Starting phenix.real_space_refine on Fri Mar 15 00:39:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzn_35089/03_2024/8hzn_35089.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzn_35089/03_2024/8hzn_35089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzn_35089/03_2024/8hzn_35089.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzn_35089/03_2024/8hzn_35089.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzn_35089/03_2024/8hzn_35089.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzn_35089/03_2024/8hzn_35089.pdb" } resolution = 3.25 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 42 5.16 5 Cl 2 4.86 5 C 6656 2.51 5 N 1684 2.21 5 O 1816 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 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 484": "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 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 303": "OE1" <-> "OE2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 484": "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 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10200 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.69, per 1000 atoms: 0.56 Number of scatterers: 10200 At special positions: 0 Unit cell: (86.818, 127.612, 117.152, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 42 16.00 O 1816 8.00 N 1684 7.00 C 6656 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: 4.16 Conformation dependent library (CDL) restraints added in 1.9 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... Secondary structure from input PDB file: 64 helices and 7 sheets defined 67.6% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.527A pdb=" N CYS A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 69 removed outlier: 3.873A pdb=" N ALA A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 75 removed outlier: 4.028A pdb=" N TRP A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 75 " --> pdb=" O ILE A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 75' Processing helix chain 'A' and resid 79 through 106 removed outlier: 4.870A pdb=" N LEU A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 120 removed outlier: 3.881A pdb=" N GLY A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 141 through 156 Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.838A pdb=" N HIS A 160 " --> pdb=" O PRO A 157 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 161 " --> pdb=" O ASP A 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 161' Processing helix chain 'A' and resid 179 through 206 removed outlier: 3.987A pdb=" N ALA A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 215 removed outlier: 3.599A pdb=" N VAL A 212 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR A 214 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 241 Processing helix chain 'A' and resid 251 through 263 Processing helix chain 'A' and resid 268 through 292 Processing helix chain 'A' and resid 301 through 317 removed outlier: 3.635A pdb=" N ALA A 317 " --> pdb=" O ILE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 374 Processing helix chain 'A' and resid 380 through 397 removed outlier: 3.765A pdb=" N GLU A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 416 removed outlier: 3.689A pdb=" N VAL A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A 414 " --> pdb=" O THR A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 437 removed outlier: 3.518A pdb=" N VAL A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 430 " --> pdb=" O ILE A 426 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 431 " --> pdb=" O SER A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 446 through 458 removed outlier: 3.799A pdb=" N LEU A 450 " --> pdb=" O GLN A 446 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 464 through 466 No H-bonds generated for 'chain 'A' and resid 464 through 466' Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 475 through 492 removed outlier: 3.547A pdb=" N ALA A 479 " --> pdb=" O ASN A 475 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE A 490 " --> pdb=" O CYS A 486 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 515 removed outlier: 3.552A pdb=" N LEU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 571 Processing helix chain 'A' and resid 573 through 595 removed outlier: 3.814A pdb=" N TYR A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 686 removed outlier: 3.784A pdb=" N SER A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 706 removed outlier: 3.715A pdb=" N LYS A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 718 removed outlier: 3.557A pdb=" N ARG A 717 " --> pdb=" O ARG A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 736 removed outlier: 3.830A pdb=" N ALA A 725 " --> pdb=" O THR A 721 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 726 " --> pdb=" O VAL A 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.588A pdb=" N ALA B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 69 removed outlier: 3.757A pdb=" N ALA B 61 " --> pdb=" O SER B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 removed outlier: 4.021A pdb=" N TRP B 74 " --> pdb=" O PRO B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 105 removed outlier: 3.537A pdb=" N SER B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 92 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 110 Processing helix chain 'B' and resid 113 through 127 removed outlier: 3.984A pdb=" N LEU B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 141 through 156 removed outlier: 3.627A pdb=" N VAL B 151 " --> pdb=" O MET B 147 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.615A pdb=" N HIS B 160 " --> pdb=" O PRO B 157 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 161 " --> pdb=" O ASP B 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 157 through 161' Processing helix chain 'B' and resid 180 through 206 removed outlier: 3.896A pdb=" N ALA B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 215 removed outlier: 3.630A pdb=" N VAL B 212 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR B 214 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 241 removed outlier: 3.728A pdb=" N ILE B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 268 through 292 removed outlier: 3.534A pdb=" N THR B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 317 removed outlier: 3.503A pdb=" N ALA B 317 " --> pdb=" O ILE B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 376 removed outlier: 3.763A pdb=" N SER B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR B 361 " --> pdb=" O ALA B 357 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS B 374 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS B 375 " --> pdb=" O TYR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 397 removed outlier: 3.941A pdb=" N GLU B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 397 " --> pdb=" O VAL B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 416 removed outlier: 3.651A pdb=" N VAL B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 437 removed outlier: 3.613A pdb=" N VAL B 436 " --> pdb=" O MET B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 443 Processing helix chain 'B' and resid 446 through 458 removed outlier: 3.783A pdb=" N LEU B 450 " --> pdb=" O GLN B 446 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 467 through 474 Processing helix chain 'B' and resid 475 through 492 removed outlier: 3.554A pdb=" N ALA B 479 " --> pdb=" O ASN B 475 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE B 490 " --> pdb=" O CYS B 486 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 492 " --> pdb=" O MET B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 515 removed outlier: 3.546A pdb=" N LEU B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 499 " --> pdb=" O ASP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 571 Processing helix chain 'B' and resid 573 through 595 removed outlier: 3.835A pdb=" N TYR B 578 " --> pdb=" O ALA B 574 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG B 587 " --> pdb=" O LYS B 583 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE B 588 " --> pdb=" O ALA B 584 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS B 593 " --> pdb=" O GLN B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 685 removed outlier: 4.617A pdb=" N SER B 675 " --> pdb=" O VAL B 671 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 676 " --> pdb=" O GLY B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 706 removed outlier: 3.990A pdb=" N LYS B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 718 removed outlier: 3.556A pdb=" N ARG B 717 " --> pdb=" O ARG B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 736 removed outlier: 3.732A pdb=" N ALA B 725 " --> pdb=" O THR B 721 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 726 " --> pdb=" O VAL B 722 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 25 removed outlier: 3.618A pdb=" N VAL A 22 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL B 22 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA3, first strand: chain 'A' and resid 522 through 523 Processing sheet with id=AA4, first strand: chain 'A' and resid 545 through 549 removed outlier: 6.550A pdb=" N LYS A 546 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ASP A 661 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU A 548 " --> pdb=" O ASP A 661 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 138 through 139 Processing sheet with id=AA6, first strand: chain 'B' and resid 522 through 523 Processing sheet with id=AA7, first strand: chain 'B' and resid 545 through 549 removed outlier: 6.604A pdb=" N LYS B 546 " --> pdb=" O VAL B 659 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ASP B 661 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU B 548 " --> pdb=" O ASP B 661 " (cutoff:3.500A) 575 hydrogen bonds defined for protein. 1677 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: 3.14 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3214 1.34 - 1.46: 2258 1.46 - 1.58: 4864 1.58 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 10400 Sorted by residual: bond pdb=" CA LEU B 162 " pdb=" CB LEU B 162 " ideal model delta sigma weight residual 1.526 1.537 -0.011 1.25e-02 6.40e+03 7.62e-01 bond pdb=" CA PHE A 121 " pdb=" C PHE A 121 " ideal model delta sigma weight residual 1.519 1.528 -0.009 1.01e-02 9.80e+03 7.28e-01 bond pdb=" CA ASP A 669 " pdb=" C ASP A 669 " ideal model delta sigma weight residual 1.532 1.524 0.008 9.60e-03 1.09e+04 7.22e-01 bond pdb=" CA ASP B 669 " pdb=" C ASP B 669 " ideal model delta sigma weight residual 1.532 1.524 0.008 9.60e-03 1.09e+04 7.18e-01 bond pdb=" C VAL A 653 " pdb=" N PRO A 654 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.05e-01 ... (remaining 10395 not shown) Histogram of bond angle deviations from ideal: 100.81 - 107.45: 302 107.45 - 114.09: 6177 114.09 - 120.73: 4426 120.73 - 127.37: 3157 127.37 - 134.01: 74 Bond angle restraints: 14136 Sorted by residual: angle pdb=" N VAL A 699 " pdb=" CA VAL A 699 " pdb=" C VAL A 699 " ideal model delta sigma weight residual 111.81 108.71 3.10 8.60e-01 1.35e+00 1.30e+01 angle pdb=" N VAL B 699 " pdb=" CA VAL B 699 " pdb=" C VAL B 699 " ideal model delta sigma weight residual 111.81 108.83 2.98 8.60e-01 1.35e+00 1.20e+01 angle pdb=" N ILE B 686 " pdb=" CA ILE B 686 " pdb=" C ILE B 686 " ideal model delta sigma weight residual 111.91 109.18 2.73 8.90e-01 1.26e+00 9.39e+00 angle pdb=" N ILE A 686 " pdb=" CA ILE A 686 " pdb=" C ILE A 686 " ideal model delta sigma weight residual 111.91 109.22 2.69 8.90e-01 1.26e+00 9.11e+00 angle pdb=" C ASP A 669 " pdb=" N VAL A 670 " pdb=" CA VAL A 670 " ideal model delta sigma weight residual 121.97 126.31 -4.34 1.80e+00 3.09e-01 5.81e+00 ... (remaining 14131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 5982 16.84 - 33.68: 163 33.68 - 50.52: 28 50.52 - 67.36: 4 67.36 - 84.20: 5 Dihedral angle restraints: 6182 sinusoidal: 2346 harmonic: 3836 Sorted by residual: dihedral pdb=" N LYS A 681 " pdb=" CA LYS A 681 " pdb=" CB LYS A 681 " pdb=" CG LYS A 681 " ideal model delta sinusoidal sigma weight residual -180.00 -120.67 -59.33 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ASP A 669 " pdb=" C ASP A 669 " pdb=" N VAL A 670 " pdb=" CA VAL A 670 " ideal model delta harmonic sigma weight residual -180.00 -164.65 -15.35 0 5.00e+00 4.00e-02 9.43e+00 dihedral pdb=" N LEU A 668 " pdb=" CA LEU A 668 " pdb=" CB LEU A 668 " pdb=" CG LEU A 668 " ideal model delta sinusoidal sigma weight residual -180.00 -126.82 -53.18 3 1.50e+01 4.44e-03 9.18e+00 ... (remaining 6179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 919 0.023 - 0.047: 438 0.047 - 0.070: 241 0.070 - 0.093: 77 0.093 - 0.117: 43 Chirality restraints: 1718 Sorted by residual: chirality pdb=" CA ILE B 379 " pdb=" N ILE B 379 " pdb=" C ILE B 379 " pdb=" CB ILE B 379 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.39e-01 chirality pdb=" CA VAL A 524 " pdb=" N VAL A 524 " pdb=" C VAL A 524 " pdb=" CB VAL A 524 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.31e-01 chirality pdb=" CA VAL A 688 " pdb=" N VAL A 688 " pdb=" C VAL A 688 " pdb=" CB VAL A 688 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.30e-01 ... (remaining 1715 not shown) Planarity restraints: 1758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 552 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO B 553 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 553 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 553 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 552 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO A 553 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 553 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 553 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 111 " 0.023 5.00e-02 4.00e+02 3.44e-02 1.90e+00 pdb=" N PRO A 112 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " 0.019 5.00e-02 4.00e+02 ... (remaining 1755 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 401 2.73 - 3.27: 11150 3.27 - 3.81: 16502 3.81 - 4.36: 20154 4.36 - 4.90: 33850 Nonbonded interactions: 82057 Sorted by model distance: nonbonded pdb=" OH TYR A 78 " pdb=" OD2 ASP A 87 " model vdw 2.182 2.440 nonbonded pdb=" O ASP A 669 " pdb=" N GLY A 672 " model vdw 2.242 2.520 nonbonded pdb=" OH TYR A 118 " pdb=" O GLY A 334 " model vdw 2.247 2.440 nonbonded pdb=" O THR A 485 " pdb=" OG SER A 489 " model vdw 2.261 2.440 nonbonded pdb=" OD1 ASN B 475 " pdb=" OG1 THR B 477 " model vdw 2.272 2.440 ... (remaining 82052 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.030 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 30.710 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 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 0.024 10400 Z= 0.116 Angle : 0.492 7.088 14136 Z= 0.300 Chirality : 0.037 0.117 1718 Planarity : 0.003 0.035 1758 Dihedral : 8.512 84.204 3710 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.22 % Favored : 94.70 % Rotamer: Outliers : 3.12 % Allowed : 4.01 % Favored : 92.87 % 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: -3.99 (0.19), residues: 1322 helix: -2.17 (0.14), residues: 876 sheet: -2.92 (0.77), residues: 34 loop : -3.36 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 83 HIS 0.001 0.000 HIS A 723 PHE 0.009 0.001 PHE A 555 TYR 0.008 0.001 TYR A 127 ARG 0.001 0.000 ARG B 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 411 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 376 time to evaluate : 1.229 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: A 38 ARG cc_start: 0.7730 (mtp-110) cc_final: 0.7165 (mtp-110) REVERT: A 66 LYS cc_start: 0.8511 (tppt) cc_final: 0.8077 (tptp) REVERT: A 160 HIS cc_start: 0.7819 (t-90) cc_final: 0.7602 (t-170) REVERT: A 258 ILE cc_start: 0.8499 (mm) cc_final: 0.8098 (mm) REVERT: A 273 ILE cc_start: 0.8310 (mt) cc_final: 0.8072 (tp) REVERT: A 318 ASN cc_start: 0.6901 (t0) cc_final: 0.6696 (t0) REVERT: A 350 LEU cc_start: 0.6272 (OUTLIER) cc_final: 0.5837 (tm) REVERT: A 369 LYS cc_start: 0.7845 (mmtt) cc_final: 0.7399 (mmtt) REVERT: A 385 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.7460 (t80) REVERT: A 394 PHE cc_start: 0.8222 (t80) cc_final: 0.7248 (t80) REVERT: A 398 PHE cc_start: 0.6554 (m-80) cc_final: 0.6246 (m-80) REVERT: A 432 MET cc_start: 0.7964 (tpt) cc_final: 0.7697 (tpp) REVERT: A 464 GLN cc_start: 0.7704 (mt0) cc_final: 0.7046 (mt0) REVERT: A 475 ASN cc_start: 0.7767 (t0) cc_final: 0.6663 (t0) REVERT: A 478 ASP cc_start: 0.6770 (m-30) cc_final: 0.6337 (m-30) REVERT: A 486 CYS cc_start: 0.8410 (t) cc_final: 0.8181 (t) REVERT: A 569 THR cc_start: 0.8596 (t) cc_final: 0.8192 (m) REVERT: A 580 LYS cc_start: 0.7866 (mmtt) cc_final: 0.7422 (mmmm) REVERT: A 684 GLN cc_start: 0.7917 (tp40) cc_final: 0.7698 (tp40) REVERT: A 717 ARG cc_start: 0.8563 (ttm-80) cc_final: 0.8279 (ttm170) REVERT: B 66 LYS cc_start: 0.8505 (tppt) cc_final: 0.8123 (tppt) REVERT: B 78 TYR cc_start: 0.6781 (t80) cc_final: 0.6320 (t80) REVERT: B 87 ASP cc_start: 0.7044 (m-30) cc_final: 0.6580 (m-30) REVERT: B 114 GLN cc_start: 0.7744 (tt0) cc_final: 0.7510 (pt0) REVERT: B 246 ASN cc_start: 0.8239 (p0) cc_final: 0.8037 (p0) REVERT: B 268 ASN cc_start: 0.8327 (t0) cc_final: 0.7490 (t0) REVERT: B 271 ASP cc_start: 0.7882 (m-30) cc_final: 0.7245 (m-30) REVERT: B 287 GLU cc_start: 0.7275 (tp30) cc_final: 0.6919 (tp30) REVERT: B 290 ASP cc_start: 0.7559 (t0) cc_final: 0.7345 (t0) REVERT: B 303 GLU cc_start: 0.7401 (mp0) cc_final: 0.6897 (mp0) REVERT: B 305 ILE cc_start: 0.8590 (tp) cc_final: 0.8219 (pt) REVERT: B 318 ASN cc_start: 0.6926 (t0) cc_final: 0.6521 (t0) REVERT: B 320 GLU cc_start: 0.6331 (tp30) cc_final: 0.6119 (tp30) REVERT: B 350 LEU cc_start: 0.6532 (OUTLIER) cc_final: 0.6179 (tm) REVERT: B 355 SER cc_start: 0.8717 (m) cc_final: 0.8092 (p) REVERT: B 394 PHE cc_start: 0.8319 (t80) cc_final: 0.7527 (t80) REVERT: B 446 GLN cc_start: 0.8192 (mt0) cc_final: 0.7889 (mt0) REVERT: B 464 GLN cc_start: 0.8030 (mt0) cc_final: 0.7336 (mt0) REVERT: B 475 ASN cc_start: 0.7764 (t0) cc_final: 0.6830 (t0) REVERT: B 478 ASP cc_start: 0.6896 (m-30) cc_final: 0.6325 (m-30) REVERT: B 580 LYS cc_start: 0.7676 (mmtt) cc_final: 0.7274 (mmmm) REVERT: B 717 ARG cc_start: 0.8420 (ttm-80) cc_final: 0.7987 (ttm170) REVERT: B 727 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.7982 (mt) outliers start: 35 outliers final: 11 residues processed: 402 average time/residue: 0.2532 time to fit residues: 136.2483 Evaluate side-chains 315 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 300 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 727 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 119 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 413 GLN A 474 GLN A 514 GLN A 656 HIS A 705 GLN A 723 HIS A 731 ASN B 34 GLN B 160 HIS B 262 GLN B 464 GLN B 514 GLN B 656 HIS B 705 GLN B 728 HIS B 730 GLN B 731 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10400 Z= 0.288 Angle : 0.647 8.191 14136 Z= 0.331 Chirality : 0.044 0.182 1718 Planarity : 0.005 0.048 1758 Dihedral : 5.924 79.163 1444 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.81 % Favored : 93.12 % Rotamer: Outliers : 3.48 % Allowed : 13.28 % Favored : 83.24 % 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: -1.97 (0.22), residues: 1322 helix: -0.43 (0.17), residues: 872 sheet: -2.68 (0.87), residues: 36 loop : -2.99 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 518 HIS 0.009 0.002 HIS B 656 PHE 0.022 0.002 PHE A 130 TYR 0.025 0.002 TYR B 361 ARG 0.005 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 357 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 318 time to evaluate : 1.126 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: A 66 LYS cc_start: 0.8540 (tppt) cc_final: 0.8140 (tptp) REVERT: A 160 HIS cc_start: 0.7955 (t-90) cc_final: 0.7742 (t70) REVERT: A 258 ILE cc_start: 0.8562 (mm) cc_final: 0.8275 (mm) REVERT: A 273 ILE cc_start: 0.8354 (mt) cc_final: 0.8102 (tp) REVERT: A 318 ASN cc_start: 0.7399 (t0) cc_final: 0.7098 (t0) REVERT: A 348 ASP cc_start: 0.5558 (OUTLIER) cc_final: 0.4281 (p0) REVERT: A 369 LYS cc_start: 0.7998 (mmtt) cc_final: 0.7540 (mmpt) REVERT: A 371 TYR cc_start: 0.8110 (m-80) cc_final: 0.7749 (m-80) REVERT: A 394 PHE cc_start: 0.8309 (t80) cc_final: 0.7447 (t80) REVERT: A 398 PHE cc_start: 0.6748 (m-80) cc_final: 0.6438 (m-80) REVERT: A 432 MET cc_start: 0.7699 (tpt) cc_final: 0.7357 (tpp) REVERT: A 436 VAL cc_start: 0.8437 (p) cc_final: 0.8151 (m) REVERT: A 486 CYS cc_start: 0.8358 (t) cc_final: 0.8031 (t) REVERT: A 569 THR cc_start: 0.8668 (t) cc_final: 0.8376 (t) REVERT: A 573 ASP cc_start: 0.7286 (t0) cc_final: 0.7076 (t0) REVERT: A 580 LYS cc_start: 0.7793 (mmtt) cc_final: 0.7322 (mmmm) REVERT: A 684 GLN cc_start: 0.7836 (tp40) cc_final: 0.7621 (tp-100) REVERT: B 27 TYR cc_start: 0.7694 (m-10) cc_final: 0.7399 (m-10) REVERT: B 66 LYS cc_start: 0.8745 (tppt) cc_final: 0.8232 (tppt) REVERT: B 246 ASN cc_start: 0.8246 (p0) cc_final: 0.8003 (p0) REVERT: B 250 ILE cc_start: 0.8410 (mm) cc_final: 0.8045 (tp) REVERT: B 268 ASN cc_start: 0.8408 (t0) cc_final: 0.7291 (t0) REVERT: B 271 ASP cc_start: 0.7680 (m-30) cc_final: 0.7108 (m-30) REVERT: B 303 GLU cc_start: 0.7315 (mp0) cc_final: 0.7105 (mp0) REVERT: B 305 ILE cc_start: 0.8412 (tp) cc_final: 0.8163 (pt) REVERT: B 318 ASN cc_start: 0.7497 (t0) cc_final: 0.7297 (t0) REVERT: B 350 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6362 (tm) REVERT: B 361 TYR cc_start: 0.8369 (t80) cc_final: 0.7746 (t80) REVERT: B 366 SER cc_start: 0.8655 (t) cc_final: 0.8352 (p) REVERT: B 369 LYS cc_start: 0.8264 (mmtt) cc_final: 0.8041 (mmtt) REVERT: B 377 TYR cc_start: 0.7512 (p90) cc_final: 0.7299 (p90) REVERT: B 385 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.7838 (m-80) REVERT: B 394 PHE cc_start: 0.8364 (t80) cc_final: 0.7772 (t80) REVERT: B 398 PHE cc_start: 0.7166 (m-80) cc_final: 0.6762 (m-80) REVERT: B 414 GLU cc_start: 0.7271 (tm-30) cc_final: 0.6793 (tm-30) REVERT: B 475 ASN cc_start: 0.7594 (t0) cc_final: 0.6510 (t0) REVERT: B 478 ASP cc_start: 0.6763 (m-30) cc_final: 0.6229 (m-30) REVERT: B 528 ASP cc_start: 0.8345 (p0) cc_final: 0.8137 (p0) REVERT: B 556 TYR cc_start: 0.8630 (p90) cc_final: 0.8057 (p90) REVERT: B 580 LYS cc_start: 0.7778 (mmtt) cc_final: 0.7351 (mmmm) REVERT: B 687 ASP cc_start: 0.7678 (t0) cc_final: 0.7477 (t0) REVERT: B 717 ARG cc_start: 0.8424 (ttm-80) cc_final: 0.8002 (ttm170) outliers start: 39 outliers final: 18 residues processed: 338 average time/residue: 0.2609 time to fit residues: 116.9126 Evaluate side-chains 307 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 286 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 541 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 33 optimal weight: 0.2980 chunk 120 optimal weight: 0.5980 chunk 129 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 119 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 96 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN A 656 HIS A 731 ASN B 160 HIS B 413 GLN B 656 HIS B 731 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10400 Z= 0.219 Angle : 0.579 7.050 14136 Z= 0.298 Chirality : 0.042 0.147 1718 Planarity : 0.004 0.043 1758 Dihedral : 5.473 80.218 1437 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.98 % Favored : 93.95 % Rotamer: Outliers : 3.92 % Allowed : 15.78 % Favored : 80.30 % 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: -1.16 (0.23), residues: 1322 helix: 0.25 (0.17), residues: 872 sheet: -2.28 (0.94), residues: 36 loop : -2.80 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 482 HIS 0.009 0.001 HIS B 656 PHE 0.017 0.001 PHE A 121 TYR 0.020 0.002 TYR B 377 ARG 0.006 0.000 ARG A 714 *********************** 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 334 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 290 time to evaluate : 1.214 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: A 21 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8315 (p) REVERT: A 66 LYS cc_start: 0.8580 (tppt) cc_final: 0.8248 (tptp) REVERT: A 114 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7448 (pt0) REVERT: A 250 ILE cc_start: 0.8355 (mm) cc_final: 0.7998 (tp) REVERT: A 258 ILE cc_start: 0.8590 (mm) cc_final: 0.8318 (mm) REVERT: A 273 ILE cc_start: 0.8357 (mt) cc_final: 0.8093 (tp) REVERT: A 314 SER cc_start: 0.8618 (t) cc_final: 0.8417 (p) REVERT: A 318 ASN cc_start: 0.7449 (t0) cc_final: 0.7089 (t0) REVERT: A 348 ASP cc_start: 0.5618 (OUTLIER) cc_final: 0.4255 (p0) REVERT: A 369 LYS cc_start: 0.7910 (mmtt) cc_final: 0.7411 (mmtt) REVERT: A 371 TYR cc_start: 0.8020 (m-80) cc_final: 0.7644 (m-80) REVERT: A 394 PHE cc_start: 0.8327 (t80) cc_final: 0.7496 (t80) REVERT: A 398 PHE cc_start: 0.6729 (m-80) cc_final: 0.6404 (m-80) REVERT: A 405 THR cc_start: 0.8300 (p) cc_final: 0.7986 (t) REVERT: A 432 MET cc_start: 0.7749 (tpt) cc_final: 0.7366 (tpp) REVERT: A 436 VAL cc_start: 0.8481 (p) cc_final: 0.8188 (m) REVERT: A 475 ASN cc_start: 0.7308 (t0) cc_final: 0.6220 (t0) REVERT: A 486 CYS cc_start: 0.8356 (t) cc_final: 0.8005 (t) REVERT: A 569 THR cc_start: 0.8667 (t) cc_final: 0.8238 (m) REVERT: A 573 ASP cc_start: 0.7308 (t0) cc_final: 0.7084 (t0) REVERT: A 580 LYS cc_start: 0.7837 (mmtt) cc_final: 0.7369 (mmmm) REVERT: A 702 LYS cc_start: 0.8134 (tppt) cc_final: 0.7901 (tppt) REVERT: B 23 SER cc_start: 0.8656 (OUTLIER) cc_final: 0.8256 (p) REVERT: B 27 TYR cc_start: 0.7851 (m-10) cc_final: 0.7482 (m-10) REVERT: B 66 LYS cc_start: 0.8645 (tppt) cc_final: 0.8098 (tppt) REVERT: B 153 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8299 (mt) REVERT: B 246 ASN cc_start: 0.8268 (p0) cc_final: 0.8047 (p0) REVERT: B 250 ILE cc_start: 0.8516 (mm) cc_final: 0.8158 (tp) REVERT: B 268 ASN cc_start: 0.8302 (t0) cc_final: 0.7844 (t0) REVERT: B 289 ASN cc_start: 0.8054 (t0) cc_final: 0.7677 (t0) REVERT: B 303 GLU cc_start: 0.7360 (mp0) cc_final: 0.7074 (mp0) REVERT: B 305 ILE cc_start: 0.8421 (tp) cc_final: 0.8151 (pt) REVERT: B 318 ASN cc_start: 0.7549 (t0) cc_final: 0.7136 (t0) REVERT: B 348 ASP cc_start: 0.6026 (OUTLIER) cc_final: 0.5016 (p0) REVERT: B 350 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6470 (tm) REVERT: B 361 TYR cc_start: 0.8432 (t80) cc_final: 0.7694 (t80) REVERT: B 377 TYR cc_start: 0.7671 (p90) cc_final: 0.7438 (p90) REVERT: B 385 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.7806 (m-80) REVERT: B 394 PHE cc_start: 0.8318 (t80) cc_final: 0.7622 (t80) REVERT: B 398 PHE cc_start: 0.7163 (m-80) cc_final: 0.6623 (m-80) REVERT: B 414 GLU cc_start: 0.7165 (tm-30) cc_final: 0.6788 (tm-30) REVERT: B 475 ASN cc_start: 0.7227 (t0) cc_final: 0.6542 (t0) REVERT: B 556 TYR cc_start: 0.8600 (p90) cc_final: 0.8130 (p90) REVERT: B 573 ASP cc_start: 0.7223 (t0) cc_final: 0.6806 (t0) REVERT: B 580 LYS cc_start: 0.7764 (mmtt) cc_final: 0.7328 (mmmm) REVERT: B 687 ASP cc_start: 0.7655 (t0) cc_final: 0.7406 (t0) REVERT: B 717 ARG cc_start: 0.8443 (ttm-80) cc_final: 0.8039 (ttm170) outliers start: 44 outliers final: 20 residues processed: 317 average time/residue: 0.2658 time to fit residues: 111.4000 Evaluate side-chains 318 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 290 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 541 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.88 > 50: distance: 49 - 55: 12.641 distance: 55 - 56: 22.070 distance: 56 - 57: 13.161 distance: 56 - 59: 12.935 distance: 57 - 58: 17.394 distance: 57 - 64: 24.652 distance: 59 - 60: 15.400 distance: 61 - 62: 8.138 distance: 62 - 63: 9.279 distance: 64 - 65: 8.147 distance: 65 - 66: 17.350 distance: 66 - 67: 21.351 distance: 66 - 72: 5.489 distance: 68 - 69: 16.498 distance: 69 - 70: 22.486 distance: 69 - 71: 16.945 distance: 72 - 73: 17.903 distance: 73 - 74: 13.201 distance: 73 - 76: 21.606 distance: 74 - 75: 37.066 distance: 74 - 80: 4.966 distance: 76 - 77: 17.923 distance: 77 - 78: 23.622 distance: 77 - 79: 30.247 distance: 80 - 81: 15.761 distance: 81 - 82: 13.818 distance: 81 - 84: 13.719 distance: 82 - 83: 5.239 distance: 82 - 89: 44.237 distance: 84 - 85: 15.965 distance: 85 - 86: 7.160 distance: 86 - 87: 7.207 distance: 86 - 88: 7.439 distance: 89 - 90: 17.303 distance: 90 - 91: 15.019 distance: 90 - 93: 22.378 distance: 91 - 92: 17.225 distance: 91 - 98: 4.318 distance: 93 - 94: 15.924 distance: 94 - 95: 19.601 distance: 95 - 96: 13.206 distance: 95 - 97: 17.867 distance: 98 - 99: 22.877 distance: 98 - 104: 30.063 distance: 99 - 100: 7.734 distance: 99 - 102: 30.811 distance: 100 - 105: 9.697 distance: 102 - 103: 11.491 distance: 103 - 104: 32.109 distance: 105 - 106: 5.285 distance: 106 - 107: 7.634 distance: 106 - 109: 14.347 distance: 107 - 108: 7.904 distance: 107 - 114: 7.358 distance: 109 - 110: 10.246 distance: 110 - 111: 14.357 distance: 111 - 112: 12.270 distance: 111 - 113: 9.504 distance: 114 - 115: 16.060 distance: 115 - 116: 6.072 distance: 116 - 117: 21.019 distance: 116 - 118: 13.885 distance: 118 - 119: 10.273 distance: 119 - 120: 3.312 distance: 119 - 122: 11.309 distance: 120 - 121: 20.591 distance: 120 - 125: 15.359 distance: 122 - 123: 10.681 distance: 122 - 124: 18.957 distance: 125 - 126: 6.243 distance: 126 - 127: 13.145 distance: 126 - 129: 21.682 distance: 127 - 128: 21.945 distance: 127 - 134: 15.808 distance: 129 - 130: 28.315 distance: 130 - 131: 7.343 distance: 131 - 132: 10.874 distance: 132 - 133: 16.758