Starting phenix.real_space_refine (version: dev) on Sun Feb 19 23:50:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijz_9682/02_2023/6ijz_9682.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijz_9682/02_2023/6ijz_9682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijz_9682/02_2023/6ijz_9682.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijz_9682/02_2023/6ijz_9682.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijz_9682/02_2023/6ijz_9682.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijz_9682/02_2023/6ijz_9682.pdb" } resolution = 3.68 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.014 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 Process input model Symmetric amino acids flipped Residue "A ARG 29": "NH1" <-> "NH2" Residue "A ARG 36": "NH1" <-> "NH2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 197": "NH1" <-> "NH2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 207": "NH1" <-> "NH2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "B ARG 29": "NH1" <-> "NH2" Residue "B ARG 36": "NH1" <-> "NH2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B ARG 207": "NH1" <-> "NH2" Residue "B ARG 675": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 10964 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5482 Classifications: {'peptide': 683} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'CIS': 1, 'PTRANS': 36, 'TRANS': 645} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 5482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5482 Classifications: {'peptide': 683} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'CIS': 1, 'PTRANS': 36, 'TRANS': 645} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 6.16, per 1000 atoms: 0.56 Number of scatterers: 10964 At special positions: 0 Unit cell: (95.411, 139.849, 108.481, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1872 8.00 N 1778 7.00 C 7264 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 - 3.50 Amino acid : False - 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: 4.54 Conformation dependent library (CDL) restraints added in 1.6 seconds 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2636 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 2 sheets defined 69.2% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 3 through 30 removed outlier: 3.804A pdb=" N VAL A 9 " --> pdb=" O GLN A 5 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 39 through 45 Processing helix chain 'A' and resid 77 through 81 removed outlier: 3.656A pdb=" N LYS A 81 " --> pdb=" O GLU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 91 Processing helix chain 'A' and resid 93 through 125 removed outlier: 3.744A pdb=" N VAL A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Proline residue: A 111 - end of helix removed outlier: 3.891A pdb=" N VAL A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 121 " --> pdb=" O TRP A 117 " (cutoff:3.500A) Proline residue: A 122 - end of helix Processing helix chain 'A' and resid 158 through 193 removed outlier: 4.010A pdb=" N HIS A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL A 164 " --> pdb=" O TRP A 160 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TRP A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS A 174 " --> pdb=" O THR A 170 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 185 " --> pdb=" O TYR A 181 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N MET A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 229 removed outlier: 4.040A pdb=" N LEU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 267 removed outlier: 3.546A pdb=" N GLN A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR A 266 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 267 " --> pdb=" O GLN A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 310 removed outlier: 5.250A pdb=" N ALA A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 337 removed outlier: 3.562A pdb=" N ALA A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 389 removed outlier: 3.595A pdb=" N ARG A 374 " --> pdb=" O SER A 370 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE A 382 " --> pdb=" O MET A 378 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 387 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 401 removed outlier: 3.508A pdb=" N ILE A 393 " --> pdb=" O PHE A 389 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A 396 " --> pdb=" O PRO A 392 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 399 " --> pdb=" O PHE A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 420 through 428 Processing helix chain 'A' and resid 428 through 438 Processing helix chain 'A' and resid 440 through 452 removed outlier: 3.961A pdb=" N GLU A 452 " --> pdb=" O MET A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 475 removed outlier: 4.215A pdb=" N ARG