Starting phenix.real_space_refine on Sun Nov 17 21:21:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbg_23254/11_2024/7lbg_23254.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbg_23254/11_2024/7lbg_23254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbg_23254/11_2024/7lbg_23254.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbg_23254/11_2024/7lbg_23254.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbg_23254/11_2024/7lbg_23254.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbg_23254/11_2024/7lbg_23254.cif" } resolution = 2.6 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= -0.027 sd= 0.763 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 9289 2.51 5 N 2453 2.21 5 O 2779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 14586 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5118 Classifications: {'peptide': 635} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 602} Chain breaks: 6 Chain: "B" Number of atoms: 1843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1843 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2462 Classifications: {'peptide': 296} Link IDs: {'PCIS': 3, 'PTRANS': 14, 'TRANS': 278} Chain breaks: 3 Chain: "D" Number of atoms: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1235 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 7, 'TRANS': 148} Chain breaks: 1 Chain: "E" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Chain: "F" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 927 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "G" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 850 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1005 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 8.60, per 1000 atoms: 0.59 Number of scatterers: 14586 At special positions: 0 Unit cell: (96.7788, 174.441, 163.688, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 2779 8.00 N 2453 7.00 C 9289 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS B 47 " distance=2.03 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 211 " distance=2.02 Simple disulfide: pdb=" SG CYS A 495 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 624 " distance=2.02 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS C 343 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 141 " - pdb=" SG CYS C 149 " distance=2.04 Simple disulfide: pdb=" SG CYS C 167 " - pdb=" SG CYS C 218 " distance=2.03 Simple disulfide: pdb=" SG CYS D 52 " - pdb=" SG CYS D 197 " distance=2.03 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 111 " distance=2.03 Simple disulfide: pdb=" SG CYS F 45 " - pdb=" SG CYS F 119 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 116 " distance=2.03 Simple disulfide: pdb=" SG CYS H 45 " - pdb=" SG CYS H 119 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 ALPHA1-2 " MAN J 4 " - " MAN J 5 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " MAN J 6 " - " MAN J 7 " ALPHA1-6 " BMA J 3 " - " MAN J 6 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG A 801 " - " ASN A 192 " " NAG A 802 " - " ASN A 67 " " NAG A 803 " - " ASN A 62 " " NAG A 804 " - " ASN A 55 " " NAG A 805 " - " ASN A 700 " " NAG B 301 " - " ASN B 74 " " NAG C 601 " - " ASN C 85 " " NAG C 602 " - " ASN C 101 " " NAG C 603 " - " ASN C 155 " " NAG C 604 " - " ASN C 217 " " NAG C 605 " - " ASN C 240 " " NAG C 606 " - " ASN C 348 " " NAG C 607 " - " ASN C 365 " " NAG C 608 " - " ASN C 383 " " NAG C 609 " - " ASN C 452 " " NAG C 610 " - " ASN C 128 " " NAG C 611 " - " ASN C 169 " " NAG J 1 " - " ASN C 160 " Time building additional restraints: 4.10 Conformation dependent library (CDL) restraints added in 2.1 seconds 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3394 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 27 sheets defined 29.4% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'A' and resid 93 through 98 Processing helix chain 'A' and resid 99 through 107 removed outlier: 3.710A pdb=" N PHE A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 122 Processing helix chain 'A' and resid 263 through 266 Processing helix chain 'A' and resid 285 through 294 removed outlier: 4.221A pdb=" N SER A 290 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N TYR A 291 " --> pdb=" O ARG A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 316 through 328 Processing helix chain 'A' and resid 334 through 352 Processing helix chain 'A' and resid 362 through 384 Processing helix chain 'A' and resid 396 through 409 Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.586A pdb=" N LEU A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 436 through 454 removed outlier: 3.709A pdb=" N LEU A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 475 removed outlier: 3.816A pdb=" N HIS A 475 " --> pdb=" O GLY A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 494 Processing helix chain 'A' and resid 496 through 507 Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 531 through 538 removed outlier: 3.598A pdb=" N LEU A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 671 through 680 Processing helix chain 'A' and resid 681 through 684 Processing helix chain 'A' and resid 707 through 710 removed outlier: 3.788A pdb=" N VAL A 710 " --> pdb=" O THR A 707 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 707 through 710' Processing helix chain 'B' and resid 46 through 56 