Starting phenix.real_space_refine on Thu May 1 02:31:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r8u_19011/05_2025/8r8u_19011.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r8u_19011/05_2025/8r8u_19011.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/cci-nas-00/data/ceres_data/8r8u_19011/05_2025/8r8u_19011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r8u_19011/05_2025/8r8u_19011.map" model { file = "/net/cci-nas-00/data/ceres_data/8r8u_19011/05_2025/8r8u_19011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r8u_19011/05_2025/8r8u_19011.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= 0.001 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 10 9.91 5 S 74 5.16 5 C 6462 2.51 5 N 1706 2.21 5 O 1888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 10140 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 4944 Classifications: {'peptide': 628} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 42, 'TRANS': 585} Chain breaks: 4 Chain: "D" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 121 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 1, 'TRANS': 11} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 121 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 1, 'TRANS': 11} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 4944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 4944 Classifications: {'peptide': 628} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 42, 'TRANS': 585} Chain breaks: 4 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' CA': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' CA': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 6.34, per 1000 atoms: 0.63 Number of scatterers: 10140 At special positions: 0 Unit cell: (99.75, 141.55, 73.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 10 19.99 S 74 16.00 O 1888 8.00 N 1706 7.00 C 6462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 2.56 Conformation dependent library (CDL) restraints added in 1.1 seconds 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2404 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 26 sheets defined 22.5% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 164 through 168 removed outlier: 4.128A pdb=" N ASP A 168 " --> pdb=" O ASP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 180 removed outlier: 3.642A pdb=" N ASP A 179 " --> pdb=" O ASP A 176 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET A 180 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 347 through 351 removed outlier: 3.837A pdb=" N GLU A 351 " --> pdb=" O TRP A 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 347 through 351' Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 402 through 406 removed outlier: 3.536A pdb=" N ASP A 405 " --> pdb=" O SER A 402 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER A 406 " --> pdb=" O GLY A 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 402 through 406' Processing helix chain 'A' and resid 444 through 454 Processing helix chain 'A' and resid 471 through 474 Processing helix chain 'A' and resid 494 through 507 Processing helix chain 'A' and resid 526 through 531 Processing helix chain 'A' and resid 532 through 558 Processing helix chain 'A' and resid 560 through 562 No H-bonds generated for 'chain 'A' and resid 560 through 562' Processing helix chain 'A' and resid 575 through 577 No H-bonds generated for 'chain 'A' and resid 575 through 577' Processing helix chain 'A' and resid 611 through 621 Processing helix chain 'A' and resid 622 through 624 No H-bonds generated for 'chain 'A' and resid 622 through 624' Processing helix chain 'A' and resid 643 through 647 Processing helix chain 'A' and resid 657 through 661 Processing helix chain 'B' and resid 164 through 168 removed outlier: 4.127A pdb=" N ASP B 168 " --> pdb=" O ASP B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 180 removed outlier: 3.642A pdb=" N ASP B 179 " --> pdb=" O ASP B 176 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET B 180 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'B' and resid 317 through 331 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 347 through 351 removed outlier: 3.837A pdb=" N GLU B 351 " --> pdb=" O TRP B 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 347 through 351' Processing helix chain 'B' and resid 378 through 383 Processing helix chain 'B' and resid 402 through 406 removed outlier: 3.536A pdb=" N ASP B 405 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER B 406 " --> pdb=" O GLY B 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 402 through 406' Processing helix chain 'B' and resid 444 through 454 Processing helix chain 'B' and resid 471 through 474 Processing helix chain 'B' and resid 494 through 507 Processing helix chain 'B' and resid 526 through 531 Processing helix chain 'B' and resid 532 through 558 Processing helix chain 'B' and resid 560 through 562 No H-bonds generated for 'chain 'B' and resid 560 through 562' Processing helix chain 'B' and resid 575 through 577 No H-bonds generated for 'chain 'B' and resid 575 through 577' Processing helix