Starting phenix.real_space_refine on Tue Nov 19 04:09:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syd_25522/11_2024/7syd_25522.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syd_25522/11_2024/7syd_25522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syd_25522/11_2024/7syd_25522.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syd_25522/11_2024/7syd_25522.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syd_25522/11_2024/7syd_25522.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syd_25522/11_2024/7syd_25522.cif" } resolution = 3.1 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= -0.000 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10192 atoms to isotropic. 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 134 5.16 5 C 6316 2.51 5 N 1810 2.21 5 O 1956 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 10216 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4723 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 614, 4723 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 30, 'TRANS': 583} Chain: "C" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 385 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "B" Number of atoms: 4723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4723 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 30, 'TRANS': 583} Chain: "D" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 385 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Time building chain proxies: 6.67, per 1000 atoms: 0.65 Number of scatterers: 10216 At special positions: 0 Unit cell: (82.0344, 141.401, 126.29, 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 134 16.00 O 1956 8.00 N 1810 7.00 C 6316 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=56, symmetry=0 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS A 34 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 175 " distance=2.03 Simple disulfide: pdb=" SG CYS A 170 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 199 " distance=2.02 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 224 " distance=2.03 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 267 " distance=2.03 Simple disulfide: pdb=" SG CYS A 271 " - pdb=" SG CYS A 283 " distance=2.02 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 302 " distance=2.02 Simple disulfide: pdb=" SG CYS A 305 " - pdb=" SG CYS A 309 " distance=2.04 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 338 " distance=2.03 Simple disulfide: pdb=" SG CYS A 446 " - pdb=" SG CYS A 475 " distance=2.04 Simple disulfide: pdb=" SG CYS A 482 " - pdb=" SG CYS A 491 " distance=2.02 Simple disulfide: pdb=" SG CYS A 486 " - pdb=" SG CYS A 499 " distance=2.02 Simple disulfide: pdb=" SG CYS A 502 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 547 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 555 " distance=2.03 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 593 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS A 600 " - pdb=" SG CYS A 612 " distance=2.04 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 20 " distance=2.04 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 31 " distance=2.03 Simple disulfide: pdb=" SG CYS C 33 " - pdb=" SG CYS C 42 " distance=2.02 Simple disulfide: pdb=" SG CYS B 7 " - pdb=" SG CYS B 34 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 166 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 170 " - pdb=" SG CYS B 183 " distance=2.04 Simple disulfide: pdb=" SG CYS B 191 " - pdb=" SG CYS B 199 " distance=2.03 Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 224 " distance=2.02 Simple disulfide: pdb=" SG CYS B 227 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 267 " distance=2.03 Simple disulfide: pdb=" SG CYS B 271 " - pdb=" SG CYS B 283 " distance=2.02 Simple disulfide: pdb=" SG CYS B 287 " - pdb=" SG CYS B 302 " distance=2.03 Simple disulfide: pdb=" SG CYS B 305 " - pdb=" SG CYS B 309 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 338 " distance=2.03 Simple disulfide: pdb=" SG CYS B 446 " - pdb=" SG CYS B 475 " distance=2.03 Simple disulfide: pdb=" SG CYS B 482 " - pdb=" SG CYS B 491 " distance=2.04 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 499 " distance=2.04 Simple disulfide: pdb=" SG CYS B 502 " - pdb=" SG CYS B 511 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 531 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 547 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 555 " distance=2.05 Simple disulfide: pdb=" SG CYS B 558 " - pdb=" SG CYS B 567 " distance=2.06 Simple disulfide: pdb=" SG CYS B 571 " - pdb=" SG CYS B 593 " distance=2.05 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS B 600 " - pdb=" SG CYS B 612 " distance=2.05 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 