Starting phenix.real_space_refine (version: dev) on Mon Dec 12 15:30:17 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijz_9682/12_2022/6ijz_9682.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijz_9682/12_2022/6ijz_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_9682/12_2022/6ijz_9682.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijz_9682/12_2022/6ijz_9682.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijz_9682/12_2022/6ijz_9682.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijz_9682/12_2022/6ijz_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 Convert atoms to be neutral 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-4807/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: 6.00, per 1000 atoms: 0.55 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: 4.61 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: 0.51 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: 3.02 Time building geometry restraints manager: 4.91 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: 0.310 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: 2.970 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.090 Process input model: 30.010 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.230 ------------------------------------------------------------------------------- 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 : 1.191 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: 0.2166 time to fit residues: 116.3105 Evaluate side-chains 257 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 251 time to evaluate : 1.337 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1118 time to fit residues: 3.0104 ------------------------------------------------------------------------------- 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 10.912 15348 Z= 0.376 Chirality : 0.045 0.179 1744 Planarity : 0.006 0.059 1914 Dihedral : 6.347 39.806 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 : 3.19 % 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 347 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 310 time to evaluate : 1.276 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: 37 outliers final: 23 residues processed: 332 average time/residue: 0.2155 time to fit residues: 103.4770 Evaluate side-chains 271 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 248 time to evaluate : 1.489 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1125 time to fit residues: 6.5531 ------------------------------------------------------------------------------- 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: 1.9990 chunk 102 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 42 optimal weight: 0.3980 chunk 99 optimal weight: 0.5980 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 151 ASN A 567 ASN A 615 GLN A 639 GLN B 14 ASN B 151 ASN B 567 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 11272 Z= 0.193 Angle : 0.676 10.764 15348 Z= 0.346 Chirality : 0.044 0.173 1744 Planarity : 0.005 0.059 1914 Dihedral : 5.814 36.925 1464 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.68 % Favored : 90.18 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.65 (0.22), residues: 1354 helix: -0.73 (0.17), residues: 878 sheet: -3.28 (1.06), residues: 30 loop : -3.72 (0.25), residues: 446 *********************** 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 306 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 279 time to evaluate : 1.204 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 outliers start: 27 outliers final: 14 residues processed: 298 average time/residue: 0.1989 time to fit residues: 88.2048 Evaluate side-chains 253 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 239 time to evaluate : 1.296 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1013 time to fit residues: 4.4304 ------------------------------------------------------------------------------- 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: 0.8980 chunk 93 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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: 0.8037 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 11272 Z= 0.224 Angle : 0.679 11.091 15348 Z= 0.344 Chirality : 0.044 0.161 1744 Planarity : 0.005 0.048 1914 Dihedral : 5.581 32.544 1464 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.68 % Favored : 90.18 % Rotamer Outliers : 2.41 % 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: -1.95 (0.23), residues: 1354 helix: -0.21 (0.18), residues: 894 sheet: -3.34 (1.05), residues: 30 loop : -3.46 (0.27), residues: 430 *********************** 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 289 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 261 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 14 residues processed: 275 average time/residue: 0.2032 time to fit residues: 81.9687 Evaluate side-chains 245 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 231 time to evaluate : 1.288 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.1109 time to fit residues: 4.5310 ------------------------------------------------------------------------------- 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: 0.0870 chunk 1 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 112 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 615 GLN B 138 ASN B 151 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 11272 Z= 0.201 Angle : 0.673 10.844 15348 Z= 0.337 Chirality : 0.044 0.156 1744 Planarity : 0.005 0.045 1914 Dihedral : 5.385 26.688 1464 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.45 % Favored : 90.40 % Rotamer Outliers : 1.72 % 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: -1.50 (0.23), residues: 1354 helix: 0.14 (0.18), residues: 894 sheet: -3.17 (1.09), residues: 30 loop : -3.29 (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 265 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 245 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 6 residues processed: 258 average time/residue: 0.2023 time to fit residues: 79.2874 Evaluate side-chains 233 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 227 time to evaluate : 1.266 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1128 time to fit residues: 3.0380 ------------------------------------------------------------------------------- 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: 0.9990 chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 32 optimal weight: 0.0070 chunk 131 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 10 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 126 optimal weight: 0.1980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 GLN B 14 ASN B 397 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3874 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= 0.177 Angle : 0.662 10.799 15348 Z= 0.330 Chirality : 0.043 0.158 1744 Planarity : 0.005 0.043 1914 Dihedral : 5.188 22.957 1464 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.45 % Favored : 90.47 % Rotamer Outliers : 2.16 % 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: -1.25 (0.24), residues: 1354 helix: 0.35 (0.18), residues: 894 sheet: -3.07 (1.08), residues: 30 loop : -3.23 (0.28), 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 281 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 256 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 9 residues processed: 272 average time/residue: 0.1931 time to fit residues: 79.2705 Evaluate side-chains 240 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 231 time to evaluate : 1.246 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1019 time to fit residues: 3.4992 ------------------------------------------------------------------------------- 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: 0.9980 chunk 74 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 110 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN ** B 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 11272 Z= 0.217 Angle : 0.687 10.915 15348 Z= 0.343 Chirality : 0.044 0.159 1744 Planarity : 0.005 0.048 1914 Dihedral : 5.141 24.059 1464 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.53 % Favored : 90.32 % Rotamer Outliers : 1.12 % 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: -1.04 (0.24), residues: 1354 helix: 0.52 (0.18), residues: 894 sheet: -3.12 (1.05), residues: 30 loop : -3.15 (0.29), residues: 430 *********************** 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 259 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 246 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 252 average time/residue: 0.1943 time to fit residues: 74.1043 Evaluate side-chains 238 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 231 time to evaluate : 1.248 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1145 time to fit residues: 3.1020 ------------------------------------------------------------------------------- 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: 0.9990 chunk 25 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 12 optimal weight: 0.0770 chunk 103 optimal weight: 1.9990 chunk 119 optimal weight: 0.2980 chunk 125 optimal weight: 3.9990 chunk 114 optimal weight: 0.2980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 GLN ** B 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 11272 Z= 0.177 Angle : 0.670 10.693 15348 Z= 0.333 Chirality : 0.043 0.166 1744 Planarity : 0.005 0.045 1914 Dihedral : 5.016 21.504 1464 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.16 % Favored : 90.77 % 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: -0.88 (0.24), residues: 1354 helix: 0.63 (0.18), residues: 900 sheet: -2.96 (1.08), residues: 30 loop : -3.11 (0.29), residues: 424 *********************** 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 269 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 257 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 263 average time/residue: 0.1828 time to fit residues: 72.7348 Evaluate side-chains 246 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 240 time to evaluate : 1.302 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1010 time to fit residues: 2.8753 ------------------------------------------------------------------------------- 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: 0.2980 chunk 125 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 53 optimal weight: 0.0060 chunk 95 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 110 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 80 optimal weight: 0.0770 chunk 129 optimal weight: 0.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 11272 Z= 0.177 Angle : 0.691 11.267 15348 Z= 0.343 Chirality : 0.043 0.161 1744 Planarity : 0.005 0.050 1914 Dihedral : 4.935 21.436 1464 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.38 % Favored : 90.55 % Rotamer Outliers : 0.52 % 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: 0.76 (0.18), residues: 900 sheet: -1.88 (1.07), residues: 34 loop : -3.10 (0.29), residues: 420 *********************** 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 258 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 252 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 254 average time/residue: 0.2031 time to fit residues: 77.7440 Evaluate side-chains 239 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 238 time to evaluate : 1.152 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1021 time to fit residues: 1.8606 ------------------------------------------------------------------------------- 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: 5.9990 chunk 61 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 107 optimal weight: 0.3980 chunk 11 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 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 ** B 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4498 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= 0.198 Angle : 0.690 10.740 15348 Z= 0.344 Chirality : 0.044 0.188 1744 Planarity : 0.005 0.047 1914 Dihedral : 4.927 22.684 1464 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.45 % Favored : 90.40 % Rotamer Outliers : 0.52 % 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: -0.55 (0.24), residues: 1354 helix: 0.89 (0.18), residues: 888 sheet: -1.92 (1.05), residues: 34 loop : -2.97 (0.30), residues: 432 ********************** 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 250 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 244 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 247 average time/residue: 0.1870 time to fit residues: 70.0438 Evaluate side-chains 247 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 243 time to evaluate : 1.312 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1156 time to fit residues: 2.6000 ------------------------------------------------------------------------------- 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: 0.0370 chunk 99 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 108 optimal weight: 0.0270 chunk 45 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 6 optimal weight: 0.0010 overall best weight: 0.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.147822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.121116 restraints weight = 18514.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.124405 restraints weight = 9848.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.126501 restraints weight = 6639.988| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4668 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= 0.171 Angle : 0.685 10.530 15348 Z= 0.341 Chirality : 0.044 0.178 1744 Planarity : 0.005 0.052 1914 Dihedral : 4.853 25.923 1464 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.23 % Favored : 90.62 % 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: -0.44 (0.24), residues: 1354 helix: 0.95 (0.18), residues: 888 sheet: -1.80 (1.08), residues: 34 loop : -2.89 (0.30), residues: 432 =============================================================================== Job complete usr+sys time: 2276.56 seconds wall clock time: 41 minutes 56.26 seconds (2516.26 seconds total)