Starting phenix.real_space_refine on Sat Dec 9 05:42:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk7_32561/12_2023/7wk7_32561_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk7_32561/12_2023/7wk7_32561.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk7_32561/12_2023/7wk7_32561.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk7_32561/12_2023/7wk7_32561.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk7_32561/12_2023/7wk7_32561_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk7_32561/12_2023/7wk7_32561_updated.pdb" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 6658 2.51 5 N 1684 2.21 5 O 1822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 39": "NH1" <-> "NH2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 586": "NH1" <-> "NH2" Residue "A ARG 587": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 79": "NH1" <-> "NH2" Residue "B PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 586": "NH1" <-> "NH2" Residue "B ARG 587": "NH1" <-> "NH2" Residue "B PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10206 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5099 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 26, 'TRANS': 638} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5099 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 26, 'TRANS': 638} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'BCT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'BCT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.52, per 1000 atoms: 0.54 Number of scatterers: 10206 At special positions: 0 Unit cell: (86.818, 127.612, 118.198, 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 42 16.00 O 1822 8.00 N 1684 7.00 C 6658 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: 4.14 Conformation dependent library (CDL) restraints added in 2.0 seconds 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 2 sheets defined 59.2% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'A' and resid 30 through 33 No H-bonds generated for 'chain 'A' and resid 30 through 33' Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 58 through 68 Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.910A pdb=" N TRP A 74 " --> pdb=" O ILE A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 107 removed outlier: 4.950A pdb=" N LEU A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LEU A 107 " --> pdb=" O MET A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 119 removed outlier: 3.591A pdb=" N LEU A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 142 through 155 Processing helix chain 'A' and resid 180 through 205 Processing helix chain 'A' and resid 210 through 214 removed outlier: 3.921A pdb=" N TYR A 214 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 240 Processing helix chain 'A' and resid 252 through 263 Processing helix chain 'A' and resid 269 through 291 Processing helix chain 'A' and resid 302 through 316 Processing helix chain 'A' and resid 350 through 373 Processing helix chain 'A' and resid 381 through 398 removed outlier: 3.537A pdb=" N PHE A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 415 removed outlier: 3.901A pdb=" N GLN A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.610A pdb=" N ILE A 430 " --> pdb=" O ILE A 426 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 431 " --> pdb=" O SER A 427 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 436 " --> pdb=" O MET A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 444 Proline residue: A 444 - end of helix No H-bonds generated for 'chain 'A' and resid 441 through 444' Processing helix chain 'A' and resid 447 through 473 removed outlier: 3.757A pdb=" N VAL A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS A 459 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N MET A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN A 464 " --> pdb=" O GLY A 460 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL A 465 " --> pdb=" O MET A 461 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N CYS A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ASP A 467 " --> pdb=" O MET A 463 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL A 468 " --> pdb=" O GLN A 464 " (cutoff:3.500A) Proline residue: A 469 - end of helix removed outlier: 3.676A pdb=" N LYS A 473 " --> pdb=" O PRO A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 491 removed outlier: 3.786A pdb=" N ILE A 490 " --> pdb=" O CYS A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 514 removed outlier: 3.696A pdb=" N LEU A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 570 Processing helix chain 'A' and resid 574 through 594 removed outlier: 3.834A pdb=" N TYR A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 586 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ARG A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS A 590 " --> pdb=" O ARG A 586 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 685 