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 102 through 113 removed outlier: 3.575A pdb=" N LEU B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 163 through 167 removed outlier: 3.835A pdb=" N LEU B 167 " --> pdb=" O LEU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 218 through 236 removed outlier: 3.974A pdb=" N PHE B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 252 removed outlier: 3.952A pdb=" N ARG B 244 " --> pdb=" O PRO B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'C' and resid 112 through 115 Processing helix chain 'C' and resid 146 through 159 Processing helix chain 'C' and resid 198 through 214 removed outlier: 3.640A pdb=" N ARG C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 217 No H-bonds generated for 'chain 'C' and resid 215 through 217' Processing helix chain 'C' and resid 222 through 230 removed outlier: 3.555A pdb=" N ARG C 230 " --> pdb=" O ASN C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 251 Processing helix chain 'C' and resid 321 through 335 Processing helix chain 'C' and resid 336 through 343 removed outlier: 6.741A pdb=" N GLU C 340 " --> pdb=" O TYR C 337 " (cutoff:3.500A) Proline residue: C 341 - end of helix Processing helix chain 'C' and resid 353 through 360 Processing helix chain 'C' and resid 361 through 364 Processing helix chain 'C' and resid 377 through 379 No H-bonds generated for 'chain 'C' and resid 377 through 379' Processing helix chain 'C' and resid 413 through 435 Processing helix chain 'C' and resid 452 through 458 removed outlier: 3.555A pdb=" N LEU C 456 " --> pdb=" O ASN C 452 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER C 458 " --> pdb=" O SER C 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 removed outlier: 3.829A pdb=" N GLY D 59 " --> pdb=" O GLY D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 144 Processing helix chain 'D' and resid 156 through 169 Processing helix chain 'E' and resid 102 through 106 removed outlier: 3.525A pdb=" N VAL E 106 " --> pdb=" O PRO E 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 88 removed outlier: 3.555A pdb=" N GLN F 88 " --> pdb=" O GLN F 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 85 through 88' Processing helix chain 'F' and resid 110 through 114 Processing helix chain 'G' and resid 107 through 111 removed outlier: 3.884A pdb=" N VAL G 111 " --> pdb=" O THR G 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 114 Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 52 Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 66 removed outlier: 4.220A pdb=" N SER A 64 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR A 88 " --> pdb=" O PHE A 81 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N PHE A 81 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE A 90 " --> pdb=" O ASN A 79 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ASN A 79 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N MET A 92 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N SER A 77 " --> pdb=" O MET A 92 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N SER A 77 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N LEU B 183 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASN A 79 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N HIS B 177 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL B 192 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE B 181 " --> pdb=" O ASN B 190 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASN B 190 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU B 183 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU B 188 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE B 189 " --> pdb=" O VAL B 210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 removed outlier: 5.797A pdb=" N ILE A 268 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL A 279 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG A 270 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 194 through 197 Processing sheet with id=AA5, first strand: chain 'A' and resid 527 through 528 Processing sheet with id=AA6, first strand: chain 'A' and resid 637 through 638 removed outlier: 6.647A pdb=" N THR A 637 " --> pdb=" O GLU A 705 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASP A 658 " --> pdb=" O VAL A 663 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N VAL A 663 " --> pdb=" O ASP A 658 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 82 through 83 removed outlier: 6.507A pdb=" N LEU B 82 " --> pdb=" O GLY B 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 99 through 100 removed outlier: 6.328A pdb=" N VAL B 99 " --> pdb=" O ARG C 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 151 through 155 Processing sheet with id=AB1, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.675A pdb=" N TYR C 124 " --> pdb=" O ARG C 137 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N TYR C 122 " --> pdb=" O PRO C 139 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 117 through 118 removed outlier: 6.632A pdb=" N VAL D 83 " --> pdb=" O HIS D 113 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LYS D 115 " --> pdb=" O VAL D 83 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU D 85 " --> pdb=" O LYS D 115 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN D 88 " --> pdb=" O ILE D 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 171 through 172 Processing sheet with id=AB4, first strand: chain 'C' and resid 184 through 189 removed outlier: 3.838A pdb=" N THR C 192 " --> pdb=" O VAL C 189 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 369 through 370 Processing sheet with id=AB6, first strand: chain 'C' and resid 381 through 382 Processing sheet with id=AB7, first strand: chain 'D' and resid 50 through 51 removed outlier: 6.334A pdb=" N GLU D 63 " --> pdb=" O VAL D 101 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU D 103 " --> pdb=" O GLU D 63 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N HIS D 65 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ASN D 105 " --> pdb=" O HIS D 65 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU D 67 " --> pdb=" O ASN D 105 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL D 100 " --> pdb=" O LEU D 126 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LEU D 128 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE D 102 " --> pdb=" O LEU D 128 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 27 through 30 Processing sheet with id=AB9, first strand: chain 'E' and resid 33 through 35 removed outlier: 6.524A pdb=" N LEU E 56 " --> pdb=" O TYR E 72 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR E 72 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TRP E 58 " --> pdb=" O LEU E 70 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 26 through 29 Processing sheet with id=AC2, first strand: chain 'F' and resid 33 through 34 removed outlier: 6.600A pdb=" N ARG F 61 " --> pdb=" O TRP F 70 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N TRP F 70 " --> pdb=" O ARG F 61 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 33 through 34 removed outlier: 3.928A pdb=" N ASP F 135 " --> pdb=" O ARG F 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 27 through 30 Processing sheet with id=AC5, first strand: chain 'G' and resid 33 through 35 removed outlier: 5.939A pdb=" N LEU G 34 " --> pdb=" O GLU G 133 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY G 112 " --> pdb=" O VAL G 132 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU G 61 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR G 77 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TRP G 63 " --> pdb=" O LEU G 75 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 33 through 35 removed outlier: 5.939A pdb=" N LEU G 34 " --> pdb=" O GLU G 133 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY G 112 " --> pdb=" O VAL G 132 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR G 125 " --> pdb=" O GLN G 118 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 26 through 30 Processing sheet with id=AC8, first strand: chain 'H' and resid 34 through 35 removed outlier: 4.013A pdb=" N SER H 56 " --> pdb=" O ASP H 122 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL H 57 " --> pdb=" O SER H 73 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER H 73 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP H 59 " --> pdb=" O VAL H 71 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 34 through 35 removed outlier: 3.874A pdb=" N VAL H 142 " --> pdb=" O ARG H 121 " (cutoff:3.500A) 585 hydrogen bonds defined for protein. 1509 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: 5.46 Time building geometry restraints manager: 4.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4621 1.34 - 1.46: 3656 1.46 - 1.58: 6549 1.58 - 1.70: 0 1.70 - 1.82: 97 Bond restraints: 14923 Sorted by residual: bond pdb=" C1 NAG C 605 " pdb=" O5 NAG C 605 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.22e+00 bond pdb=" C1 NAG C 603 " pdb=" O5 NAG C 603 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.81e+00 bond pdb=" C1 MAN J 7 " pdb=" C2 MAN J 7 " ideal model delta sigma weight residual 1.526 1.569 -0.043 2.00e-02 2.50e+03 4.60e+00 bond pdb=" C1 NAG C 610 " pdb=" O5 NAG C 610 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.72e+00 bond pdb=" C1 MAN J 5 " pdb=" C2 MAN J 5 " ideal model delta sigma weight residual 1.526 1.564 -0.038 2.00e-02 2.50e+03 3.64e+00 ... (remaining 14918 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 19592 1.39 - 2.77: 540 2.77 - 4.16: 135 4.16 - 5.55: 17 5.55 - 6.94: 6 Bond angle restraints: 20290 Sorted by residual: angle pdb=" CB LYS B 64 " pdb=" CG LYS B 64 " pdb=" CD LYS B 64 " ideal model delta sigma weight residual 111.30 116.61 -5.31 2.30e+00 1.89e-01 5.32e+00 angle pdb=" CA ASN C 101 " pdb=" CB ASN C 101 " pdb=" CG ASN C 101 " ideal model delta sigma weight residual 112.60 114.88 -2.28 1.00e+00 1.00e+00 5.19e+00 angle pdb=" C3 MAN J 4 " pdb=" C2 MAN J 4 " pdb=" O2 MAN J 4 " ideal model delta sigma weight residual 111.77 104.94 6.83 3.00e+00 1.11e-01 5.19e+00 angle pdb=" C ASN A 85 " pdb=" CA ASN A 85 " pdb=" CB ASN A 85 " ideal model delta sigma weight residual 111.80 108.48 3.32 1.46e+00 4.69e-01 5.16e+00 angle pdb=" C3 MAN J 6 " pdb=" C2 MAN J 6 " pdb=" O2 MAN J 6 " ideal model delta sigma weight residual 111.77 105.24 6.53 3.00e+00 1.11e-01 4.74e+00 ... (remaining 20285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.35: 8839 22.35 - 44.70: 331 44.70 - 67.04: 59 67.04 - 89.39: 27 89.39 - 111.74: 4 Dihedral angle restraints: 9260 sinusoidal: 4007 harmonic: 5253 Sorted by residual: dihedral pdb=" CB CYS D 52 " pdb=" SG CYS D 52 " pdb=" SG CYS D 197 " pdb=" CB CYS D 197 " ideal model delta sinusoidal sigma weight residual -86.00 -167.27 81.27 1 1.00e+01 1.00e-02 8.14e+01 dihedral pdb=" CA PRO C 145 " pdb=" C PRO C 145 " pdb=" N SER C 146 " pdb=" CA SER C 146 " ideal model delta harmonic sigma weight residual 180.00 153.60 26.40 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA ALA B 194 " pdb=" C ALA B 194 " pdb=" N ILE B 195 " pdb=" CA ILE B 195 " ideal model delta harmonic sigma weight residual 180.00 155.35 24.65 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 9257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2011 0.053 - 0.105: 278 0.105 - 0.158: 86 0.158 - 0.210: 1 0.210 - 0.263: 3 Chirality restraints: 2379 Sorted by residual: chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C1 NAG C 611 " pdb=" ND2 ASN C 169 " pdb=" C2 NAG C 611 " pdb=" O5 NAG C 611 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ASN C 101 " pdb=" N ASN C 101 " pdb=" C ASN C 101 " pdb=" CB ASN C 101 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 2376 not shown) Planarity restraints: 2560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 344 " 0.059 5.00e-02 4.00e+02 8.89e-02 1.26e+01 pdb=" N PRO C 345 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO C 345 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 345 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 94 " 0.236 9.50e-02 1.11e+02 1.06e-01 7.47e+00 pdb=" NE ARG A 94 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 94 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 94 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 94 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 253 " -0.229 9.50e-02 1.11e+02 1.03e-01 7.25e+00 pdb=" NE ARG C 253 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG C 253 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG C 253 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG C 253 " -0.003 2.00e-02 2.50e+03 ... (remaining 2557 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 189 2.65 - 3.21: 13461 3.21 - 3.77: 22227 3.77 - 4.34: 33742 4.34 - 4.90: 53996 Nonbonded interactions: 123615 Sorted by model distance: nonbonded pdb=" NH2 ARG A 365 " pdb=" OD2 ASP A 368 " model vdw 2.085 3.120 nonbonded pdb=" ND1 HIS C 360 " pdb=" O LEU C 459 " model vdw 2.192 3.120 nonbonded pdb=" O LEU G 34 " pdb=" N GLU G 133 " model vdw 2.209 3.120 nonbonded pdb=" OG SER B 83 " pdb=" OE1 GLU B 176 " model vdw 2.259 3.040 nonbonded pdb=" OD1 ASP E 128 " pdb=" N ILE E 129 " model vdw 2.283 3.120 ... (remaining 123610 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.420 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: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 35.600 Find NCS groups from input model: 0.180 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: 0.010 Load rotamer database and sin/cos tables:12.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 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 : 0.003 0.057 14923 Z= 0.217 Angle : 0.580 6.937 20290 Z= 0.282 Chirality : 0.043 0.263 2379 Planarity : 0.006 0.106 2542 Dihedral : 12.952 111.738 5827 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.75 % 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: 0.44 (0.20), residues: 1750 helix: 0.45 (0.25), residues: 402 sheet: 0.37 (0.24), residues: 432 loop : 0.34 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 460 HIS 0.005 0.001 HIS A 187 PHE 0.027 0.002 PHE H 52 TYR 0.020 0.002 TYR A 344 ARG 0.015 0.002 ARG C 253 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 317 LYS cc_start: 0.7993 (mmtt) cc_final: 0.7694 (mmtm) REVERT: D 96 HIS cc_start: 0.7843 (t70) cc_final: 0.7576 (t70) REVERT: D 115 LYS cc_start: 0.7382 (mmpt) cc_final: 0.6495 (pttp) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 1.5720 time to fit residues: 481.9262 Evaluate side-chains 217 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 137 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 83 optimal weight: 0.0270 chunk 102 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 overall best weight: 0.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 480 HIS B 203 ASN C 215 GLN D 155 HIS D 157 ASN D 202 ASN D 207 ASN E 26 GLN G 81 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14923 Z= 0.219 Angle : 0.592 6.931 20290 Z= 0.303 Chirality : 0.044 0.244 2379 Planarity : 0.004 0.058 2542 Dihedral : 7.910 82.681 2490 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.51 % Allowed : 8.81 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.75 % 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: 0.96 (0.20), residues: 1750 helix: 1.40 (0.25), residues: 406 sheet: 0.54 (0.24), residues: 422 loop : 0.47 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 460 HIS 0.005 0.001 HIS B 236 PHE 0.029 0.002 PHE H 52 TYR 0.028 0.002 TYR A 84 ARG 0.007 0.001 ARG C 216 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 229 time to evaluate : 1.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 317 LYS cc_start: 0.8075 (mmtt) cc_final: 0.7613 (mmtm) outliers start: 24 outliers final: 8 residues processed: 241 average time/residue: 1.6114 time to fit residues: 422.4568 Evaluate side-chains 229 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 221 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 ASN D 155 HIS G 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1640 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: