.66), residues: 67 loop : -1.78 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 92 TYR 0.010 0.001 TYR G 39 PHE 0.012 0.001 PHE E 67 TRP 0.006 0.001 TRP L 364 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00366 (16995) covalent geometry : angle 0.60677 (24218) hydrogen bonds : bond 0.04293 ( 809) hydrogen bonds : angle 3.05680 ( 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 160 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: L 277 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7778 (mp10) REVERT: L 323 ILE cc_start: 0.8310 (mt) cc_final: 0.7971 (mt) REVERT: L 325 GLU cc_start: 0.8481 (mm-30) cc_final: 0.7659 (tm-30) REVERT: L 351 ILE cc_start: 0.7824 (mt) cc_final: 0.7528 (tt) REVERT: L 433 MET cc_start: 0.8300 (ttm) cc_final: 0.7806 (ttt) REVERT: L 437 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7747 (pt0) REVERT: L 465 LEU cc_start: 0.5778 (mt) cc_final: 0.5495 (pt) REVERT: L 470 MET cc_start: 0.9081 (tpt) cc_final: 0.8550 (tpp) REVERT: L 570 LYS cc_start: 0.8908 (mttt) cc_final: 0.8558 (tptt) REVERT: L 609 MET cc_start: 0.8782 (tpt) cc_final: 0.8491 (tpp) REVERT: A 59 GLU cc_start: 0.8811 (pm20) cc_final: 0.8369 (pm20) REVERT: A 120 MET cc_start: 0.8636 (mmm) cc_final: 0.8206 (mtp) REVERT: B 63 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8578 (mt-10) REVERT: B 93 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7327 (mp-120) REVERT: C 84 GLN cc_start: 0.9454 (tp40) cc_final: 0.9021 (tp-100) REVERT: C 95 LYS cc_start: 0.9489 (tptm) cc_final: 0.9247 (tppt) REVERT: E 41 TYR cc_start: 0.8030 (m-80) cc_final: 0.7782 (m-80) REVERT: E 42 ARG cc_start: 0.7626 (mmm160) cc_final: 0.7400 (mmm-85) REVERT: E 51 ILE cc_start: 0.8868 (mt) cc_final: 0.8557 (mt) REVERT: E 97 GLU cc_start: 0.8760 (tt0) cc_final: 0.8509 (mt-10) REVERT: F 80 THR cc_start: 0.9411 (m) cc_final: 0.9092 (p) REVERT: G 92 GLU cc_start: 0.8587 (pm20) cc_final: 0.8193 (pm20) REVERT: H 44 GLN cc_start: 0.9051 (tm-30) cc_final: 0.8803 (tm-30) REVERT: H 68 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8448 (tp30) outliers start: 19 outliers final: 13 residues processed: 156 average time/residue: 0.1285 time to fit residues: 30.3063 Evaluate side-chains 152 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 82 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 18 SER 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 E residue 112 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain H residue 86 ILE 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: 8.9990 chunk 148 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 145 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.087414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.057604 restraints weight = 58595.354| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.30 r_work: 0.2874 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16995 Z= 0.203 Angle : 0.648 9.640 24218 Z= 0.365 Chirality : 0.038 0.167 2754 Planarity : 0.004 0.046 2054 Dihedral : 29.809 175.693 4590 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.04 % Allowed : 15.33 % Favored : 82.62 % 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: 0.37 (0.25), residues: 1238 helix: 1.37 (0.20), residues: 742 sheet: -0.41 (0.65), residues: 67 loop : -1.69 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 39 TYR 0.014 0.001 TYR F 98 PHE 0.012 0.001 PHE E 67 TRP 0.009 0.001 TRP L 600 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00459 (16995) covalent geometry : angle 0.64823 (24218) hydrogen bonds : bond 0.04972 ( 809) hydrogen bonds : angle 3.17806 ( 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 154 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 277 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7899 (mp10) REVERT: L 323 ILE cc_start: 0.8328 (mt) cc_final: 0.8005 (mp) REVERT: L 351 ILE cc_start: 0.7932 (mt) cc_final: 0.7637 (tt) REVERT: L 433 MET cc_start: 0.8399 (ttm) cc_final: 0.7895 (ttt) REVERT: L 437 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7611 (pt0) REVERT: L 470 MET cc_start: 0.9116 (tpt) cc_final: 0.8563 (tpp) REVERT: L 570 LYS cc_start: 0.8871 (mttt) cc_final: 0.8543 (tptt) REVERT: L 609 MET cc_start: 0.8778 (tpt) cc_final: 0.8439 (tpp) REVERT: A 