20 " distance=2.04 Simple disulfide: pdb=" SG CYS D 14 " - pdb=" SG CYS D 31 " distance=2.03 Simple disulfide: pdb=" SG CYS D 33 " - pdb=" SG CYS D 42 " distance=2.02 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 Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 1.5 seconds 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2428 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 29 sheets defined 13.2% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.513A pdb=" N LEU A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 91 removed outlier: 4.140A pdb=" N ASN A 91 " --> pdb=" O TYR A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 145 through 149 removed outlier: 3.526A pdb=" N LEU A 149 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 174 Processing helix chain 'A' and resid 220 through 224 removed outlier: 4.106A pdb=" N CYS A 224 " --> pdb=" O GLU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 322 removed outlier: 3.527A pdb=" N LYS A 322 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 336 removed outlier: 3.619A pdb=" N LYS A 336 " --> pdb=" O LYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 374 removed outlier: 3.523A pdb=" N ASP A 369 " --> pdb=" O GLN A 366 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 370 " --> pdb=" O GLU A 367 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR A 373 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 410 removed outlier: 3.773A pdb=" N GLY A 410 " --> pdb=" O LYS A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 407 through 410' Processing helix chain 'A' and resid 471 through 477 removed outlier: 3.787A pdb=" N LYS A 476 " --> pdb=" O GLU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 499 removed outlier: 3.860A pdb=" N CYS A 499 " --> pdb=" O PRO A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 555 removed outlier: 4.257A pdb=" N ASN A 554 " --> pdb=" O GLY A 551 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N CYS A 555 " --> pdb=" O PRO A 552 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 551 through 555' Processing helix chain 'C' and resid 7 through 11 Processing helix chain 'B' and resid 19 through 32 Processing helix chain 'B' and resid 52 through 57 removed outlier: 3.544A pdb=" N LYS B 56 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR B 57 " --> pdb=" O PHE B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 91 removed outlier: 4.204A pdb=" N ASN B 91 " --> pdb=" O TYR B 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 88 through 91' Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.512A pdb=" N GLY B 173 " --> pdb=" O CYS B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 336 Processing helix chain 'B' and resid 348 through 354 removed outlier: 4.261A pdb=" N PHE B 352 " --> pdb=" O LEU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 374 removed outlier: 3.823A pdb=" N ASP B 369 " --> pdb=" O GLN B 366 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR B 373 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 397 removed outlier: 3.637A pdb=" N GLU B 397 " --> pdb=" O HIS B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 410 Processing helix chain 'B' and resid 452 through 457 removed outlier: 4.121A pdb=" N LEU B 456 " --> pdb=" O ASN B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 478 removed outlier: 3.729A pdb=" N THR B 478 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 555 removed outlier: 3.802A pdb=" N CYS B 555 " --> pdb=" O PRO B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 581 removed outlier: 3.947A pdb=" N ASN B 580 " --> pdb=" O GLY B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 612 removed outlier: 3.656A pdb=" N GLY B 611 " --> pdb=" O PRO B 607 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS B 612 " --> pdb=" O GLY B 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 607 through 612' Processing helix chain 'D' and resid 7 through 11 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 44 removed outlier: 5.627A pdb=" N ALA A 123 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 95 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A 124 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA4, first strand: chain 'A' and resid 244 through 247 removed outlier: 3.734A pdb=" N GLN A 252 " --> pdb=" O ASN A 247 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 261 through 263 Processing sheet with id=AA6, first strand: chain 'A' and resid 276 through 277 Processing sheet with id=AA7, first strand: chain 'A' and resid 291 through 296 Processing sheet with id=AA8, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.730A pdb=" N CYS A 313 " --> pdb=" O SER A 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 345 through 347 removed