chain 'B' and resid 611 through 621 Processing helix chain 'B' and resid 622 through 624 No H-bonds generated for 'chain 'B' and resid 622 through 624' Processing helix chain 'B' and resid 643 through 647 Processing helix chain 'B' and resid 657 through 661 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 5.851A pdb=" N THR A 5 " --> pdb=" O GLN A 26 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASP A 28 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE A 7 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR A 25 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL A 76 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 20 removed outlier: 5.969A pdb=" N THR A 15 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N THR A 111 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA A 17 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL A 113 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N CYS A 19 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE A 115 " --> pdb=" O CYS A 19 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER A 39 " --> pdb=" O TYR A 97 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TRP A 68 " --> pdb=" O PHE A 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 20 removed outlier: 5.969A pdb=" N THR A 15 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N THR A 111 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA A 17 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL A 113 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N CYS A 19 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE A 115 " --> pdb=" O CYS A 19 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASP A 248 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL A 213 " --> pdb=" O VAL A 228 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 148 through 150 removed outlier: 3.531A pdb=" N ALA A 148 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU A 271 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN A 286 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE A 269 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER A 288 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU A 267 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL A 290 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE A 265 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU A 199 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 333 through 337 removed outlier: 3.574A pdb=" N LYS A 333 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 359 Processing sheet with id=AA7, first strand: chain 'A' and resid 410 through 412 removed outlier: 6.442A pdb=" N ILE A 428 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU A 462 " --> pdb=" O ILE A 428 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE A 430 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 416 through 418 Processing sheet with id=AA9, first strand: chain 'A' and resid 476 through 480 removed outlier: 8.149A pdb=" N ILE A 565 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU A 489 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE A 567 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU A 491 " --> pdb=" O ILE A 567 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 513 through 514 Processing sheet with id=AB2, first strand: chain 'A' and resid 571 through 573 Processing sheet with id=AB3, first strand: chain 'A' and resid 590 through 592 removed outlier: 5.842A pdb=" N LEU A 596 " --> pdb=" O THR A 628 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE A 630 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE A 598 " --> pdb=" O ILE A 630 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 605 through 606 Processing sheet with id=AB5, first strand: chain 'B' and resid 5 through 8 removed outlier: 5.851A pdb=" N THR B 5 " --> pdb=" O GLN B 26 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASP B 28 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE B 7 " --> pdb=" O ASP B 28 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR B 25 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL B 76 " --> pdb=" O LEU B 27 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 15 through 20 removed outlier: 5.970A pdb=" N THR B 15 " --> pdb=" O TYR B 109 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N THR B 111 " --> pdb=" O THR B 15 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA B 17 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL B 113 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N CYS B 19 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE B 115 " --> pdb=" O CYS B 19 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER B 39 " --> pdb=" O TYR B 97 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP B 68 " --> pdb=" O PHE B 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 15 through 20 removed outlier: 5.970A pdb=" N THR B 15 " --> pdb=" O TYR B 109 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N THR B 111 " --> pdb=" O THR B 15 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA B 17 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL B 113 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N CYS B 19 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE B 115 " --> pdb=" O CYS B 19 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASP B 248 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL B 213 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 148 through 150 removed outlier: 3.532A pdb=" N ALA B 148 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU B 271 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN B 286 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE B 269 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER B 288 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU B 267 " --> pdb=" O SER B 288 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL B 290 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE B 265 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU B 199 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 333 through 337 removed outlier: 3.574A pdb=" N LYS B 333 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 352 through 359 Processing sheet with id=AC2, first strand: chain 'B' and resid 410 through 412 removed outlier: 6.442A pdb=" N ILE B 428 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU B 462 " --> pdb=" O ILE B 428 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE B 430 " --> pdb=" O LEU B 462 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 416 through 418 Processing sheet with id=AC4, first strand: chain 'B' and resid 476 through 480 removed outlier: 8.148A pdb=" N ILE B 565 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU B 489 " --> pdb=" O ILE B 565 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE B 567 " --> pdb=" O LEU B 489 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU B 491 " --> pdb=" O ILE B 567 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 513 through 514 Processing sheet with id=AC6, first strand: chain 'B' and resid 571 through 573 Processing sheet with id=AC7, first strand: chain 'B' and resid 590 through 592 removed outlier: 5.841A pdb=" N LEU B 596 " --> pdb=" O THR B 628 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE B 630 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE B 598 " --> pdb=" O ILE B 630 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 605 through 606 344 hydrogen bonds defined for protein. 888 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: 4.18 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3292 1.34 - 1.46: 2108 1.46 - 1.58: 4868 1.58 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 10376 Sorted by residual: bond pdb=" N ARG B 650 " pdb=" CA ARG B 650 " ideal model delta sigma weight residual 1.456 1.485 -0.028 1.23e-02 6.61e+03 5.37e+00 bond pdb=" N ARG A 650 " pdb=" CA ARG A 650 " ideal model delta sigma weight residual 1.456 1.485 -0.028 1.23e-02 6.61e+03 5.37e+00 bond pdb=" N ARG B 495 " pdb=" CA ARG B 495 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.05e+00 bond pdb=" N ARG A 495 " pdb=" CA ARG A 495 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.05e+00 bond pdb=" N ARG B 488 " pdb=" CA ARG B 488 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.26e-02 6.30e+03 4.40e+00 ... (remaining 10371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 13445 0.98 - 1.95: 469 1.95 - 2.93: 125 2.93 - 3.90: 27 3.90 - 4.88: 8 Bond angle restraints: 14074 Sorted by residual: angle pdb=" CA ARG A 123 " pdb=" C ARG A 123 " pdb=" O ARG A 123 " ideal model delta sigma weight residual 121.28 118.04 3.24 1.19e+00 7.06e-01 7.41e+00 angle pdb=" CA ARG B 123 " pdb=" C ARG B 123 " pdb=" O ARG B 123 " ideal model delta sigma weight residual 121.28 118.04 3.24 1.19e+00 7.06e-01 7.41e+00 angle pdb=" CA ARG A 650 " pdb=" C ARG A 650 " pdb=" O ARG A 650 " ideal model delta sigma weight residual 120.43 117.61 2.82 1.09e+00 8.42e-01 6.69e+00 angle pdb=" CA ARG B 495 " pdb=" C ARG B 495 " pdb=" O ARG B 495 " ideal model delta sigma weight residual 120.82 118.12 2.70 1.05e+00 9.07e-01 6.59e+00 angle pdb=" CA ARG B 650 " pdb=" C ARG B 650 " pdb=" O ARG B 650 " ideal model delta sigma weight residual 120.43 117.63 2.80 1.09e+00 8.42e-01 6.58e+00 ... (remaining 14069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 5372 16.11 - 32.21: 598 32.21 - 48.32: 192 48.32 - 64.43: 86 64.43 - 80.53: 10 Dihedral angle restraints: 6258 sinusoidal: 2552 harmonic: 3706 Sorted by residual: dihedral pdb=" CA PHE B 407 " pdb=" C PHE B 407 " pdb=" N GLY B 408 " pdb=" CA GLY B 408 " ideal model delta harmonic sigma weight residual 180.00 161.38 18.62 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA PHE A 407 " pdb=" C PHE A 407 " pdb=" N GLY A 408 " pdb=" CA GLY A 408 " ideal model delta harmonic sigma weight residual 180.00 161.38 18.62 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA ASP B 405 " pdb=" CB ASP B 405 " pdb=" CG ASP B 405 " pdb=" OD1 ASP B 405 " ideal model delta sinusoidal sigma weight residual -30.00 -86.39 56.39 1 2.00e+01 2.50e-03 1.07e+01 ... (remaining 6255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 912 0.028 - 0.057: 