59 GLU cc_start: 0.8880 (pm20) cc_final: 0.8496 (pm20) REVERT: A 120 MET cc_start: 0.8682 (mmm) cc_final: 0.8325 (mtp) REVERT: B 88 TYR cc_start: 0.8925 (m-10) cc_final: 0.8450 (m-80) REVERT: B 93 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8588 (mm110) REVERT: C 18 SER cc_start: 0.9110 (OUTLIER) cc_final: 0.8704 (t) REVERT: C 95 LYS cc_start: 0.9496 (tptm) cc_final: 0.9227 (tppt) REVERT: D 32 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8262 (mm-30) REVERT: E 41 TYR cc_start: 0.8067 (m-80) cc_final: 0.7814 (m-80) REVERT: E 51 ILE cc_start: 0.8938 (mt) cc_final: 0.8666 (mt) REVERT: E 97 GLU cc_start: 0.8767 (tt0) cc_final: 0.8487 (mt-10) REVERT: F 80 THR cc_start: 0.9379 (m) cc_final: 0.9018 (p) REVERT: H 44 GLN cc_start: 0.9037 (tm-30) cc_final: 0.8715 (tm-30) REVERT: H 68 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8357 (tp30) outliers start: 22 outliers final: 12 residues processed: 149 average time/residue: 0.1315 time to fit residues: 29.2816 Evaluate side-chains 136 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain H residue 86 ILE 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: 0.6980 chunk 72 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 78 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 76 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 358 ASN C 24 GLN D 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.088129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.058510 restraints weight = 58225.565| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.39 r_work: 0.2870 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16995 Z= 0.163 Angle : 0.610 9.933 24218 Z= 0.346 Chirality : 0.037 0.161 2754 Planarity : 0.004 0.049 2054 Dihedral : 29.645 175.885 4590 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.30 % Allowed : 16.54 % Favored : 82.16 % 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: 0.54 (0.25), residues: 1238 helix: 1.52 (0.20), residues: 742 sheet: -0.28 (0.66), residues: 67 loop : -1.64 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 30 TYR 0.010 0.001 TYR L 191 PHE 0.012 0.001 PHE E 67 TRP 0.006 0.001 TRP L 364 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00363 (16995) covalent geometry : angle 0.61022 (24218) hydrogen bonds : bond 0.04307 ( 809) hydrogen bonds : angle 3.03082 ( 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: 14 poor density : 129 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 219 LEU cc_start: 0.8726 (tp) cc_final: 0.8404 (tp) REVERT: L 277 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7812 (mp10) REVERT: L 323 ILE cc_start: 0.8208 (mt) cc_final: 0.7883 (mp) REVERT: L 351 ILE cc_start: 0.7776 (mt) cc_final: 0.7541 (tt) REVERT: L 433 MET cc_start: 0.8366 (ttm) cc_final: 0.7852 (ttt) REVERT: L 437 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7804 (pt0) REVERT: L 470 MET cc_start: 0.9115 (tpt) cc_final: 0.8551 (tpp) REVERT: L 570 LYS cc_start: 0.8915 (mttt) cc_final: 0.8556 (tptt) REVERT: L 609 MET cc_start: 0.8829 (tpt) cc_final: 0.8583 (tpt) REVERT: A 59 GLU cc_start: 0.8949 (pm20) cc_final: 0.8501 (pm20) REVERT: A 120 MET cc_start: 0.8650 (mmm) cc_final: 0.8217 (mtp) REVERT: B 88 TYR cc_start: 0.8916 (m-10) cc_final: 0.8427 (m-80) REVERT: C 18 SER cc_start: 0.9151 (m) cc_final: 0.8746 (t) REVERT: C 95 LYS cc_start: 0.9462 (tptm) cc_final: 0.9189 (tppt) REVERT: E 51 ILE cc_start: 0.8794 (mt) cc_final: 0.8492 (mt) REVERT: E 97 GLU cc_start: 0.8849 (tt0) cc_final: 0.8555 (mt-10) REVERT: F 80 THR cc_start: 0.9389 (m) cc_final: 0.9068 (p) REVERT: H 44 GLN cc_start: 0.9027 (tm-30) cc_final: 0.8679 (tm-30) REVERT: H 68 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8449 (tp30) outliers start: 14 outliers final: 9 residues processed: 141 average time/residue: 0.1262 time to fit residues: 26.7850 Evaluate side-chains 136 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 277 GLN Chi-restraints excluded: chain L residue 437 GLN 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 101 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain H residue 86 ILE 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: 0.8980 chunk 28 optimal weight: 30.0000 chunk 111 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 