removed outlier: 4.131A pdb=" N SER A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 705 removed outlier: 3.624A pdb=" N LYS A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 717 No H-bonds generated for 'chain 'A' and resid 715 through 717' Processing helix chain 'A' and resid 722 through 735 removed outlier: 3.553A pdb=" N ILE A 726 " --> pdb=" O VAL A 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'B' and resid 46 through 53 removed outlier: 3.805A pdb=" N LEU B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 68 removed outlier: 3.540A pdb=" N VAL B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 removed outlier: 3.794A pdb=" N TRP B 74 " --> pdb=" O ILE B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 109 removed outlier: 3.633A pdb=" N LEU B 84 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LEU B 85 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 92 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU B 107 " --> pdb=" O MET B 103 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA B 109 " --> pdb=" O TYR B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 120 removed outlier: 3.818A pdb=" N TYR B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 119 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 114 through 120' Processing helix chain 'B' and resid 122 through 128 removed outlier: 3.652A pdb=" N PHE B 128 " --> pdb=" O ILE B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 155 removed outlier: 3.685A pdb=" N VAL B 151 " --> pdb=" O MET B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 181 through 205 removed outlier: 3.738A pdb=" N ARG B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 212 No H-bonds generated for 'chain 'B' and resid 210 through 212' Processing helix chain 'B' and resid 217 through 240 removed outlier: 3.627A pdb=" N PHE B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 262 Processing helix chain 'B' and resid 269 through 291 removed outlier: 3.617A pdb=" N ALA B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 316 removed outlier: 3.727A pdb=" N THR B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 373 removed outlier: 3.941A pdb=" N SER B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR B 361 " --> pdb=" O ALA B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 398 removed outlier: 3.876A pdb=" N PHE B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE B 397 " --> pdb=" O VAL B 393 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 415 removed outlier: 3.552A pdb=" N VAL B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.539A pdb=" N VAL B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 436 " --> pdb=" O MET B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 473 removed outlier: 4.015A pdb=" N VAL B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN B 457 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 458 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LYS B 459 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLY B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N MET B 461 " --> pdb=" O ASN B 457 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN B 464 " --> pdb=" O GLY B 460 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL B 465 " --> pdb=" O MET B 461 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N CYS B 466 " --> pdb=" O PHE B 462 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ASP B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N VAL B 468 " --> pdb=" O GLN B 464 " (cutoff:3.500A) Proline residue: B 469 - end of helix removed outlier: 3.651A pdb=" N LYS B 473 " --> pdb=" O PRO B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 491 removed outlier: 3.770A pdb=" N ILE B 490 " --> pdb=" O CYS B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 514 removed outlier: 3.646A pdb=" N LEU B 499 " --> pdb=" O ASP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 570 removed outlier: 3.612A pdb=" N LYS B 563 " --> pdb=" O VAL B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 594 removed outlier: 3.885A pdb=" N TYR B 578 " --> pdb=" O ALA B 574 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ARG B 587 " --> pdb=" O LYS B 583 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE B 588 " --> pdb=" O ALA B 584 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS B 590 " --> pdb=" O ARG B 586 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS B 593 " --> pdb=" O GLN B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 685 removed outlier: 4.855A pdb=" N SER B 675 " --> pdb=" O VAL B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 705 removed outlier: 3.824A pdb=" N LYS B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 717 No H-bonds generated for 'chain 'B' and resid 715 through 717' Processing helix chain 'B' and resid 722 through 735 removed outlier: 3.513A pdb=" N ILE B 726 " --> pdb=" O VAL B 722 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 545 through 549 removed outlier: 6.666A pdb=" N SER A 657 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LEU A 548 " --> pdb=" O SER A 657 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL A 659 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ASN A 689 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU A 660 " --> pdb=" O ASN A 689 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TYR A 691 " --> pdb=" O LEU A 660 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 545 through 549 removed outlier: 6.739A pdb=" N SER B 657 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N LEU B 548 " --> pdb=" O SER B 657 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL B 659 " --> pdb=" O LEU B 548 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASN B 689 " --> pdb=" O LEU B 658 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU B 660 " --> pdb=" O ASN B 689 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR B 691 " --> pdb=" O LEU B 660 " (cutoff:3.500A) No H-bonds generated for sheet with id= B 469 hydrogen bonds defined for protein. 1329 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: 2.80 Time building geometry restraints manager: 4.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3203 1.34 - 1.46: 1355 1.46 - 1.57: 5784 1.57 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 10406 Sorted by residual: bond pdb=" C BCT B 800 " pdb=" O3 BCT B 800 " ideal model delta sigma weight residual 1.389 1.436 -0.047 2.00e-02 2.50e+03 5.50e+00 bond pdb=" C BCT A 800 " pdb=" O3 BCT A 800 " ideal model delta sigma weight residual 1.389 1.435 -0.046 2.00e-02 2.50e+03 5.34e+00 bond pdb=" C VAL B 653 " pdb=" N PRO B 654 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.24e-01 bond pdb=" C VAL A 653 " pdb=" N PRO A 654 " ideal model delta sigma weight residual 1.334 1.354 -0.021 2.34e-02 1.83e+03 7.75e-01 bond pdb=" N ASN A 167 " pdb=" CA ASN A 167 " ideal model delta sigma weight residual 1.457 1.468 -0.010 1.29e-02 6.01e+03 6.27e-01 ... (remaining 10401 not shown) Histogram of bond angle deviations from ideal: 100.76 - 107.42: 296 107.42 - 114.08: 6183 114.08 - 120.74: 4476 120.74 - 127.39: 3110 127.39 - 134.05: 77 Bond angle restraints: 14142 Sorted by residual: angle pdb=" C ARG B 79 " pdb=" N VAL B 80 " pdb=" CA VAL B 80 " ideal model delta sigma weight residual 120.62 124.97 -4.35 1.64e+00 3.72e-01 7.03e+00 angle pdb=" N LEU A 521 " pdb=" CA LEU A 521 " pdb=" C LEU A 521 " ideal model delta sigma weight residual 110.42 113.96 -3.54 1.46e+00 4.69e-01 5.86e+00 angle pdb=" N LEU B 521 " pdb=" CA LEU B 521 " pdb=" C LEU B 521 " ideal model delta sigma weight residual 110.42 113.93 -3.51 1.46e+00 4.69e-01 5.79e+00 angle pdb=" C ALA B 434 " pdb=" N ILE B 435 " pdb=" CA ILE B 435 " ideal model delta sigma weight residual 122.66 120.34 2.32 9.70e-01 1.06e+00 5.71e+00 angle pdb=" C GLY A 520 " pdb=" N LEU A 521 " pdb=" CA LEU A 521 " ideal model delta sigma weight residual 121.56 125.25 -3.69 1.56e+00 4.11e-01 5.59e+00 ... (remaining 14137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 5994 17.24 - 34.49: 153 34.49 - 51.73: 24 51.73 - 68.97: 3 68.97 - 86.22: 8 Dihedral angle restraints: 6182 sinusoidal: 2346 harmonic: 3836 Sorted by residual: dihedral pdb=" N LEU A 496 " pdb=" CA LEU A 496 " pdb=" CB LEU A 496 " pdb=" CG LEU A 496 " ideal model delta sinusoidal sigma weight residual -180.00 -123.81 -56.19 3 1.50e+01 4.44e-03 9.39e+00 dihedral pdb=" CB GLU A 303 " pdb=" CG GLU A 303 " pdb=" CD GLU A 303 " pdb=" OE1 GLU A 303 " ideal model delta sinusoidal sigma weight residual 0.00 -82.21 82.21 1 3.00e+01 1.11e-03 9.22e+00 dihedral pdb=" N LEU B 727 " pdb=" CA LEU B 727 " pdb=" CB LEU B 727 " pdb=" CG LEU B 727 " ideal model delta sinusoidal sigma weight residual -180.00 -127.36 -52.64 3 1.50e+01 4.44e-03 9.13e+00 ... (remaining 6179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 975 0.026 - 0.052: 469 0.052 - 0.077: 181 0.077 - 0.103: 75 0.103 - 0.129: 18 Chirality restraints: 1718 Sorted by residual: chirality pdb=" CA PRO B 553 " pdb=" N PRO B 553 " pdb=" C PRO B 553 " pdb=" CB PRO B 553 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA PRO A 553 " pdb=" N PRO A 553 " pdb=" C PRO A 553 " pdb=" CB PRO A 553 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA LEU A 668 " pdb=" N LEU A 668 " pdb=" C LEU A 668 " pdb=" CB LEU A 668 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.86e-01 ... (remaining 1715 not shown) Planarity restraints: 1760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 552 " 0.021 5.00e-02 4.00e+02 3.14e-02 1.57e+00 pdb=" N PRO B 553 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 553 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 553 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 552 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO A 553 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 553 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 553 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 300 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO B 301 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 301 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 301 " 0.017 5.00e-02 4.00e+02 ... (remaining 1757 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1095 2.74 - 3.28: 10921 3.28 - 3.82: 16714 3.82 - 4.36: 19786 4.36 - 4.90: 33419 Nonbonded interactions: 81935 Sorted by model distance: nonbonded pdb=" OH TYR A 78 " pdb=" OD2 ASP A 87 " model vdw 2.206 2.440 nonbonded pdb=" OG SER A 90 " pdb=" O GLY A 417 " model vdw 2.221 2.440 nonbonded pdb=" OD1 ASN B 475 " pdb=" OG1 THR B 477 " model vdw 2.227 2.440 nonbonded pdb=" OD1 ASN A 475 " pdb=" OG1 THR A 477 " model vdw 2.229 2.440 nonbonded pdb=" O THR A 485 " pdb=" OG SER A 489 " model vdw 2.237 2.440 ... (remaining 81930 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 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: 7.180 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 30.430 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 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 : 0.002 0.047 10406 Z= 0.116 Angle : 0.440 5.051 14142 Z= 0.246 Chirality : 0.037 0.129 1718 Planarity : 0.003 0.031 1760 Dihedral : 8.683 86.216 3710 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.54 % Favored : 95.39 % Rotamer: Outliers : 3.12 % Allowed : 5.17 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -3.90 (0.18), residues: 1322 helix: -2.07 (0.14), residues: 838 sheet: -4.06 (0.61), residues: 34 loop : -3.22 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 83 HIS 0.001 0.000 HIS B 656 PHE 0.009 0.001 PHE B 555 TYR 0.009 0.001 TYR A 127 ARG 0.001 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 438 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 9 residues processed: 464 average time/residue: 0.2673 time to fit residues: 164.3460 Evaluate side-chains 348 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 339 time to evaluate : 1.205 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1230 time to fit residues: 3.3501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.0980 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 chunk 77 optimal weight: 0.0970 chunk 119 optimal weight: 0.6980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 382 ASN A 656 HIS B 101 GLN ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 ASN B 464 GLN B 474 GLN B 731 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10406 Z= 0.206 Angle : 0.620 8.315 14142 Z= 0.313 Chirality : 0.043 0.200 1718 Planarity : 0.005 0.039 1760 Dihedral : 3.580 17.522 1416 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.30 % Allowed : 18.09 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.27 (0.22), residues: 1322 helix: -0.66 (0.17), residues: 846 sheet: -3.52 (0.75), residues: 36 loop : -2.89 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 74 HIS 0.013 0.001 HIS A 656 PHE 0.028 0.002 PHE A 394 TYR 0.027 0.002 TYR A 361 ARG 0.006 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 373 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 20 residues processed: 391 average time/residue: 0.2811 time to fit residues: 144.7034 Evaluate side-chains 338 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 318 time to evaluate : 1.161 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1113 time to fit residues: 5.5177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 119 optimal weight: 0.2980 chunk 40 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN A 382 ASN A 731 ASN B 101 GLN B 160 HIS B 446 GLN B 457 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 10406 Z= 0.288 Angle : 0.654 9.487 14142 Z= 0.334 Chirality : 0.044 0.196 1718 Planarity : 0.005 0.045 1760 Dihedral : 3.866 20.448 1416 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.12 % Allowed : 22.28 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.87 (0.22), residues: 1322 helix: -0.43 (0.17), residues: 856 sheet: -2.86 (0.90), residues: 36 loop : -2.64 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 74 HIS 0.011 0.001 HIS B 160 PHE 0.020 0.002 PHE B 272 TYR 0.034 0.002 TYR A 361 ARG 0.009 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 342 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 14 residues processed: 361 average time/residue: 0.2580 time to fit residues: 125.3026 Evaluate side-chains 321 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 307 time to evaluate : 1.225 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1259 time to fit residues: 4.6114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 80 optimal weight: 0.2980 chunk 120 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 chunk 114 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 106 optimal weight: 6.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 457 ASN A 656 HIS B 33 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10406 Z= 0.230 Angle : 0.643 9.747 14142 Z= 0.327 Chirality : 0.044 0.176 1718 Planarity : 0.004 0.042 1760 Dihedral : 3.950 18.565 1416 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.05 % Favored : 93.87 % Rotamer: Outliers : 2.41 % Allowed : 24.24 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.47 (0.23), residues: 1322 helix: -0.14 (0.18), residues: 846 sheet: -2.59 (0.91), residues: 36 loop : -2.40 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 74 HIS 0.012 0.001 HIS A 656 PHE 0.030 0.001 PHE A 385 TYR 0.034 0.002 TYR A 361 ARG 0.009 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 322 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 334 average time/residue: 0.2497 time to fit residues: 113.2056 Evaluate side-chains 312 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 299 time to evaluate : 1.194 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0994 time to fit residues: 4.0028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 114 optimal weight: 0.5980 chunk 32 optimal weight: 0.1980 chunk 42 optimal weight: 0.0050 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 656 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10406 Z= 0.210 Angle : 0.657 9.592 14142 Z= 0.331 Chirality : 0.044 0.303 1718 Planarity : 0.004 0.041 1760 Dihedral : 3.982 18.519 1416 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.67 % Favored : 94.25 % Rotamer: Outliers : 1.96 % Allowed : 25.40 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.34 (0.23), residues: 1322 helix: -0.09 (0.18), residues: 848 sheet: -2.27 (0.95), residues: 36 loop : -2.26 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 482 HIS 0.006 0.001 HIS A 656 PHE 0.027 0.001 PHE A 385 TYR 0.026 0.002 TYR B 105 ARG 0.010 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 311 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 324 average time/residue: 0.2624 time to fit residues: 115.4224 Evaluate side-chains 310 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 300 time to evaluate : 1.122 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1594 time to fit residues: 4.1029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 0.1980 chunk 31 optimal weight: 0.0030 chunk 127 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 10 optimal weight: 0.0980 chunk 42 optimal weight: 0.7980 chunk 67 optimal weight: 0.1980 chunk 123 optimal weight: 0.7980 overall best weight: 0.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 656 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10406 Z= 0.186 Angle : 0.642 10.344 14142 Z= 0.324 Chirality : 0.043 0.171 1718 Planarity : 0.004 0.043 1760 Dihedral : 3.987 19.214 1416 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.67 % Favored : 94.25 % Rotamer: Outliers : 2.05 % Allowed : 26.83 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.14 (0.23), residues: 1322 helix: 0.04 (0.18), residues: 848 sheet: -1.73 (1.04), residues: 36 loop : -2.14 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 482 HIS 0.006 0.001 HIS A 656 PHE 0.022 0.001 PHE A 385 TYR 0.025 0.001 TYR B 105 ARG 0.010 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 311 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 10 residues processed: 323 average time/residue: 0.2586 time to fit residues: 111.5897 Evaluate side-chains 308 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 298 time to evaluate : 1.111 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1065 time to fit residues: 3.3841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.0980 chunk 72 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 71 optimal weight: 0.3980 chunk 127 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 50 optimal weight: 0.0870 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 656 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10406 Z= 0.208 Angle : 0.663 10.785 14142 Z= 0.330 Chirality : 0.043 0.196 1718 Planarity : 0.004 0.043 1760 Dihedral : 4.009 19.129 1416 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.75 % Favored : 94.18 % Rotamer: Outliers : 1.34 % Allowed : 28.34 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.14 (0.23), residues: 1322 helix: 0.05 (0.18), residues: 854 sheet: -1.53 (1.08), residues: 36 loop : -2.23 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 482 HIS 0.004 0.000 HIS A 656 PHE 0.045 0.001 PHE A 385 TYR 0.029 0.002 TYR B 105 ARG 0.013 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 299 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 4 residues processed: 307 average time/residue: 0.2577 time to fit residues: 105.9928 Evaluate side-chains 295 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 291 time to evaluate : 1.217 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1057 time to fit residues: 2.3877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 24 optimal weight: 0.3980 