A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 489 removed outlier: 3.822A pdb=" N ALA A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N PHE A 487 " --> pdb=" O ALA A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 496 removed outlier: 3.609A pdb=" N GLN A 496 " --> pdb=" O SER A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 512 removed outlier: 3.739A pdb=" N ILE A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 509 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Proline residue: A 510 - end of helix Processing helix chain 'A' and resid 513 through 523 Processing helix chain 'A' and resid 524 through 530 Processing helix chain 'A' and resid 534 through 547 removed outlier: 4.112A pdb=" N MET A 540 " --> pdb=" O LYS A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 560 removed outlier: 3.514A pdb=" N ALA A 558 " --> pdb=" O ARG A 555 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET A 559 " --> pdb=" O GLU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 583 removed outlier: 3.848A pdb=" N ILE A 573 " --> pdb=" O GLY A 569 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN A 574 " --> pdb=" O GLU A 570 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 612 removed outlier: 3.948A pdb=" N ILE A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 647 removed outlier: 3.773A pdb=" N GLY A 629 " --> pdb=" O PRO A 625 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY A 644 " --> pdb=" O LEU A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 655 removed outlier: 3.838A pdb=" N ALA A 654 " --> pdb=" O ALA A 651 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA A 655 " --> pdb=" O ALA A 652 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 651 through 655' Processing helix chain 'A' and resid 659 through 676 removed outlier: 3.852A pdb=" N VAL A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 666 " --> pdb=" O PRO A 662 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 674 " --> pdb=" O HIS A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 680 Processing helix chain 'A' and resid 684 through 699 removed outlier: 3.636A pdb=" N ASP A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 709 removed outlier: 3.582A pdb=" N GLN A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 30 removed outlier: 3.804A pdb=" N VAL B 9 " --> pdb=" O GLN B 5 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL B 20 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 39 through 45 Processing helix chain 'B' and resid 77 through 81 removed outlier: 3.656A pdb=" N LYS B 81 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 91 Processing helix chain 'B' and resid 93 through 125 removed outlier: 3.744A pdb=" N VAL B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Proline residue: B 111 - end of helix removed outlier: 3.891A pdb=" N VAL B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 121 " --> pdb=" O TRP B 117 " (cutoff:3.500A) Proline residue: B 122 - end of helix Processing helix chain 'B' and resid 158 through 193 removed outlier: 4.009A pdb=" N HIS B 162 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL B 164 " --> pdb=" O TRP B 160 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TRP B 172 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA B 185 " --> pdb=" O TYR B 181 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N MET B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 229 removed outlier: 4.040A pdb=" N LEU B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL B 227 " --> pdb=" O HIS B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 267 removed outlier: 3.546A pdb=" N GLN B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR B 266 " --> pdb=" O TYR B 262 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 267 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 310 removed outlier: 5.250A pdb=" N ALA B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 306 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 337 removed outlier: 3.561A pdb=" N ALA B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 370 through 389 removed outlier: 3.596A pdb=" N ARG B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 380 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE B 382 " --> pdb=" O MET B 378 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE B 387 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 401 removed outlier: 3.508A pdb=" N ILE B 393 " --> pdb=" O PHE B 389 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 396 " --> pdb=" O PRO B 392 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 399 " --> pdb=" O PHE B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 Processing helix chain 'B' and resid 420 through 428 Processing helix chain 'B' and resid 428 through 438 Processing helix chain 'B' and resid 440 through 452 removed outlier: 