outlier: 6.120A pdb=" N LEU A 345 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N PHE A 412 " --> pdb=" O ASP A 436 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE A 438 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU A 414 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N SER A 440 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL A 416 " --> pdb=" O SER A 440 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 376 through 377 Processing sheet with id=AB2, first strand: chain 'A' and resid 505 through 507 Processing sheet with id=AB3, first strand: chain 'A' and resid 524 through 527 removed outlier: 3.651A pdb=" N GLU A 527 " --> pdb=" O GLU A 530 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 575 through 576 Processing sheet with id=AB5, first strand: chain 'C' and resid 19 through 23 removed outlier: 3.571A pdb=" N VAL C 19 " --> pdb=" O ASN C 32 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 37 through 38 Processing sheet with id=AB7, first strand: chain 'B' and resid 6 through 7 Processing sheet with id=AB8, first strand: chain 'B' and resid 16 through 17 removed outlier: 3.504A pdb=" N LYS D 28 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL D 19 " --> pdb=" O ASN D 32 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 41 through 44 removed outlier: 6.381A pdb=" N LEU B 41 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ALA B 68 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE B 43 " --> pdb=" O ALA B 68 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ALA B 123 " --> pdb=" O TYR B 93 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 95 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL B 124 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 230 through 231 Processing sheet with id=AC2, first strand: chain 'B' and resid 244 through 247 removed outlier: 3.653A pdb=" N GLN B 252 " --> pdb=" O ASN B 247 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 261 through 263 Processing sheet with id=AC4, first strand: chain 'B' and resid 283 through 284 removed outlier: 3.534A pdb=" N VAL B 277 " --> pdb=" O ARG B 300 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N CYS B 302 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS B 301 " --> pdb=" O MET B 294 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 345 through 347 removed outlier: 6.204A pdb=" N LEU B 345 " --> pdb=" O LEU B 382 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N PHE B 412 " --> pdb=" O ASP B 436 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ILE B 438 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU B 414 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N SER B 440 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL B 416 " --> pdb=" O SER B 440 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL B 437 " --> pdb=" O LYS B 465 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 376 through 377 Processing sheet with id=AC7, first strand: chain 'B' and resid 505 through 506 removed outlier: 3.573A pdb=" N VAL B 505 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 524 through 527 removed outlier: 3.530A pdb=" N GLU B 527 " --> pdb=" O GLU B 530 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 561 through 563 Processing sheet with id=AD1, first strand: chain 'B' and resid 585 through 587 Processing sheet with id=AD2, first strand: chain 'D' and resid 37 through 38 155 hydrogen bonds defined for protein. 300 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: 3.63 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3094 1.33 - 1.45: 1748 1.45 - 1.58: 5424 1.58 - 1.70: 0 1.70 - 1.82: 156 Bond restraints: 10422 Sorted by residual: bond pdb=" N CYS B 571 " pdb=" CA CYS B 571 " ideal model delta sigma weight residual 1.454 1.497 -0.043 1.14e-02 7.69e+03 1.43e+01 bond pdb=" N LEU B 595 " pdb=" CA LEU B 595 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.25e-02 6.40e+03 9.88e+00 bond pdb=" N THR A 601 " pdb=" CA THR A 601 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.26e-02 6.30e+03 9.32e+00 bond pdb=" N CYS B 183 " pdb=" CA CYS B 183 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.29e-02 6.01e+03 8.96e+00 bond pdb=" N CYS B 558 " pdb=" CA CYS B 558 " ideal model delta sigma weight residual 1.453 1.492 -0.039 1.31e-02 5.83e+03 8.90e+00 ... (remaining 10417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 13635 1.97 - 3.95: 417 3.95 - 5.92: 41 5.92 - 7.90: 6 7.90 - 9.87: 1 Bond angle restraints: 14100 Sorted by residual: angle pdb=" N ILE B 556 " pdb=" CA ILE B 556 " pdb=" C ILE B 556 " ideal model delta sigma weight residual 110.53 106.22 4.31 9.40e-01 1.13e+00 2.10e+01 angle pdb=" C ASN B 182 " pdb=" N CYS B 183 " pdb=" CA CYS B 183 " ideal model delta sigma weight