Starting phenix.real_space_refine on Thu Jun 27 08:47:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gce_29932/06_2024/8gce_29932.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gce_29932/06_2024/8gce_29932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gce_29932/06_2024/8gce_29932.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gce_29932/06_2024/8gce_29932.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gce_29932/06_2024/8gce_29932.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gce_29932/06_2024/8gce_29932.pdb" } resolution = 3.12 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= 0.049 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: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 Mg 1 5.21 5 S 98 5.16 5 C 7697 2.51 5 N 2116 2.21 5 O 2425 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 683": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 12343 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7007 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 912, 6966 Classifications: {'peptide': 912} Link IDs: {'PCIS': 2, 'PTRANS': 59, 'TRANS': 850} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 912, 6966 Classifications: {'peptide': 912} Link IDs: {'PCIS': 2, 'PTRANS': 59, 'TRANS': 850} Chain breaks: 2 bond proxies already assigned to first conformer: 7082 Chain: "B" Number of atoms: 5195 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 676, 5191 Classifications: {'peptide': 676} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 643} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 676, 5191 Classifications: {'peptide': 676} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 643} Chain breaks: 2 bond proxies already assigned to first conformer: 5277 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 32 Unusual residues: {' CA': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 72 residue: pdb=" N AGLN A 177 " occ=0.51 ... (16 atoms not shown) pdb=" NE2BGLN A 177 " occ=0.49 residue: pdb=" N AARG A 276 " occ=0.92 ... (20 atoms not shown) pdb=" NH2BARG A 276 " occ=0.08 residue: pdb=" N AHIS A 587 " occ=0.40 ... (18 atoms not shown) pdb=" NE2BHIS A 587 " occ=0.60 residue: pdb=" N PRO B 605 " occ=0.71 ... (5 atoms not shown) pdb=" CD PRO B 605 " occ=0.71 residue: pdb=" N ASP B 606 " occ=0.49 ... (6 atoms not shown) pdb=" OD2 ASP B 606 " occ=0.49 residue: pdb=" N ALA B 607 " occ=0.70 ... (3 atoms not shown) pdb=" CB ALA B 607 " occ=0.70 residue: pdb=" N CYS B 608 " occ=0.50 ... (4 atoms not shown) pdb=" SG CYS B 608 " occ=0.50 residue: pdb=" N THR B 609 " occ=0.56 ... (5 atoms not shown) pdb=" CG2 THR B 609 " occ=0.56 residue: pdb=" N PHE B 610 " occ=0.93 ... (9 atoms not shown) pdb=" CZ PHE B 610 " occ=0.93 residue: pdb=" N LYS B 611 " occ=0.77 ... (7 atoms not shown) pdb=" NZ LYS B 611 " occ=0.77 residue: pdb=" N LYS B 612 " occ=0.67 ... (7 atoms not shown) pdb=" NZ LYS B 612 " occ=0.67 residue: pdb=" N GLU B 613 " occ=0.76 ... (7 atoms not shown) pdb=" OE2 GLU B 613 " occ=0.76 ... (remaining 60 not shown) Time building chain proxies: 11.86, per 1000 atoms: 0.96 Number of scatterers: 12343 At special positions: 0 Unit cell: (104.86, 123.05, 129.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 98 16.00 Mg 1 11.99 O 2425 8.00 N 2116 7.00 C 7697 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 167 " distance=2.02 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 545 " distance=2.03 Simple disulfide: pdb=" SG CYS A 602 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 674 " - pdb=" SG CYS A 687 " distance=2.04 Simple disulfide: pdb=" SG CYS A 826 " - pdb=" SG CYS A 890 " distance=2.03 Simple disulfide: pdb=" SG CYS A 880 " - pdb=" SG CYS A 885 " distance=2.03 Simple disulfide: pdb=" SG CYS B 5 " - pdb=" SG CYS B 23 " distance=2.03 Simple disulfide: pdb=" SG CYS B 13 " - pdb=" SG CYS B 435 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 38 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 49 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 184 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 386 " distance=2.04 Simple disulfide: pdb=" SG CYS B 406 " - pdb=" SG CYS B 433 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 448 " - pdb=" SG CYS B 460 " distance=2.03 Simple disulfide: pdb=" SG CYS B 462 " - pdb=" SG CYS B 471 " distance=2.03 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 503 " distance=2.03 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 501 " distance=2.03 Simple disulfide: pdb=" SG CYS B 495 " - pdb=" SG CYS B 506 " distance=2.03 Simple disulfide: pdb=" SG CYS B 508 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 523 " - pdb=" SG CYS B 544 " distance=2.03 Simple disulfide: pdb=" SG CYS B 528 " - pdb=" SG CYS B 542 " distance=2.04 