3.961A pdb=" N GLU B 452 " --> pdb=" O MET B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 475 removed outlier: 4.215A pdb=" N ARG B 462 " --> pdb=" O SER B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 489 removed outlier: 3.822A pdb=" N ALA B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA B 486 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N PHE B 487 " --> pdb=" O ALA B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 496 removed outlier: 3.608A pdb=" N GLN B 496 " --> pdb=" O SER B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 512 removed outlier: 3.739A pdb=" N ILE B 505 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 509 " --> pdb=" O ILE B 505 " (cutoff:3.500A) Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 513 through 523 Processing helix chain 'B' and resid 524 through 530 Processing helix chain 'B' and resid 534 through 547 removed outlier: 4.112A pdb=" N MET B 540 " --> pdb=" O LYS B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 560 removed outlier: 3.514A pdb=" N ALA B 558 " --> pdb=" O ARG B 555 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET B 559 " --> pdb=" O GLU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 583 removed outlier: 3.848A pdb=" N ILE B 573 " --> pdb=" O GLY B 569 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN B 574 " --> pdb=" O GLU B 570 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR B 583 " --> pdb=" O LEU B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 612 removed outlier: 3.947A pdb=" N ILE B 603 " --> pdb=" O ALA B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 647 removed outlier: 3.773A pdb=" N GLY B 629 " --> pdb=" O PRO B 625 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY B 644 " --> pdb=" O LEU B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 655 removed outlier: 3.837A pdb=" N ALA B 654 " --> pdb=" O ALA B 651 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA B 655 " --> pdb=" O ALA B 652 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 651 through 655' Processing helix chain 'B' and resid 659 through 676 removed outlier: 3.852A pdb=" N VAL B 663 " --> pdb=" O ILE B 659 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE B 666 " --> pdb=" O PRO B 662 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY B 674 " --> pdb=" O HIS B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 680 Processing helix chain 'B' and resid 684 through 699 removed outlier: 3.636A pdb=" N ASP B 692 " --> pdb=" O ALA B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 709 removed outlier: 3.581A pdb=" N GLN B 709 " --> pdb=" O LYS B 705 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 203 through 205 removed outlier: 4.859A pdb=" N VAL A 239 " --> pdb=" O MET A 320 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 203 through 205 removed outlier: 4.860A pdb=" N VAL B 239 " --> pdb=" O MET B 320 " (cutoff:3.500A) 557 hydrogen bonds defined for protein. 1653 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.33 Time building geometry restraints manager: 4.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3027 1.33 - 1.45: 2070 1.45 - 1.57: 6083 1.57 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 11272 Sorted by residual: bond pdb=" CB TRP A 624 " pdb=" CG TRP A 624 " ideal model delta sigma weight residual 1.498 1.404 0.094 3.10e-02 1.04e+03 9.10e+00 bond pdb=" CB TRP B 624 " pdb=" CG TRP B 624 " ideal model delta sigma weight residual 1.498 1.405 0.093 3.10e-02 1.04e+03 9.04e+00 bond pdb=" CB PRO B 111 " pdb=" CG PRO B 111 " ideal model delta sigma weight residual 1.492 1.398 0.094 5.00e-02 4.00e+02 3.54e+00 bond pdb=" CB PRO A 111 " pdb=" CG PRO A 111 " ideal model delta sigma weight residual 1.492 1.398 0.094 5.00e-02 4.00e+02 3.54e+00 bond pdb=" CB TRP B 172 " pdb=" CG TRP B 172 " ideal model delta sigma weight residual 1.498 1.443 0.055 3.10e-02 1.04e+03 3.15e+00 ... (remaining 11267 not shown) Histogram of bond angle deviations from ideal: 98.52 - 105.64: 302 105.64 - 112.77: 5738 112.77 - 119.89: 4337 119.89 - 127.02: 4797 127.02 - 134.14: 174 Bond angle restraints: 15348 Sorted by residual: angle pdb=" C VAL A 206 " pdb=" N ARG A 207 " pdb=" CA ARG A 207 " ideal model delta sigma weight residual 121.54 130.94 -9.40 1.91e+00 2.74e-01 2.42e+01 angle pdb=" C VAL B 206 " pdb=" N ARG B 207 " pdb=" CA ARG B 207 " ideal model delta sigma weight residual 121.54 130.89 -9.35 1.91e+00 2.74e-01 2.40e+01 angle pdb=" CA TRP B 624 " pdb=" CB TRP B 624 " pdb=" CG TRP B 624 " ideal model delta sigma weight residual 113.60 104.68 8.92 1.90e+00 2.77e-01 2.20e+01 angle pdb=" CA TRP A 624 " pdb=" CB TRP A 624 " pdb=" CG TRP A 624 " ideal model delta sigma weight residual 113.60 104.69 8.91 1.90e+00 2.77e-01 2.20e+01 angle pdb=" N VAL B 586 " pdb=" CA VAL B 586 " pdb=" C VAL B 586 " ideal model delta