133 optimal weight: 8.9990 chunk 45 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN G 73 ASN H 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.087796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.058543 restraints weight = 58195.024| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.46 r_work: 0.2838 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16995 Z= 0.184 Angle : 0.631 10.331 24218 Z= 0.355 Chirality : 0.037 0.165 2754 Planarity : 0.004 0.048 2054 Dihedral : 29.694 176.076 4590 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.49 % Allowed : 16.17 % Favored : 82.34 % 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: 0.60 (0.25), residues: 1238 helix: 1.54 (0.20), residues: 741 sheet: -0.17 (0.66), residues: 67 loop : -1.58 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 30 TYR 0.012 0.001 TYR F 98 PHE 0.011 0.001 PHE E 67 TRP 0.007 0.001 TRP L 364 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00415 (16995) covalent geometry : angle 0.63085 (24218) hydrogen bonds : bond 0.04565 ( 809) hydrogen bonds : angle 3.08427 ( 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 143 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 277 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7900 (mp10) REVERT: L 323 ILE cc_start: 0.8254 (mt) cc_final: 0.7973 (mt) REVERT: L 351 ILE cc_start: 0.7766 (mt) cc_final: 0.7530 (tt) REVERT: L 433 MET cc_start: 0.8356 (ttm) cc_final: 0.7840 (ttt) REVERT: L 437 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7637 (pt0) REVERT: L 470 MET cc_start: 0.9132 (tpt) cc_final: 0.8572 (tpp) REVERT: L 570 LYS cc_start: 0.8987 (mttt) cc_final: 0.8596 (tptt) REVERT: L 609 MET cc_start: 0.8847 (tpt) cc_final: 0.8605 (tpt) REVERT: A 59 GLU cc_start: 0.8975 (pm20) cc_final: 0.8512 (pm20) REVERT: A 120 MET cc_start: 0.8720 (mmm) cc_final: 0.8340 (mtp) REVERT: B 88 TYR cc_start: 0.8962 (m-10) cc_final: 0.8472 (m-80) REVERT: B 93 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.7565 (mp-120) REVERT: C 18 SER cc_start: 0.9170 (OUTLIER) cc_final: 0.8767 (t) REVERT: C 95 LYS cc_start: 0.9472 (tptm) cc_final: 0.9206 (tppt) REVERT: E 51 ILE cc_start: 0.8813 (mt) cc_final: 0.8539 (mt) REVERT: E 97 GLU cc_start: 0.8868 (tt0) cc_final: 0.8580 (mt-10) REVERT: F 80 THR cc_start: 0.9386 (m) cc_final: 0.9030 (p) REVERT: H 44 GLN cc_start: 0.9064 (tm-30) cc_final: 0.8713 (tm-30) REVERT: H 68 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8477 (tp30) outliers start: 16 outliers final: 12 residues processed: 140 average time/residue: 0.1261 time to fit residues: 26.6764 Evaluate side-chains 136 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 277 GLN Chi-restraints excluded: chain L residue 437 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 86 ILE 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: 8.9990 chunk 119 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 51 optimal weight: 0.0270 chunk 46 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 24 optimal weight: 8.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 44 GLN G 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.087841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.058652 restraints weight = 57974.680| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.42 r_work: 0.2840 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.210 16995 Z= 0.226 Angle : 0.887 59.122 24218 Z= 0.531 Chirality : 0.056 2.163 2754 Planarity : 0.005 0.134 2054 Dihedral : 29.694 176.078 4590 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.39 % Allowed : 15.99 % Favored : 82.62 % Cbeta Deviations : 0.17 % 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: 0.62 (0.25), residues: 1238 helix: 1.56 (0.20), residues: 741 sheet: -0.16 (0.66), residues: 67 loop : -1.58 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 81 TYR 0.011 0.001 TYR F 98 PHE 0.011 0.001 PHE E 67 TRP 0.006 0.001 TRP L 364 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00496 (16995) covalent geometry : angle 0.88698 (24218) hydrogen bonds : bond 0.04586 ( 809) hydrogen bonds : angle 3.08080 ( 2080) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3978.83 seconds wall clock time: 68 minutes 40.69 seconds (4120.69 seconds total)