382 0.057 - 0.085: 118 0.085 - 0.113: 115 0.113 - 0.141: 35 Chirality restraints: 1562 Sorted by residual: chirality pdb=" CA ILE B 94 " pdb=" N ILE B 94 " pdb=" C ILE B 94 " pdb=" CB ILE B 94 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ILE A 94 " pdb=" N ILE A 94 " pdb=" C ILE A 94 " pdb=" CB ILE A 94 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA VAL B 203 " pdb=" N VAL B 203 " pdb=" C VAL B 203 " pdb=" CB VAL B 203 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 1559 not shown) Planarity restraints: 1818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 449 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.13e+00 pdb=" CG ASP B 449 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASP B 449 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP B 449 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 449 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" CG ASP A 449 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASP A 449 " 0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP A 449 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 488 " 0.147 9.50e-02 1.11e+02 6.60e-02 2.70e+00 pdb=" NE ARG B 488 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG B 488 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 488 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 488 " 0.006 2.00e-02 2.50e+03 ... (remaining 1815 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 32 2.41 - 3.04: 5637 3.04 - 3.66: 14068 3.66 - 4.28: 22381 4.28 - 4.90: 39446 Nonbonded interactions: 81564 Sorted by model distance: nonbonded pdb=" CA UNK C 0 " pdb=" SG CYS C 12 " model vdw 1.792 3.830 nonbonded pdb=" CA UNK D 0 " pdb=" SG CYS D 12 " model vdw 1.792 3.830 nonbonded pdb=" OH TYR A 435 " pdb=" OE2 GLU B 281 " model vdw 2.229 3.040 nonbonded pdb=" OE2 GLU A 281 " pdb=" OH TYR B 435 " model vdw 2.231 3.040 nonbonded pdb=" OG SER B 84 " pdb=" OG1 THR B 111 " model vdw 2.254 3.040 ... (remaining 81559 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=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: 0.010 Normalize map: mean=0, sd=1: 1.940 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: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 26.320 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10376 Z= 0.120 Angle : 0.481 4.875 14074 Z= 0.267 Chirality : 0.044 0.141 1562 Planarity : 0.005 0.066 1818 Dihedral : 16.319 80.534 3854 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 21.37 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.24), residues: 1256 helix: 0.82 (0.36), residues: 218 sheet: 1.06 (0.26), residues: 402 loop : -0.47 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 347 HIS 0.002 0.001 HIS A 236 PHE 0.011 0.001 PHE B 583 TYR 0.010 0.001 TYR B 391 ARG 0.003 0.000 ARG B 488 Details of bonding type rmsd hydrogen bonds : bond 0.12840 ( 344) hydrogen bonds : angle 5.15727 ( 888) covalent geometry : bond 0.00229 (10376) covalent geometry : angle 0.48108 (14074) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.408 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.3114 time to fit residues: 65.6425 Evaluate side-chains 143 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 64 optimal weight: 0.2980 chunk 51 optimal weight: 0.5980 chunk 98 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN B 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.130640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.098239 restraints weight = 11207.739| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.81 r_work: 0.2779 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.0606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10376 Z= 0.133 Angle : 0.497 4.881 14074 Z= 0.261 Chirality : 0.045 0.135 1562 Planarity : 0.004 0.037 1818 Dihedral : 4.037 19.928 1358 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.84 % Allowed : 19.53 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.24), residues: 1256 helix: 1.23 (0.37), residues: 206 sheet: 0.97 (0.26), residues: 410 loop : -0.36 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 659 HIS 0.004 0.001 HIS B 202 PHE 0.013 0.001 PHE B 583 TYR 0.010 0.001 TYR A 391 ARG 0.004 0.000 ARG A 372 Details of bonding type rmsd hydrogen bonds : bond 0.04212 ( 344) hydrogen bonds : angle 4.79858 ( 888) covalent geometry : bond 0.00326 (10376) covalent geometry : angle 0.49661 (14074) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.903 Fit side-chains REVERT: A 19 CYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7924 (m) REVERT: B 19 CYS cc_start: 0.8459 (OUTLIER) cc_final: 0.7935 (m) outliers start: 21 outliers final: 15 residues processed: 170 average time/residue: 0.2269 time to fit residues: 54.3769 Evaluate side-chains 170 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 534 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 100 optimal weight: 0.0040 chunk 89 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.128649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.096777 restraints weight = 11424.577| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.80 r_work: 