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 547 " distance=2.03 Simple disulfide: pdb=" SG CYS B 549 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 560 " - pdb=" SG CYS B 583 " distance=2.03 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 581 " distance=2.02 Simple disulfide: pdb=" SG CYS B 575 " - pdb=" SG CYS B 586 " distance=2.03 Simple disulfide: pdb=" SG CYS B 588 " - pdb=" SG CYS B 598 " distance=2.03 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 655 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 631 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1105 " - " ASN A 15 " " NAG A1106 " - " ASN A 570 " " NAG C 1 " - " ASN B 371 " " NAG D 1 " - " ASN B 320 " " NAG E 1 " - " ASN B 99 " Time building additional restraints: 4.66 Conformation dependent library (CDL) restraints added in 4.3 seconds 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2920 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 25 sheets defined 10.2% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 199 through 204 removed outlier: 3.545A pdb=" N ILE A 203 " --> pdb=" O PRO A 199 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE A 204 " --> pdb=" O VAL A 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 199 through 204' Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.567A pdb=" N GLN A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 9 removed outlier: 3.557A pdb=" N ARG B 8 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY B 9 " --> pdb=" O CYS B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 20 removed outlier: 4.195A pdb=" N SER B 20 " --> pdb=" O CYS B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 47 Processing helix chain 'B' and resid 50 through 52 No H-bonds generated for 'chain 'B' and resid 50 through 52' Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 124 through 132 Processing helix chain 'B' and resid 135 through 143 removed outlier: 3.943A pdb=" N GLN B 141 " --> pdb=" O LYS B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 173 removed outlier: 3.636A pdb=" N LEU B 173 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.948A pdb=" N ASN B 204 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B 208 " --> pdb=" O ASN B 204 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 232 removed outlier: 4.309A pdb=" N ALA B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 258 through 264 removed outlier: 3.642A pdb=" N ARG B 261 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU B 262 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 286 removed outlier: 4.383A pdb=" N THR B 285 " --> pdb=" O SER B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 314 through 319 Processing helix chain 'B' and resid 339 through 354 Processing helix chain 'B' and resid 493 through 497 Processing helix chain 'B' and resid 534 through 538 Processing helix chain 'B' and resid 612 through 617 Processing helix chain 'B' and resid 630 through 635 removed outlier: 4.039A pdb=" N TYR B 634 " --> pdb=" O THR B 630 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N CYS B 635 " --> pdb=" O CYS B 631 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 630 through 635' Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 10 removed outlier: 3.865A pdb=" N THR A 9 " --> pdb=" O VAL A 447 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 removed outlier: 3.612A pdb=" N HIS A 26 " --> pdb=" O ALA A 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 removed outlier: 4.900A pdb=" N VAL A 53 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.399A pdb=" N GLU A 75 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA6, first strand: chain 'A' and resid 256 through 257 removed outlier: 6.522A pdb=" N VAL A 267 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG A 279 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 269 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 293 through 296 removed outlier: 3.810A pdb=" N LEU A 345 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 314 through 315 Processing sheet with id=AA9, first strand: chain 'A' and resid 360 through 364 removed outlier: 5.866A pdb=" N ASP A 373 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A 405 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 521 through 523 removed outlier: 3.672A pdb=" N LEU A 522 " --> pdb=" O PHE A 551 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 551 " --> pdb=" O LEU A 522 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 544 " --> pdb=" O VAL A 491 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A 491 " --> pdb=" O ILE A 544 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR A 494 " --> pdb=" O LYS A 455 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL A 454 " --> pdb=" O VAL A 585 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N AHIS A 587 " --> pdb=" O VAL A 454 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.678A pdb=" N CYS A 473 " --> pdb=" O VAL A 482 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL A 482 " --> pdb=" O CYS A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 530 through 536 removed outlier: 4.143A pdb=" N ASN A 505 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N SER A 572 " --> pdb=" O ASN A 505 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU A 507 " --> pdb=" O ASN A 570 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASN A 570 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLN A 509 " --> pdb=" O SER A 568 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N SER A 568 " --> pdb=" O GLN A 509 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 612 through 615 removed outlier: 3.683A pdb=" N MET A 703 " --> pdb=" O LEU A 633 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 706 " --> pdb=" O HIS A 658 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 648 through 652 removed outlier: 4.232A pdb=" N GLN A 720 " --> pdb=" O HIS A 652 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 749 through 755 removed outlier: 3.581A pdb=" N GLU A 749 " --> pdb=" O HIS A 787 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N HIS A 787 " --> pdb=" O GLU A 749 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG A 751 " --> pdb=" O GLU A 785 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 907 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS A 782 " --> pdb=" O VAL A 905 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 905 " --> pdb=" O HIS A 782 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR A 784 " --> pdb=" O VAL A 903 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 903 " --> pdb=" O TYR A 784 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N MET A 902 " --> pdb=" O PRO A 820 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR A 904 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ILE A 818 " --> pdb=" O THR A 904 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU A 906 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE A 908 " --> pdb=" O TYR A 814 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYR A 814 " --> pdb=" O PHE A 908 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 825 through 829 removed outlier: 4.338A pdb=" N GLN A 825 " --> pdb=" O ASP A 891 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 887 " --> pdb=" O GLN A 829 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU A 894 " --> pdb=" O ASN A 795 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ASN A 795 " --> pdb=" O GLU A 894 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N GLY A 796 " --> pdb=" O SER A 933 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A 933 " --> pdb=" O GLY A 796 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N HIS A 802 " --> pdb=" O HIS A 927 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N HIS A 927 " --> pdb=" O HIS A 802 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 38 through 39 Processing sheet with id=AB9, first strand: chain 'B' and resid 60 through 65 removed outlier: 3.815A pdb=" N ARG B 62 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG B 87 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE B 88 " --> pdb=" O GLN B 428 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N THR B 430 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU B 90 " --> pdb=" O THR B 430 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 414 " --> pdb=" O VAL B 427 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 97 through 102 Processing sheet with id=AC2, first strand: chain 'B' and resid 194 through 197 removed outlier: 5.923A pdb=" N THR B 195 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N PHE B 153 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE B 151 " --> pdb=" O THR B 197 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 499 through 502 Processing sheet with id=AC4, first strand: chain 'B' and resid 540 through 543 Processing sheet with id=AC5, first strand: chain 'B' and resid 581 through 582 Processing sheet with id=AC6, first strand: chain 'B' and resid 638 through 639 removed outlier: 6.184A pdb=" N GLU B 638 " --> pdb=" O LEU B 679 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 655 through 658 removed outlier: 3.673A pdb=" N TYR B 657 " --> pdb=" O VAL B 665 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL B 665 " --> pdb=" O TYR B 657 " (cutoff:3.500A) 244 hydrogen bonds defined for protein. 632 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: 3.78 Time building geometry restraints manager: 5.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2145 1.31 - 1.44: 3267 1.44 - 1.58: 7063 1.58 - 1.71: 1 1.71 - 1.85: 123 Bond restraints: 12599 Sorted by residual: bond pdb=" CA SER A 664 " pdb=" CB SER A 664 " ideal model delta sigma weight residual 1.530 1.363 0.167 1.69e-02 3.50e+03 9.75e+01 bond pdb=" CA LEU A 689 " pdb=" C LEU A 689 " ideal model delta sigma weight residual 1.523 1.422 0.101 1.34e-02 5.57e+03 5.66e+01 bond pdb=" CA ALA A 662 " pdb=" C ALA A 662 " ideal model delta sigma weight residual 1.523 1.429 0.094 1.34e-02 5.57e+03 4.90e+01 bond pdb=" CA ASN A 665 " pdb=" C ASN A 665 " ideal model delta sigma weight residual 1.524 1.427 0.096 1.59e-02 3.96e+03 3.67e+01 bond pdb=" CA ALA A 662 " pdb=" CB ALA A 662 " ideal model delta sigma weight residual 1.530 1.439 0.091 1.69e-02 3.50e+03 2.90e+01 ... (remaining 12594 not shown) Histogram of bond angle deviations from ideal: 81.57 - 94.64: 6 94.64 - 107.71: 659 107.71 - 120.78: 11929 120.78 - 133.85: 4509 133.85 - 146.92: 19 Bond angle restraints: 17122 Sorted by residual: angle pdb=" N GLN A 18 " pdb=" CA GLN A 18 " pdb=" C GLN A 18 " ideal model delta sigma weight residual 110.41 92.07 18.34 1.18e+00 7.18e-01 2.42e+02 angle pdb=" C ASN A 691 " pdb=" N PRO A 692 " pdb=" CA PRO A 692 " ideal model delta sigma weight residual 119.84 101.42 18.42 1.25e+00 6.40e-01 2.17e+02 angle pdb=" C ARG A 661 " pdb=" CA ARG A 661 " pdb=" CB ARG A 661 " ideal model delta sigma weight residual 110.42 81.57 28.85 1.99e+00 2.53e-01 2.10e+02 angle pdb=" N ASN A 665 " pdb=" CA ASN A 665 " pdb=" C ASN A 665 " ideal model delta sigma weight residual 112.97 98.69 14.28 1.06e+00 8.90e-01 1.82e+02 angle pdb=" N LEU A 689 " pdb=" CA LEU A 689 " pdb=" CB LEU A 689 " ideal model delta sigma weight residual 110.49 88.84 21.65 1.69e+00 3.50e-01 1.64e+02 ... (remaining 17117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.51: 7211 24.51 - 49.02: 525 49.02 - 73.53: 72 73.53 - 98.04: 15 98.04 - 122.55: 9 Dihedral angle restraints: 7832 sinusoidal: 3269 harmonic: 4563 Sorted by residual: dihedral pdb=" CA ASN A 691 " pdb=" C ASN A 691 " pdb=" N PRO A 692 " pdb=" CA PRO A 692 " ideal model delta harmonic sigma weight residual -180.00 -57.45 -122.55 0 5.00e+00 4.00e-02 6.01e+02 dihedral pdb=" C ARG A 661 " pdb=" N ARG A 661 " pdb=" CA ARG A 661 " pdb=" CB ARG A 661 " ideal model delta harmonic sigma weight residual -122.60 -83.31 -39.29 0 2.50e+00 1.60e-01 2.47e+02 dihedral pdb=" N LEU A 689 " pdb=" C LEU A 689 " pdb=" CA LEU A 689 " pdb=" CB LEU A 689 " ideal model delta harmonic sigma weight residual 122.80 90.01 32.79 0 2.50e+00 1.60e-01 1.72e+02 ... (remaining 7829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.215: 1899 0.215 - 0.431: 16 0.431 - 0.646: 3 0.646 - 0.862: 1 0.862 - 1.077: 3 Chirality restraints: 1922 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.32 -1.08 2.00e-02 2.50e+03 2.90e+03 chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.38e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.37e+01 ... (remaining 1919 not shown) Planarity restraints: 2264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " -0.365 2.00e-02 2.50e+03 3.08e-01 1.19e+03 pdb=" C7 NAG C 1 " 0.096 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " -0.184 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " 0.539 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " -0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 2 " 0.333 2.00e-02 2.50e+03 2.89e-01 1.04e+03 pdb=" C7 NAG C 2 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG C 2 " 0.079 2.00e-02 2.50e+03 pdb=" N2 NAG C 2 " -0.514 2.00e-02 2.50e+03 pdb=" O7 NAG C 2 " 0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.336 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG D 1 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.177 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.501 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.074 2.00e-02 2.50e+03 ... (remaining 2261 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.25: 25 2.25 - 2.91: 5679 2.91 - 3.57: 17632 3.57 - 4.24: 28454 4.24 - 4.90: 46088 Nonbonded interactions: 97878 Sorted by model distance: nonbonded pdb=" N LEU A 689 " pdb=" OD1 ASN A 691 " model vdw 1.584 2.520 nonbonded pdb=" CA LEU A 689 " pdb=" OD1 ASN A 691 " model vdw 1.759 3.470 nonbonded pdb=" C LEU A 689 " pdb=" OD1 ASN A 691 " model vdw 1.847 3.270 nonbonded pdb=" N ASN A 665 " pdb=" O GLY A 700 " model vdw 1.909 2.520 nonbonded pdb=" OE2 GLU B 220 " pdb="MG MG B2001 " model vdw 1.982 2.170 ... (remaining 97873 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 'C' selection = chain 'D' } 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=0.00 max=1.00 mean=0.98 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: 0.010 Normalize map: mean=0, sd=1: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.960 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 41.540 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5559 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 : 0.007 0.167 12599 Z= 0.479 Angle : 1.153 28.849 17122 Z= 0.659 Chirality : 0.077 1.077 1922 Planarity : 0.015 0.308 2259 Dihedral : 16.738 122.547 4804 Min Nonbonded Distance : 1.584 Molprobity Statistics. All-atom Clashscore : 31.98 Ramachandran Plot: Outliers : 1.59 % Allowed : 9.64 % Favored : 88.77 % Rotamer: Outliers : 3.38 % Allowed : 17.57 % Favored : 79.04 % Cbeta Deviations : 1.03 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 1.08 % 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: -2.30 (0.20), residues: 1587 helix: -2.13 (0.43), residues: 122 sheet: -0.83 (0.26), residues: 425 loop : -1.84 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 113 HIS 0.007 0.001 HIS B 274 PHE 0.037 0.002 PHE A 669 TYR 0.029 0.002 TYR B 164 ARG 0.038 0.001 ARG A 661 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 162 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLN cc_start: 0.7898 (mt0) cc_final: 0.7512 (tt0) REVERT: A 112 HIS cc_start: 0.4661 (m90) cc_final: 0.4455 (m170) REVERT: A 121 GLU cc_start: 0.2824 (mp0) cc_final: 0.2220 (tt0) REVERT: A 124 LYS cc_start: 0.2962 (mtmm) cc_final: 0.2582 (mtmm) REVERT: A 164 LYS cc_start: 0.5149 (pttt) cc_final: 0.4624 (pttm) REVERT: A 449 ARG cc_start: 0.5775 (mpp80) cc_final: 0.4968 (mtp180) REVERT: A 489 MET cc_start: 0.5934 (ppp) cc_final: 0.5655 (tpt) REVERT: A 660 MET cc_start: 0.4302 (mmm) cc_final: 0.3346 (mmt) REVERT: A 691 ASN cc_start: 0.7019 (OUTLIER) cc_final: 0.6490 (m110) REVERT: A 835 LEU cc_start: 0.1899 (OUTLIER) cc_final: 0.0928 (mt) REVERT: A 837 VAL cc_start: 0.1859 (OUTLIER) cc_final: 0.1241 (m) outliers start: 45 outliers final: 18 residues processed: 202 average time/residue: 0.2581 time to fit residues: 73.0345 Evaluate side-chains 115 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 PRO Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 670 GLU Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 507 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/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-5370/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-5370/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-5370/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-5370/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-5370/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-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.4467 > 50: distance: 55 - 164: 4.656 distance: 58 - 161: 6.762 distance: 68 - 148: 30.302 distance: 99 - 104: 27.682 distance: 104 - 105: 35.977 distance: 105 - 106: 17.283 distance: 105 - 108: 7.464 distance: 106 - 107: 23.979 distance: 106 - 115: 18.559 distance: 108 - 109: 21.986 distance: 109 - 110: 8.692 distance: 110 - 111: 6.518 distance: 115 - 116: 23.256 distance: 116 - 117: 17.065 distance: 116 - 119: 24.660 distance: 117 - 118: 32.571 distance: 117 - 121: 7.150 distance: 119 - 120: 12.858 distance: 121 - 122: 8.138 distance: 122 - 123: 23.225 distance: 122 - 125: 17.989 distance: 123 - 124: 28.810 distance: 123 - 132: 51.170 distance: 125 - 126: 16.882 distance: 126 - 127: 14.469 distance: 127 - 128: 10.207 distance: 128 - 129: 5.288 distance: 129 - 131: 3.582 distance: 132 - 133: 56.738 distance: 132 - 138: 53.669 distance: 133 - 134: 55.846 distance: 133 - 136: 53.246 distance: 134 - 135: 37.978 distance: 134 - 139: 28.325 distance: 136 - 137: 29.468 distance: 137 - 138: 36.219 distance: 139 - 140: 33.361 distance: 140 - 141: 24.061 distance: 140 - 143: 43.953 distance: 141 - 142: 35.330 distance: 141 - 145: 3.786 distance: 143 - 144: 31.812 distance: 145 - 146: 20.404 distance: 146 - 147: 27.068 distance: 146 - 149: 17.516 distance: 147 - 148: 27.614 distance: 147 - 154: 14.504 distance: 149 - 150: 12.607 distance: 150 - 151: 15.302 distance: 151 - 152: 13.014 distance: 151 - 153: 8.597 distance: 154 - 155: 9.411 distance: 155 - 156: 9.812 distance: 155 - 158: 14.101 distance: 156 - 157: 17.315 distance: 156 - 161: 13.376 distance: 158 - 159: 17.280 distance: 158 - 160: 13.431 distance: 161 - 162: 6.057 distance: 162 - 163: 5.036 distance: 162 - 165: 3.647 distance: 163 - 164: 4.888 distance: 163 - 169: 7.646 distance: 165 - 166: 6.667 distance: 166 - 167: 3.558 distance: 169 - 170: 4.480 distance: 170 - 171: 4.265 distance: 170 - 173: 3.651 distance: 171 - 172: 4.605 distance: 171 - 177: 6.352 distance: 173 - 174: 10.457 distance: 174 - 175: 10.121 distance: 174 - 176: 8.235 distance: 178 - 181: 4.838 distance: 179 - 180: 7.059 distance: 181 - 182: 6.133