chunk 80 optimal weight: 0.5980 chunk 86 optimal weight: 0.1980 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 0.0170 chunk 111 optimal weight: 0.8980 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10406 Z= 0.202 Angle : 0.670 10.255 14142 Z= 0.332 Chirality : 0.043 0.184 1718 Planarity : 0.004 0.042 1760 Dihedral : 4.018 18.847 1416 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.52 % Favored : 94.40 % Rotamer: Outliers : 1.25 % Allowed : 29.14 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.03 (0.24), residues: 1322 helix: 0.13 (0.18), residues: 854 sheet: -1.52 (1.07), residues: 36 loop : -2.17 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 482 HIS 0.002 0.000 HIS B 375 PHE 0.038 0.001 PHE A 385 TYR 0.026 0.001 TYR B 105 ARG 0.012 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 308 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 314 average time/residue: 0.2648 time to fit residues: 111.6494 Evaluate side-chains 297 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 290 time to evaluate : 1.249 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2717 time to fit residues: 3.9552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 93 optimal weight: 8.9990 chunk 36 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 76 optimal weight: 0.0370 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 457 ASN A 656 HIS A 684 GLN A 728 HIS B 241 ASN ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 10406 Z= 0.250 Angle : 0.701 12.825 14142 Z= 0.349 Chirality : 0.045 0.256 1718 Planarity : 0.004 0.042 1760 Dihedral : 4.107 20.580 1416 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.05 % Favored : 93.87 % Rotamer: Outliers : 1.16 % Allowed : 29.50 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.08 (0.24), residues: 1322 helix: 0.12 (0.18), residues: 852 sheet: -1.50 (1.07), residues: 36 loop : -2.26 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 518 HIS 0.004 0.001 HIS A 656 PHE 0.046 0.002 PHE B 394 TYR 0.026 0.002 TYR B 105 ARG 0.011 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 307 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 314 average time/residue: 0.2543 time to fit residues: 108.0220 Evaluate side-chains 296 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 292 time to evaluate : 1.147 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0992 time to fit residues: 2.3858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 121 optimal weight: 0.0050 chunk 104 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 32 optimal weight: 0.0050 overall best weight: 0.4408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN B 160 HIS B 241 ASN ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 ASN B 656 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10406 Z= 0.230 Angle : 0.713 12.058 14142 Z= 0.357 Chirality : 0.045 0.267 1718 Planarity : 0.004 0.039 1760 Dihedral : 4.157 20.828 1416 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.05 % Favored : 93.87 % Rotamer: Outliers : 0.98 % Allowed : 30.21 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.06 (0.24), residues: 1322 helix: 0.13 (0.18), residues: 852 sheet: -1.37 (1.09), residues: 36 loop : -2.25 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 482 HIS 0.014 0.001 HIS B 160 PHE 0.032 0.001 PHE A 385 TYR 0.025 0.002 TYR B 105 ARG 0.011 0.001 ARG B 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 303 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 308 average time/residue: 0.2646 time to fit residues: 109.6822 Evaluate side-chains 305 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 301 time to evaluate : 1.201 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3084 time to fit residues: 3.1862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.0270 chunk 15 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 75 optimal weight: 0.0980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 656 HIS ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.121385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.102346 restraints weight = 17827.041| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.82 r_work: 0.3243 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10406 Z= 0.240 Angle : 0.721 11.016 14142 Z= 0.365 Chirality : 0.045 0.235 1718 Planarity : 0.004 0.040 1760 Dihedral : 4.178 19.688 1416 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.35 % Favored : 93.57 % Rotamer: Outliers : 0.89 % Allowed : 31.28 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.05 (0.24), residues: 1322 helix: 0.13 (0.18), residues: 854 sheet: -1.44 (1.09), residues: 36 loop : -2.25 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 518 HIS 0.011 0.001 HIS B 656 PHE 0.048 0.002 PHE B 394 TYR 0.024 0.002 TYR B 105 ARG 0.009 0.001 ARG B 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3047.03 seconds wall clock time: 55 minutes 38.39 seconds (3338.39 seconds total)