0.2758 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 10376 Z= 0.166 Angle : 0.530 5.837 14074 Z= 0.277 Chirality : 0.046 0.137 1562 Planarity : 0.005 0.039 1818 Dihedral : 4.275 21.145 1358 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.33 % Allowed : 18.30 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.24), residues: 1256 helix: 1.07 (0.37), residues: 206 sheet: 0.91 (0.26), residues: 410 loop : -0.43 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 347 HIS 0.005 0.001 HIS A 202 PHE 0.013 0.001 PHE B 583 TYR 0.011 0.001 TYR B 391 ARG 0.004 0.000 ARG A 372 Details of bonding type rmsd hydrogen bonds : bond 0.04402 ( 344) hydrogen bonds : angle 4.84816 ( 888) covalent geometry : bond 0.00420 (10376) covalent geometry : angle 0.53031 (14074) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 1.220 Fit side-chains REVERT: A 19 CYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7992 (m) REVERT: B 19 CYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7987 (m) outliers start: 38 outliers final: 26 residues processed: 175 average time/residue: 0.2403 time to fit residues: 60.2642 Evaluate side-chains 176 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 570 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 0.0770 chunk 23 optimal weight: 0.3980 chunk 14 optimal weight: 0.0570 chunk 12 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.131526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.099111 restraints weight = 11233.656| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.82 r_work: 0.2795 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10376 Z= 0.093 Angle : 0.461 5.778 14074 Z= 0.241 Chirality : 0.044 0.134 1562 Planarity : 0.004 0.037 1818 Dihedral : 3.973 19.779 1358 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.80 % Allowed : 19.79 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.24), residues: 1256 helix: 1.26 (0.37), residues: 206 sheet: 1.06 (0.26), residues: 410 loop : -0.36 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 347 HIS 0.002 0.001 HIS A 202 PHE 0.010 0.001 PHE B 475 TYR 0.010 0.001 TYR B 391 ARG 0.004 0.000 ARG A 383 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 344) hydrogen bonds : angle 4.66631 ( 888) covalent geometry : bond 0.00218 (10376) covalent geometry : angle 0.46066 (14074) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 1.075 Fit side-chains REVERT: A 19 CYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7969 (m) REVERT: A 274 THR cc_start: 0.8778 (m) cc_final: 0.8491 (p) REVERT: A 626 GLN cc_start: 0.8598 (mt0) cc_final: 0.8198 (mt0) REVERT: B 19 CYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7987 (m) REVERT: B 274 THR cc_start: 0.8803 (m) cc_final: 0.8527 (p) REVERT: B 626 GLN cc_start: 0.8605 (mt0) cc_final: 0.8210 (mt0) outliers start: 32 outliers final: 19 residues processed: 175 average time/residue: 0.2370 time to fit residues: 58.2921 Evaluate side-chains 167 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 570 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.2476 > 50: distance: 98 - 102: 7.081 distance: 102 - 103: 5.850 distance: 103 - 104: 4.777 distance: 104 - 105: 22.324 distance: 104 - 110: 9.452 distance: 106 - 107: 6.088 distance: 107 - 108: 11.543 distance: 107 - 109: 16.710 distance: 111 - 112: 9.017 distance: 111 - 114: 4.800 distance: 112 - 124: 3.022 distance: 114 - 115: 7.454 distance: 115 - 116: 12.321 distance: 115 - 117: 8.065 distance: 116 - 118: 5.621 distance: 117 - 119: 13.857 distance: 117 - 120: 9.964 distance: 118 - 119: 14.081 distance: 119 - 121: 8.315 distance: 120 - 122: 4.617 distance: 121 - 123: 3.931 distance: 122 - 123: 5.982 distance: 124 - 125: 4.577 distance: 125 - 126: 3.226 distance: 125 - 128: 6.730 distance: 126 - 132: 4.314 distance: 128 - 129: 7.447 distance: 133 - 134: 4.406 distance: 133 - 136: 6.664 distance: 134 - 138: 6.478 distance: 136 - 137: 5.596 distance: 138 - 139: 10.802 distance: 139 - 140: 17.393 distance: 139 - 142: 8.886 distance: 140 - 141: 23.196 distance: 140 - 145: 9.649 distance: 142 - 143: 9.637 distance: 142 - 144: 12.883 distance: 145 - 146: 9.181 distance: 146 - 147: 42.412 distance: 147 - 148: 13.891 distance: 147 - 149: 26.228 distance: 149 - 150: 14.987 distance: 150 - 151: 10.069 distance: 150 - 153: 4.528 distance: 151 - 152: 10.643 distance: 151 - 159: 10.699 distance: 152 - 174: 6.765 distance: 153 - 154: 6.877 distance: 154 - 155: 6.850 distance: 154 - 156: 5.194 distance: 155 - 157: 5.551 distance: 156 - 158: 4.821 distance: 157 - 158: 4.510 distance: 159 - 160: 5.695 distance: 160 - 161: 6.477 distance: 160 - 163: 5.915 distance: 161 - 162: 8.619 distance: 161 - 166: 3.610 distance: 163 - 164: 4.666 distance: 163 - 165: 11.109 distance: 166 - 167: 6.163 distance: 167 - 168: 7.350 distance: 167 - 170: 5.881 distance: 168 - 169: 5.682 distance: 168 - 174: 6.355 distance: 170 - 171: 9.948 distance: 171 - 172: 12.036 distance: 171 - 173: 14.474 distance: 175 - 176: 3.879 distance: 175 - 178: 5.342 distance: 178 - 179: 6.515 distance: 179 - 180: 4.816 distance: 180 - 181: 6.082 distance: 180 - 182: 10.632