residual 122.59 115.47 7.12 1.57e+00 4.06e-01 2.06e+01 angle pdb=" N PRO A 613 " pdb=" CA PRO A 613 " pdb=" CB PRO A 613 " ideal model delta sigma weight residual 103.25 98.49 4.76 1.05e+00 9.07e-01 2.06e+01 angle pdb=" C CYS B 596 " pdb=" CA CYS B 596 " pdb=" CB CYS B 596 " ideal model delta sigma weight residual 111.71 101.84 9.87 2.23e+00 2.01e-01 1.96e+01 angle pdb=" N VAL B 526 " pdb=" CA VAL B 526 " pdb=" C VAL B 526 " ideal model delta sigma weight residual 107.75 114.15 -6.40 1.46e+00 4.69e-01 1.92e+01 ... (remaining 14095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 5761 17.82 - 35.64: 575 35.64 - 53.46: 99 53.46 - 71.28: 31 71.28 - 89.09: 14 Dihedral angle restraints: 6480 sinusoidal: 2692 harmonic: 3788 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 163 " pdb=" CB CYS A 163 " ideal model delta sinusoidal sigma weight residual 93.00 174.68 -81.68 1 1.00e+01 1.00e-02 8.21e+01 dihedral pdb=" CB CYS C 6 " pdb=" SG CYS C 6 " pdb=" SG CYS C 20 " pdb=" CB CYS C 20 " ideal model delta sinusoidal sigma weight residual 93.00 168.16 -75.16 1 1.00e+01 1.00e-02 7.14e+01 dihedral pdb=" CB CYS A 558 " pdb=" SG CYS A 558 " pdb=" SG CYS A 567 " pdb=" CB CYS A 567 " ideal model delta sinusoidal sigma weight residual -86.00 -153.51 67.51 1 1.00e+01 1.00e-02 5.93e+01 ... (remaining 6477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1206 0.063 - 0.127: 296 0.127 - 0.190: 24 0.190 - 0.253: 6 0.253 - 0.316: 2 Chirality restraints: 1534 Sorted by residual: chirality pdb=" CA CYS B 596 " pdb=" N CYS B 596 " pdb=" C CYS B 596 " pdb=" CB CYS B 596 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CA THR B 614 " pdb=" N THR B 614 " pdb=" C THR B 614 " pdb=" CB THR B 614 " both_signs ideal model delta sigma weight residual False 2.53 2.83 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA CYS B 555 " pdb=" N CYS B 555 " pdb=" C CYS B 555 " pdb=" CB CYS B 555 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 1531 not shown) Planarity restraints: 1864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 169 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.26e+00 pdb=" C SER B 169 " 0.053 2.00e-02 2.50e+03 pdb=" O SER B 169 " -0.020 2.00e-02 2.50e+03 pdb=" N CYS B 170 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 515 " -0.011 2.00e-02 2.50e+03 2.34e-02 5.46e+00 pdb=" C CYS A 515 " 0.040 2.00e-02 2.50e+03 pdb=" O CYS A 515 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN A 516 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 521 " 0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO B 522 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 522 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 522 " 0.023 5.00e-02 4.00e+02 ... (remaining 1861 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 110 2.63 - 3.20: 9182 3.20 - 3.77: 14227 3.77 - 4.33: 21466 4.33 - 4.90: 35992 Nonbonded interactions: 80977 Sorted by model distance: nonbonded pdb=" OG1 THR A 10 " pdb=" OE1 GLU A 42 " model vdw 2.068 3.040 nonbonded pdb=" OG1 THR B 10 " pdb=" OE1 GLU B 42 " model vdw 2.122 3.040 nonbonded pdb=" OD2 ASP B 167 " pdb=" OG SER B 169 " model vdw 2.217 3.040 nonbonded pdb=" O CYS B 34 " pdb=" OG1 THR B 57 " model vdw 2.230 3.040 nonbonded pdb=" OE2 GLU A 376 " pdb=" NH1 ARG A 403 " model vdw 2.231 3.120 ... (remaining 80972 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.000 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.210 Find NCS groups from input model: 0.380 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 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 0.046 10422 Z= 0.480 Angle : 0.787 9.872 14100 Z= 0.491 Chirality : 0.054 0.316 1534 Planarity : 0.004 0.042 1864 Dihedral : 14.223 89.095 3884 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.43 % Favored : 89.41 % Rotamer: Outliers : 1.99 % Allowed : 7.45 % Favored : 90.55 % Cbeta Deviations : 0.16 % 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: -3.66 (0.20), residues: 1314 helix: -4.33 (0.32), residues: 67 sheet: -3.00 (0.34), residues: 168 loop : -2.43 (0.16), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 50 HIS 0.005 0.001 HIS A 535 PHE 0.015 0.002 PHE B 380 TYR 0.013 0.002 TYR B 64 ARG 0.004 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 1.284 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 7 residues processed: 93 average time/residue: 0.2955 time to fit residues: 37.8156 Evaluate side-chains 52 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 502 CYS Chi-restraints excluded: chain A residue 597 HIS Chi-restraints excluded: chain A residue 600 CYS Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain B residue 515 CYS Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 596 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: