Starting phenix.real_space_refine on Mon Jan 20 22:23:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hk7_34848/01_2025/8hk7_34848_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hk7_34848/01_2025/8hk7_34848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hk7_34848/01_2025/8hk7_34848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hk7_34848/01_2025/8hk7_34848.map" model { file = "/net/cci-nas-00/data/ceres_data/8hk7_34848/01_2025/8hk7_34848_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hk7_34848/01_2025/8hk7_34848_trim.cif" } resolution = 3.0 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= 0.003 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 1 9.91 5 S 80 5.16 5 C 10428 2.51 5 N 2460 2.21 5 O 2796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 15765 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3872 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 12, 'TRANS': 455} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3872 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 12, 'TRANS': 455} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3872 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 12, 'TRANS': 455} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3872 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 12, 'TRANS': 455} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {' CA': 1, 'AQV': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 69 Unusual residues: {'AQV': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 69 Unusual residues: {'AQV': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 69 Unusual residues: {'AQV': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 9.00, per 1000 atoms: 0.57 Number of scatterers: 15765 At special positions: 0 Unit cell: (108.7, 108.7, 102.178, 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 1 19.99 S 80 16.00 O 2796 8.00 N 2460 7.00 C 10428 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 344 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 344 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 344 " distance=2.03 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 344 " 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 NAG-ASN " NAG A1001 " - " ASN A 328 " " NAG A1002 " - " ASN A 362 " " NAG A1003 " - " ASN A 375 " " NAG B1001 " - " ASN B 328 " " NAG B1002 " - " ASN B 362 " " NAG B1003 " - " ASN B 375 " " NAG C1001 " - " ASN C 328 " " NAG C1002 " - " ASN C 362 " " NAG C1003 " - " ASN C 375 " " NAG D1001 " - " ASN D 328 " " NAG D1002 " - " ASN D 362 " " NAG D1003 " - " ASN D 375 " Time building additional restraints: 4.26 Conformation dependent library (CDL) restraints added in 2.1 seconds 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3584 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 12 sheets defined 58.9% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 215 through 242 Processing helix chain 'A' and resid 246 through 259 removed outlier: 3.706A pdb=" N THR A 250 " --> pdb=" O VAL A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 284 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 335 through 339 removed outlier: 4.572A pdb=" N ASP A 339 " --> pdb=" O ASP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 367 removed outlier: 4.011A pdb=" N TRP A 366 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE A 367 " --> pdb=" O THR A 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 363 through 367' Processing helix chain 'A' and resid 398 through 412 Processing helix chain 'A' and resid 467 through 495 removed outlier: 3.612A pdb=" N PHE A 471 " --> pdb=" O THR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 528 removed outlier: 4.458A pdb=" N VAL A 513 " --> pdb=" O CYS A 509 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL A 515 " --> pdb=" O ASP A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 538 through 541 Processing helix chain 'A' and resid 548 through 572 Processing helix chain 'A' and resid 573 through 578 removed outlier: 3.989A pdb=" N ILE A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 585 removed outlier: 5.982A pdb=" N THR A 582 " --> pdb=" O PHE A 579 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER A 584 " --> pdb=" O ARG A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 601 removed outlier: 3.528A pdb=" N ALA A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 619 Processing helix chain 'A' and resid 623 through 628 removed outlier: 3.784A pdb=" N SER A 627 " --> pdb=" O ASP A 624 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR A 628 " --> pdb=" O ASP A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 642 removed outlier: 3.598A pdb=" N ILE A 633 " --> pdb=" O PHE A 629 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 641 " --> pdb=" O PHE A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 653 removed outlier: 3.632A pdb=" N ILE A 649 " --> pdb=" O ASN A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 687 removed outlier: 3.606A pdb=" N ILE A 659 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE A 669 " --> pdb=" O VAL A 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 242 Processing helix chain 'B' and resid 246 through 259 removed outlier: 3.704A pdb=" N THR B 250 " --> pdb=" O VAL B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 284 Processing helix chain 'B' and resid 285 through 290 Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'B' and resid 335 through 339 removed outlier: 4.558A pdb=" N ASP B 339 " --> pdb=" O ASP B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 367 removed outlier: 4.014A pdb=" N TRP B 366 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE B 367 " --> pdb=" O THR B 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 363 through 367' Processing helix chain 'B' and resid 398 through 412 removed outlier: 3.510A pdb=" N THR B 402 " --> pdb=" O THR B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 494 removed outlier: 3.610A pdb=" N PHE B 471 " --> pdb=" O THR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 528 removed outlier: 3.508A pdb=" N VAL B 512 " --> pdb=" O ASN B 508 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL B 513 " --> pdb=" O CYS B 509 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL B 515 " --> pdb=" O ASP B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 537 Processing helix chain 'B' and resid 538 through 541 Processing helix chain 'B' and resid 548 through 572 Processing helix chain 'B' and resid 573 through 578 removed outlier: 4.039A pdb=" N ILE B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 581 No H-bonds generated for 'chain 'B' and resid 579 through 581' Processing helix chain 'B' and resid 582 through 591 removed outlier: 3.721A pdb=" N LEU B 586 " --> pdb=" O THR B 582 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR B 588 " --> pdb=" O SER B 584 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N THR B 589 " --> pdb=" O GLN B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 601 Processing helix chain 'B' and resid 601 through 619 Processing helix chain 'B' and resid 623 through 628 removed outlier: 3.781A pdb=" N SER B 627 " --> pdb=" O ASP B 624 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR B 628 " --> pdb=" O ASP B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 642 removed outlier: 3.594A pdb=" N ILE B 633 " --> pdb=" O PHE B 629 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 653 removed outlier: 3.658A pdb=" N ILE B 649 " --> pdb=" O ASN B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 687 removed outlier: 3.613A pdb=" N ILE B 659 " --> pdb=" O VAL B 655 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE B 669 " --> pdb=" O VAL B 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 242 Processing helix chain 'C' and resid 246 through 259 removed outlier: 3.706A pdb=" N THR C 250 " --> pdb=" O VAL C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 284 Processing helix chain 'C' and resid 285 through 290 Processing helix chain 'C' and resid 308 through 312 Processing helix chain 'C' and resid 335 through 339 removed outlier: 4.554A pdb=" N ASP C 339 " --> pdb=" O ASP C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 367 removed outlier: 4.012A pdb=" N TRP C 366 " --> pdb=" O GLY C 363 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 367 " --> pdb=" O THR C 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 363 through 367' Processing helix chain 'C' and resid 398 through 412 Processing helix chain 'C' and resid 467 through 494 removed outlier: 3.602A pdb=" N PHE C 471 " --> pdb=" O THR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 530 removed outlier: 4.275A pdb=" N VAL C 512 " --> pdb=" O ASN C 508 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL C 513 " --> pdb=" O CYS C 509 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL C 515 " --> pdb=" O ASP C 511 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER C 530 " --> pdb=" O ILE C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 537 Processing helix chain 'C' and resid 538 through 541 Processing helix chain 'C' and resid 548 through 572 Processing helix chain 'C' and resid 573 through 578 removed outlier: 3.957A pdb=" N ILE C 577 " --> pdb=" O LEU C 573 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN C 578 " --> pdb=" O PHE C 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 573 through 578' Processing helix chain 'C' and resid 579 through 584 removed outlier: 6.004A pdb=" N THR C 582 " --> pdb=" O PHE C 579 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER C 584 " --> pdb=" O ARG C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 591 removed outlier: 3.823A pdb=" N THR C 589 " --> pdb=" O GLN C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 601 Processing helix chain 'C' and resid 601 through 619 Processing helix chain 'C' and resid 623 through 628 removed outlier: 3.806A pdb=" N SER C 627 " --> pdb=" O ASP C 624 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR C 628 " --> pdb=" O ASP C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 642 removed outlier: 3.596A pdb=" N ILE C 633 " --> pdb=" O PHE C 629 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 641 " --> pdb=" O PHE C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 653 removed outlier: 3.660A pdb=" N ILE C 649 " --> pdb=" O ASN C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 687 removed outlier: 3.595A pdb=" N ILE C 659 " --> pdb=" O VAL C 655 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE C 669 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 242 Processing helix chain 'D' and resid 246 through 259 removed outlier: 3.707A pdb=" N THR D 250 " --> pdb=" O VAL D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 285 through 290 Processing helix chain 'D' and resid 308 through 312 Processing helix chain 'D' and resid 335 through 339 removed outlier: 4.604A pdb=" N ASP D 339 " --> pdb=" O ASP D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 367 removed outlier: 4.010A pdb=" N TRP D 366 " --> pdb=" O GLY D 363 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE D 367 " --> pdb=" O THR D 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 363 through 367' Processing helix chain 'D' and resid 398 through 412 Processing helix chain 'D' and resid 467 through 494 removed outlier: 3.597A pdb=" N PHE D 471 " --> pdb=" O THR D 467 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU D 493 " --> pdb=" O VAL D 489 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU D 494 " --> pdb=" O GLU D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 528 removed outlier: 4.440A pdb=" N VAL D 513 " --> pdb=" O CYS D 509 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL D 515 " --> pdb=" O ASP D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 537 Processing helix chain 'D' and resid 538 through 541 Processing helix chain 'D' and resid 548 through 572 Processing helix chain 'D' and resid 573 through 578 removed outlier: 3.912A pdb=" N ILE D 577 " --> pdb=" O LEU D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 592 Processing helix chain 'D' and resid 601 through 619 Processing helix chain 'D' and resid 623 through 628 removed outlier: 3.779A pdb=" N SER D 627 " --> pdb=" O ASP D 624 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR D 628 " --> pdb=" O ASP D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 642 removed outlier: 3.593A pdb=" N ILE D 633 " --> pdb=" O PHE D 629 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU D 641 " --> pdb=" O PHE D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 653 removed outlier: 3.664A pdb=" N ILE D 649 " --> pdb=" O ASN D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 687 removed outlier: 3.609A pdb=" N ILE D 659 " --> pdb=" O VAL D 655 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE D 669 " --> pdb=" O VAL D 665 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 391 through 394 removed outlier: 6.685A pdb=" N ARG A 320 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE A 424 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG A 322 " --> pdb=" O THR A 422 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR A 422 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU A 324 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 435 " --> pdb=" O ASN A 430 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 391 through 394 removed outlier: 6.685A pdb=" N ARG A 320 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE A 424 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG A 322 " --> pdb=" O THR A 422 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR A 422 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU A 324 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 435 " --> pdb=" O ASN A 430 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AA4, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.688A pdb=" N ARG B 320 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE B 424 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ARG B 322 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THR B 422 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU B 324 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 435 " --> pdb=" O ASN B 430 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.688A pdb=" N ARG B 320 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE B 424 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ARG B 322 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THR B 422 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU B 324 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 435 " --> pdb=" O ASN B 430 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 379 through 380 Processing sheet with id=AA7, first strand: chain 'C' and resid 391 through 394 removed outlier: 6.684A pdb=" N ARG C 320 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE C 424 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ARG C 322 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR C 422 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU C 324 " --> pdb=" O ARG C 420 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 435 " --> pdb=" O ASN C 430 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 391 through 394 removed outlier: 6.684A pdb=" N ARG C 320 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE C 424 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ARG C 322 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR C 422 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU C 324 " --> pdb=" O ARG C 420 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 435 " --> pdb=" O ASN C 430 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 379 through 380 Processing sheet with id=AB1, first strand: chain 'D' and resid 391 through 394 removed outlier: 6.658A pdb=" N ARG D 320 " --> pdb=" O ILE D 424 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE D 424 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG D 322 " --> pdb=" O THR D 422 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N THR D 422 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU D 324 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU D 435 " --> pdb=" O ASN D 430 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 391 through 394 removed outlier: 6.658A pdb=" N ARG D 320 " --> pdb=" O ILE D 424 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE D 424 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG D 322 " --> pdb=" O THR D 422 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N THR D 422 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU D 324 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU D 435 " --> pdb=" O ASN D 430 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 379 through 380 861 hydrogen bonds defined for protein. 2463 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: 4.85 Time building geometry restraints manager: 4.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2408 1.30 - 1.43: 4742 1.43 - 1.56: 8915 1.56 - 1.68: 7 1.68 - 1.81: 124 Bond restraints: 16196 Sorted by residual: bond pdb=" C1 AQV A1005 " pdb=" C2 AQV A1005 " ideal model delta sigma weight residual 1.381 1.548 -0.167 2.00e-02 2.50e+03 6.95e+01 bond pdb=" C1 AQV D1004 " pdb=" C2 AQV D1004 " ideal model delta sigma weight residual 1.381 1.548 -0.167 2.00e-02 2.50e+03 6.94e+01 bond pdb=" C1 AQV C1004 " pdb=" C2 AQV C1004 " ideal model delta sigma weight residual 1.381 1.547 -0.166 2.00e-02 2.50e+03 6.91e+01 bond pdb=" C1 AQV B1004 " pdb=" C2 AQV B1004 " ideal model delta sigma weight residual 1.381 1.547 -0.166 2.00e-02 2.50e+03 6.90e+01 bond pdb=" C5 AQV A1005 " pdb=" C6 AQV A1005 " ideal model delta sigma weight residual 1.381 1.543 -0.162 2.00e-02 2.50e+03 6.53e+01 ... (remaining 16191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 21400 2.02 - 4.04: 497 4.04 - 6.06: 72 6.06 - 8.08: 22 8.08 - 10.10: 9 Bond angle restraints: 22000 Sorted by residual: angle pdb=" N SER B 587 " pdb=" CA SER B 587 " pdb=" C SER B 587 " ideal model delta sigma weight residual 110.97 103.01 7.96 1.09e+00 8.42e-01 5.33e+01 angle pdb=" N SER A 587 " pdb=" CA SER A 587 " pdb=" C SER A 587 " ideal model delta sigma weight residual 110.80 102.00 8.80 2.13e+00 2.20e-01 1.71e+01 angle pdb=" N THR B 589 " pdb=" CA THR B 589 " pdb=" C THR B 589 " ideal model delta sigma weight residual 111.28 115.76 -4.48 1.09e+00 8.42e-01 1.69e+01 angle pdb=" C PHE B 310 " pdb=" N TYR B 311 " pdb=" CA TYR B 311 " ideal model delta sigma weight residual 121.54 128.26 -6.72 1.91e+00 2.74e-01 1.24e+01 angle pdb=" C PHE D 310 " pdb=" N TYR D 311 " pdb=" CA TYR D 311 " ideal model delta sigma weight residual 121.54 128.16 -6.62 1.91e+00 2.74e-01 1.20e+01 ... (remaining 21995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.50: 9299 35.50 - 71.00: 191 71.00 - 106.50: 46 106.50 - 142.00: 4 142.00 - 177.49: 8 Dihedral angle restraints: 9548 sinusoidal: 4000 harmonic: 5548 Sorted by residual: dihedral pdb=" CA CYS C 331 " pdb=" C CYS C 331 " pdb=" N SER C 332 " pdb=" CA SER C 332 " ideal model delta harmonic sigma weight residual 180.00 150.30 29.70 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA CYS D 331 " pdb=" C CYS D 331 " pdb=" N SER D 332 " pdb=" CA SER D 332 " ideal model delta harmonic sigma weight residual 180.00 150.33 29.67 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA CYS B 331 " pdb=" C CYS B 331 " pdb=" N SER B 332 " pdb=" CA SER B 332 " ideal model delta harmonic sigma weight residual 180.00 150.43 29.57 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 9545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1643 0.037 - 0.074: 574 0.074 - 0.110: 189 0.110 - 0.147: 52 0.147 - 0.184: 10 Chirality restraints: 2468 Sorted by residual: chirality pdb=" CA SER A 587 " pdb=" N SER A 587 " pdb=" C SER A 587 " pdb=" CB SER A 587 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CA SER B 587 " pdb=" N SER B 587 " pdb=" C SER B 587 " pdb=" CB SER B 587 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.32e-01 chirality pdb=" CA ARG B 592 " pdb=" N ARG B 592 " pdb=" C ARG B 592 " pdb=" CB ARG B 592 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.47e-01 ... (remaining 2465 not shown) Planarity restraints: 2720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 585 " 0.012 2.00e-02 2.50e+03 2.52e-02 6.36e+00 pdb=" C GLN A 585 " -0.044 2.00e-02 2.50e+03 pdb=" O GLN A 585 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU A 586 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 585 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.25e+00 pdb=" C GLN C 585 " -0.043 2.00e-02 2.50e+03 pdb=" O GLN C 585 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU C 586 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 585 " 0.011 2.00e-02 2.50e+03 2.34e-02 5.45e+00 pdb=" C GLN B 585 " -0.040 2.00e-02 2.50e+03 pdb=" O GLN B 585 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU B 586 " 0.014 2.00e-02 2.50e+03 ... (remaining 2717 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.24: 12 2.24 - 2.91: 6670 2.91 - 3.57: 22302 3.57 - 4.24: 34906 4.24 - 4.90: 62124 Nonbonded interactions: 126014 Sorted by model distance: nonbonded pdb=" CE1 TYR A 684 " pdb=" OH TYR D 684 " model vdw 1.579 3.340 nonbonded pdb=" O GLN D 585 " pdb=" CG2 THR D 589 " model vdw 1.990 3.460 nonbonded pdb=" OH TYR D 386 " pdb=" OE1 GLU D 444 " model vdw 2.199 3.040 nonbonded pdb=" OH TYR A 386 " pdb=" OE1 GLU A 444 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR B 386 " pdb=" OE1 GLU B 444 " model vdw 2.203 3.040 ... (remaining 126009 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' and (resid 215 through 688 or resid 1001 through 1003)) selection = (chain 'B' and (resid 215 through 688 or resid 1001 through 1003)) selection = (chain 'C' and (resid 215 through 688 or resid 1001 through 1003)) selection = (chain 'D' and (resid 215 through 688 or resid 1001 through 1003)) } 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: 0.810 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: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 34.920 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.060 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:12.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4027 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 : 0.009 0.167 16196 Z= 0.553 Angle : 0.748 10.097 22000 Z= 0.403 Chirality : 0.044 0.184 2468 Planarity : 0.004 0.037 2708 Dihedral : 16.919 177.494 5952 Min Nonbonded Distance : 1.579 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.62 % Favored : 91.16 % Rotamer: Outliers : 0.53 % Allowed : 0.88 % Favored : 98.58 % 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: -0.87 (0.20), residues: 1856 helix: 0.45 (0.17), residues: 924 sheet: -1.09 (0.37), residues: 176 loop : -1.72 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 554 HIS 0.002 0.001 HIS B 501 PHE 0.028 0.001 PHE C 483 TYR 0.023 0.001 TYR D 249 ARG 0.005 0.000 ARG B 306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 458 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 MET cc_start: 0.4029 (ppp) cc_final: 0.3825 (ttt) REVERT: B 478 ILE cc_start: 0.7726 (mm) cc_final: 0.7472 (pt) REVERT: B 482 PHE cc_start: 0.8466 (m-10) cc_final: 0.7895 (t80) REVERT: B 649 ILE cc_start: 0.8323 (mt) cc_final: 0.8063 (OUTLIER) REVERT: D 256 LEU cc_start: 0.2769 (tp) cc_final: 0.2512 (mt) REVERT: D 345 TYR cc_start: 0.4546 (m-80) cc_final: 0.0840 (m-80) outliers start: 9 outliers final: 3 residues processed: 463 average time/residue: 0.9717 time to fit residues: 510.3830 Evaluate side-chains 264 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 262 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 589 THR Chi-restraints excluded: chain D residue 588 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.0770 chunk 139 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 0.0050 chunk 74 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 167 optimal weight: 20.0000 overall best weight: 1.1554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 HIS A 458 GLN ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN A 585 GLN B 313 ASN B 412 ASN B 531 ASN B 547 ASN B 636 GLN C 313 ASN C 323 GLN C 412 ASN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 636 GLN C 674 ASN D 323 GLN ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 HIS D 578 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.178845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.156406 restraints weight = 33016.590| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 4.05 r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5747 moved from start: 0.5849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16196 Z= 0.268 Angle : 0.828 11.691 22000 Z= 0.413 Chirality : 0.046 0.198 2468 Planarity : 0.005 0.058 2708 Dihedral : 17.920 169.282 2402 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.70 % Favored : 92.24 % Rotamer: Outliers : 4.42 % Allowed : 13.38 % Favored : 82.19 % 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: -0.66 (0.20), residues: 1856 helix: 0.48 (0.16), residues: 984 sheet: -0.91 (0.40), residues: 192 loop : -1.60 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 293 HIS 0.004 0.001 HIS C 379 PHE 0.048 0.003 PHE C 664 TYR 0.022 0.002 TYR A 249 ARG 0.009 0.001 ARG D 338 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 296 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.6275 (ptm) cc_final: 0.5343 (tpp) REVERT: A 583 MET cc_start: 0.5684 (ppp) cc_final: 0.5079 (ttt) REVERT: A 648 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7458 (mt-10) REVERT: B 235 CYS cc_start: 0.7265 (m) cc_final: 0.6998 (p) REVERT: B 289 ASP cc_start: 0.7361 (m-30) cc_final: 0.7076 (m-30) REVERT: B 348 TYR cc_start: 0.8415 (t80) cc_final: 0.7787 (t80) REVERT: B 372 LYS cc_start: 0.8579 (mppt) cc_final: 0.8350 (ttmt) REVERT: B 440 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7908 (tpp80) REVERT: B 482 PHE cc_start: 0.8742 (m-10) cc_final: 0.8089 (t80) REVERT: B 502 TYR cc_start: 0.6297 (t80) cc_final: 0.5883 (t80) REVERT: B 595 LYS cc_start: 0.5086 (OUTLIER) cc_final: 0.4741 (tptm) REVERT: C 307 SER cc_start: 0.8399 (OUTLIER) cc_final: 0.7867 (t) REVERT: C 310 PHE cc_start: 0.7811 (m-10) cc_final: 0.6457 (m-80) REVERT: C 644 ILE cc_start: 0.6417 (mp) cc_final: 0.6058 (tt) REVERT: D 245 ASN cc_start: 0.7686 (t0) cc_final: 0.7092 (p0) REVERT: D 259 ASP cc_start: 0.7910 (t0) cc_final: 0.7688 (t0) REVERT: D 315 LEU cc_start: 0.3440 (OUTLIER) cc_final: 0.2942 (tt) REVERT: D 484 ILE cc_start: 0.3929 (OUTLIER) cc_final: 0.3630 (pt) outliers start: 75 outliers final: 19 residues processed: 344 average time/residue: 0.8187 time to fit residues: 327.2803 Evaluate side-chains 253 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 229 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 280 TRP Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 455 TRP Chi-restraints excluded: chain B residue 481 CYS Chi-restraints excluded: chain B residue 506 PHE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 414 TRP Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 455 TRP Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 477 GLU Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 589 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 147 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 chunk 168 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN A 585 GLN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN B 559 ASN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 547 ASN D 323 GLN D 379 HIS ** D 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 557 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.165580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.141343 restraints weight = 32765.603| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 4.00 r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.8764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 16196 Z= 0.245 Angle : 0.813 11.014 22000 Z= 0.400 Chirality : 0.044 0.229 2468 Planarity : 0.005 0.054 2708 Dihedral : 16.589 175.368 2400 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 4.30 % Allowed : 18.10 % Favored : 77.59 % 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: -0.58 (0.20), residues: 1856 helix: 0.76 (0.17), residues: 972 sheet: -0.41 (0.42), residues: 168 loop : -2.00 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 293 HIS 0.002 0.001 HIS C 550 PHE 0.029 0.002 PHE B 669 TYR 0.023 0.002 TYR B 249 ARG 0.006 0.001 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 294 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 TRP cc_start: 0.6756 (OUTLIER) cc_final: 0.5799 (m-10) REVERT: A 346 ASP cc_start: 0.7806 (m-30) cc_final: 0.7522 (m-30) REVERT: A 507 TRP cc_start: 0.5357 (m100) cc_final: 0.4058 (p90) REVERT: A 583 MET cc_start: 0.5685 (ppp) cc_final: 0.5265 (ttt) REVERT: A 585 GLN cc_start: -0.1444 (OUTLIER) cc_final: -0.1878 (pt0) REVERT: B 242 MET cc_start: 0.7067 (tpt) cc_final: 0.6707 (tpp) REVERT: B 348 TYR cc_start: 0.8348 (t80) cc_final: 0.7999 (t80) REVERT: B 482 PHE cc_start: 0.8757 (m-10) cc_final: 0.8211 (t80) REVERT: B 595 LYS cc_start: 0.5350 (OUTLIER) cc_final: 0.5032 (tmtt) REVERT: C 236 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7489 (tp) REVERT: C 278 ASP cc_start: 0.7273 (m-30) cc_final: 0.6911 (m-30) REVERT: C 307 SER cc_start: 0.8831 (OUTLIER) cc_final: 0.8213 (t) REVERT: C 312 GLU cc_start: 0.7801 (pt0) cc_final: 0.7563 (pt0) REVERT: C 335 GLN cc_start: 0.7536 (tp-100) cc_final: 0.7092 (tt0) REVERT: D 241 MET cc_start: 0.6354 (tmm) cc_final: 0.6136 (ttp) REVERT: D 245 ASN cc_start: 0.8177 (t0) cc_final: 0.7731 (p0) REVERT: D 253 MET cc_start: 0.7183 (mmm) cc_final: 0.6970 (mmm) REVERT: D 293 TRP cc_start: 0.7812 (m100) cc_final: 0.7567 (m100) REVERT: D 312 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6541 (pm20) REVERT: D 485 PHE cc_start: 0.6596 (OUTLIER) cc_final: 0.6185 (t80) REVERT: D 539 LEU cc_start: 0.7451 (mm) cc_final: 0.6773 (tm) REVERT: D 593 CYS cc_start: 0.2216 (p) cc_final: 0.1986 (m) REVERT: D 660 TYR cc_start: 0.6105 (OUTLIER) cc_final: 0.4305 (t80) outliers start: 73 outliers final: 17 residues processed: 342 average time/residue: 0.7967 time to fit residues: 318.2823 Evaluate side-chains 246 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 221 