sigma weight residual 109.34 100.14 9.20 2.08e+00 2.31e-01 1.96e+01 ... (remaining 15343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.25: 5910 12.25 - 24.50: 580 24.50 - 36.75: 120 36.75 - 49.00: 32 49.00 - 61.25: 4 Dihedral angle restraints: 6646 sinusoidal: 2596 harmonic: 4050 Sorted by residual: dihedral pdb=" CA GLN B 135 " pdb=" C GLN B 135 " pdb=" N LEU B 136 " pdb=" CA LEU B 136 " ideal model delta harmonic sigma weight residual -180.00 -131.79 -48.21 0 5.00e+00 4.00e-02 9.29e+01 dihedral pdb=" CA GLN A 135 " pdb=" C GLN A 135 " pdb=" N LEU A 136 " pdb=" CA LEU A 136 " ideal model delta harmonic sigma weight residual -180.00 -131.83 -48.17 0 5.00e+00 4.00e-02 9.28e+01 dihedral pdb=" CA LYS A 134 " pdb=" C LYS A 134 " pdb=" N GLN A 135 " pdb=" CA GLN A 135 " ideal model delta harmonic sigma weight residual 180.00 148.87 31.13 0 5.00e+00 4.00e-02 3.88e+01 ... (remaining 6643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1371 0.073 - 0.146: 326 0.146 - 0.218: 34 0.218 - 0.291: 11 0.291 - 0.364: 2 Chirality restraints: 1744 Sorted by residual: chirality pdb=" CB VAL A 206 " pdb=" CA VAL A 206 " pdb=" CG1 VAL A 206 " pdb=" CG2 VAL A 206 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CB VAL B 206 " pdb=" CA VAL B 206 " pdb=" CG1 VAL B 206 " pdb=" CG2 VAL B 206 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CA TYR A 613 " pdb=" N TYR A 613 " pdb=" C TYR A 613 " pdb=" CB TYR A 613 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 1741 not shown) Planarity restraints: 1914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 233 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C TYR B 233 " -0.055 2.00e-02 2.50e+03 pdb=" O TYR B 233 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU B 234 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 233 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C TYR A 233 " 0.055 2.00e-02 2.50e+03 pdb=" O TYR A 233 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU A 234 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 612 " 0.014 2.00e-02 2.50e+03 3.01e-02 9.03e+00 pdb=" C VAL A 612 " -0.052 2.00e-02 2.50e+03 pdb=" O VAL A 612 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR A 613 " 0.018 2.00e-02 2.50e+03 ... (remaining 1911 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 52 2.58 - 3.16: 8901 3.16 - 3.74: 16886 3.74 - 4.32: 22900 4.32 - 4.90: 37417 Nonbonded interactions: 86156 Sorted by model distance: nonbonded pdb=" O VAL B 612 " pdb=" CD1 TYR B 613 " model vdw 2.000 3.340 nonbonded pdb=" O VAL A 612 " pdb=" CD1 TYR A 613 " model vdw 2.001 3.340 nonbonded pdb=" OG SER A 216 " pdb=" OE1 GLU A 219 " model vdw 2.242 2.440 nonbonded pdb=" OG SER B 216 " pdb=" OE1 GLU B 219 " model vdw 2.242 2.440 nonbonded pdb=" O PHE B 420 " pdb=" OG SER B 423 " model vdw 2.314 2.440 ... (remaining 86151 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 7264 2.51 5 N 1778 2.21 5 O 1872 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.820 Check model and map are aligned: 0.150 Process input model: 30.470 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.110 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 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 : 0.008 0.094 11272 Z= 0.486 Angle : 1.108 10.715 15348 Z= 0.585 Chirality : 0.064 0.364 1744 Planarity : 0.009 0.068 1914 Dihedral : 10.644 61.249 4010 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.93 % Favored : 88.77 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 2.78 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.03 (0.17), residues: 1354 helix: -2.86 (0.13), residues: 860 sheet: -3.31 (1.09), residues: 20 loop : -4.03 (0.23), residues: 474 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 376 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 379 average time/residue: 0.2256 time to fit residues: 120.2436 Evaluate side-chains 257 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 251 time to evaluate : 1.229 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1120 time to fit residues: 2.9098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 55 optimal weight: 0.0970 chunk 106 optimal weight: 0.0870 chunk 41 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN A 232 HIS ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN A 542 HIS A 607 HIS A 608 GLN ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN B 232 HIS ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 ASN B 489 GLN B 495 ASN B 567 ASN B 607 HIS ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 11272 Z= 0.201 Angle : 0.729 10.911 15348 Z= 0.376 Chirality : 0.045 0.179 1744 Planarity : 0.006 0.059 1914 Dihedral : 6.347 39.805 1464 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.27 % Favored : 89.66 % Rotamer Outliers : 3.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.20), residues: 1354 helix: -1.44 (0.16), residues: 858 sheet: -3.51 (0.98), residues: 30 loop : -3.84 (0.23), residues: 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 310 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 24 residues processed: 333 average time/residue: 0.2270 time to fit residues: 108.8248 Evaluate side-chains 272 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 248 time to evaluate : 1.204 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1046 time to fit residues: 6.2544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 10.0000 chunk 38 optimal weight: 0.0670 chunk 102 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 123 optimal weight: 0.0770 chunk 133 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 151 ASN A 567 ASN A 615 GLN B 14 ASN B 151 ASN B 567 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 11272 Z= 0.178 Angle : 0.669 10.658 15348 Z= 0.342 Chirality : 0.044 0.170 1744 Planarity : 0.005 0.058 1914 Dihedral : 5.780 36.489 1464 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.82 % Favored : 90.03 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.22), residues: 1354 helix: -0.74 (0.17), residues: 882 sheet: -3.21 (1.07), residues: 30 loop : -3.68 (0.25), residues: 442 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 288 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 9 residues processed: 304 average time/residue: 0.2005 time to fit residues: 89.5098 Evaluate side-chains 246 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 237 time to evaluate : 1.263 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1027 time to fit residues: 3.4509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 131 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 35 optimal weight: 0.2980 chunk 109 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 138 ASN A 151 ASN A 489 GLN ** A 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 11272 Z= 0.186 Angle : 0.668 10.785 15348 Z= 0.335 Chirality : 0.043 0.162 1744 Planarity : 0.005 0.046 1914 Dihedral : 5.507 32.025 1464 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.75 % Favored : 90.10 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.23), residues: 1354 helix: -0.18 (0.18), residues: 892 sheet: -3.20 (1.08), residues: 30 loop : -3.42 (0.27), residues: 432 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 258 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 18 residues processed: 274 average time/residue: 0.2050 time to fit residues: 82.3107 Evaluate side-chains 254 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 236 time to evaluate : 1.389 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1134 time to fit residues: 5.6007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 0.0000 chunk 1 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 112 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 117 optimal weight: 0.2980 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN A 615 GLN B 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 11272 Z= 0.171 Angle : 0.657 10.705 15348 Z= 0.328 Chirality : 0.043 0.160 1744 Planarity : 0.005 0.045 1914 Dihedral : 5.286 26.351 1464 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.45 % Favored : 90.40 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.23), residues: 1354 helix: 0.14 (0.18), residues: 894 sheet: -2.99 (1.11), residues: 30 loop : -3.26 (0.28), residues: 430 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 252 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 262 average time/residue: 0.1899 time to fit residues: 75.0206 Evaluate side-chains 239 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 232 time to evaluate : 1.254 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1125 time to fit residues: 3.1311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 131 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 ASN B 151 ASN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 11272 Z= 0.249 Angle : 0.678 11.109 15348 Z= 0.343 Chirality : 0.044 0.153 1744 Planarity : 0.005 0.091 1914 Dihedral : 5.198 22.909 1464 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.12 % Favored : 89.81 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.24), residues: 1354 helix: 0.41 (0.18), residues: 894 sheet: -3.02 (1.07), residues: 30 loop : -3.18 (0.29), residues: 430 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 243 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 12 residues processed: 262 average time/residue: 0.1991 time to fit residues: 78.4366 Evaluate side-chains 242 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 230 time to evaluate : 1.356 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1111 time to fit residues: 4.2982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 60 optimal weight: 0.6980 chunk 81 optimal weight: 0.4980 chunk 52 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 11272 Z= 0.195 Angle : 0.674 10.912 15348 Z= 0.336 Chirality : 0.044 0.160 1744 Planarity : 0.005 0.091 1914 Dihedral : 5.107 23.616 1464 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.38 % Favored : 90.47 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.24), residues: 1354 helix: 0.62 (0.18), residues: 896 sheet: -2.98 (1.06), residues: 30 loop : -3.09 (0.29), residues: 428 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 251 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 258 average time/residue: 0.1989 time to fit residues: 77.3199 Evaluate side-chains 241 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 235 time to evaluate : 1.354 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1189 time to fit residues: 3.2651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 11272 Z= 0.194 Angle : 0.673 10.990 15348 Z= 0.335 Chirality : 0.044 0.165 1744 Planarity : 0.005 0.085 1914 Dihedral : 5.025 22.634 1464 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.23 % Favored : 90.62 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.24), residues: 1354 helix: 0.74 (0.18), residues: 894 sheet: -3.00 (1.05), residues: 30 loop : -3.02 (0.29), residues: 430 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 247 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 256 average time/residue: 0.1896 time to fit residues: 74.2459 Evaluate side-chains 246 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 237 time to evaluate : 1.176 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1039 time to fit residues: 3.4036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 53 optimal weight: 0.0000 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 115 optimal weight: 10.0000 chunk 121 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 11272 Z= 0.191 Angle : 0.683 11.620 15348 Z= 0.340 Chirality : 0.044 0.163 1744 Planarity : 0.005 0.082 1914 Dihedral : 4.966 20.702 1464 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.45 % Favored : 90.40 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.24), residues: 1354 helix: 0.78 (0.18), residues: 900 sheet: -2.96 (1.05), residues: 30 loop : -3.04 (0.29), residues: 424 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 252 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 257 average time/residue: 0.2243 time to fit residues: 85.7880 Evaluate side-chains 244 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 237 time to evaluate : 1.518 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1274 time to fit residues: 3.4142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 83 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 114 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 11272 Z= 0.191 Angle : 0.700 10.897 15348 Z= 0.349 Chirality : 0.045 0.192 1744 Planarity : 0.005 0.081 1914 Dihedral : 4.917 20.334 1464 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.45 % Favored : 90.40 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.24), residues: 1354 helix: 0.87 (0.18), residues: 888 sheet: -2.95 (1.05), residues: 30 loop : -2.90 (0.29), residues: 436 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 251 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 254 average time/residue: 0.1909 time to fit residues: 73.7754 Evaluate side-chains 244 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 242 time to evaluate : 1.298 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1122 time to fit residues: 2.1959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 0.0770 chunk 99 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 108 optimal weight: 0.0670 chunk 45 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 6 optimal weight: 0.0270 overall best weight: 0.3334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 GLN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.147168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.120071 restraints weight = 18448.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.123364 restraints weight = 9838.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.125468 restraints weight = 6639.851| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 11272 Z= 0.172 Angle : 0.687 10.721 15348 Z= 0.340 Chirality : 0.043 0.187 1744 Planarity : 0.005 0.080 1914 Dihedral : 4.843 23.541 1464 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.49 % Favored : 91.43 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.24), residues: 1354 helix: 0.97 (0.18), residues: 882 sheet: -2.87 (1.07), residues: 30 loop : -2.80 (0.29), residues: 442 =============================================================================== Job complete usr+sys time: 2319.13 seconds wall clock time: 43 minutes 8.76 seconds (2588.76 seconds total)