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 280 TRP Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 506 PHE Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 506 PHE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 477 GLU Chi-restraints excluded: chain D residue 485 PHE Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 660 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 167 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 90 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 154 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 GLN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 559 ASN C 613 GLN D 456 GLN D 636 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.147000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.121395 restraints weight = 31811.336| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 3.75 r_work: 0.3719 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 1.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 16196 Z= 0.292 Angle : 0.903 25.096 22000 Z= 0.432 Chirality : 0.049 0.507 2468 Planarity : 0.005 0.055 2708 Dihedral : 16.781 177.005 2400 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 4.72 % Allowed : 21.58 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.76 (0.19), residues: 1856 helix: 0.70 (0.16), residues: 964 sheet: -0.91 (0.41), residues: 164 loop : -2.08 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 455 HIS 0.005 0.001 HIS A 379 PHE 0.028 0.002 PHE D 279 TYR 0.021 0.002 TYR C 249 ARG 0.007 0.001 ARG A 581 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 290 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.6638 (OUTLIER) cc_final: 0.6315 (tpp) REVERT: A 458 GLN cc_start: 0.8291 (pp30) cc_final: 0.7954 (tm-30) REVERT: A 460 LEU cc_start: 0.8545 (tp) cc_final: 0.8117 (mt) REVERT: A 585 GLN cc_start: -0.0535 (OUTLIER) cc_final: -0.0776 (pt0) REVERT: A 598 PHE cc_start: 0.6670 (OUTLIER) cc_final: 0.6458 (m-80) REVERT: A 617 LEU cc_start: 0.8828 (tp) cc_final: 0.8603 (mm) REVERT: A 669 PHE cc_start: 0.7297 (OUTLIER) cc_final: 0.6811 (t80) REVERT: A 675 MET cc_start: 0.6526 (ppp) cc_final: 0.6245 (pp-130) REVERT: B 312 GLU cc_start: 0.8312 (pt0) cc_final: 0.7796 (pm20) REVERT: B 482 PHE cc_start: 0.8693 (m-10) cc_final: 0.8304 (t80) REVERT: B 503 PHE cc_start: 0.5180 (p90) cc_final: 0.4962 (m-10) REVERT: B 582 THR cc_start: 0.3833 (OUTLIER) cc_final: 0.3611 (p) REVERT: B 595 LYS cc_start: 0.5597 (OUTLIER) cc_final: 0.5253 (tmtt) REVERT: B 611 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.8242 (t80) REVERT: B 650 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8056 (tm-30) REVERT: B 669 PHE cc_start: 0.6160 (p90) cc_final: 0.5943 (m-10) REVERT: C 236 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7743 (tp) REVERT: C 242 MET cc_start: 0.7615 (tpp) cc_final: 0.7159 (tpp) REVERT: C 251 ARG cc_start: 0.9110 (tmm-80) cc_final: 0.8723 (ttt90) REVERT: C 252 MET cc_start: 0.8299 (tmm) cc_final: 0.7676 (mpp) REVERT: C 253 MET cc_start: 0.9000 (tpt) cc_final: 0.8613 (tpp) REVERT: C 259 ASP cc_start: 0.8777 (m-30) cc_final: 0.8452 (m-30) REVERT: C 278 ASP cc_start: 0.8260 (m-30) cc_final: 0.7768 (m-30) REVERT: C 312 GLU cc_start: 0.8184 (pt0) cc_final: 0.7970 (pt0) REVERT: C 335 GLN cc_start: 0.7930 (tp-100) cc_final: 0.7456 (tt0) REVERT: C 336 ASP cc_start: 0.8342 (t0) cc_final: 0.7477 (m-30) REVERT: D 245 ASN cc_start: 0.8586 (t0) cc_final: 0.8372 (p0) REVERT: D 255 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8567 (pp30) REVERT: D 312 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7159 (pm20) REVERT: D 324 LEU cc_start: 0.7566 (mt) cc_final: 0.7330 (mm) REVERT: D 344 CYS cc_start: 0.4282 (OUTLIER) cc_final: 0.3225 (t) REVERT: D 413 VAL cc_start: 0.5730 (t) cc_final: 0.5499 (m) REVERT: D 414 TRP cc_start: 0.6634 (OUTLIER) cc_final: 0.6262 (t60) REVERT: D 471 PHE cc_start: 0.6711 (m-80) cc_final: 0.5434 (t80) REVERT: D 485 PHE cc_start: 0.7099 (OUTLIER) cc_final: 0.6602 (t80) REVERT: D 545 PHE cc_start: 0.6175 (OUTLIER) cc_final: 0.5940 (m-80) REVERT: D 590 MET cc_start: 0.6510 (tpp) cc_final: 0.6079 (tpp) REVERT: D 593 CYS cc_start: 0.3518 (p) cc_final: 0.3219 (m) REVERT: D 611 TYR cc_start: 0.8221 (OUTLIER) cc_final: 0.7049 (t80) outliers start: 80 outliers final: 17 residues processed: 345 average time/residue: 0.8490 time to fit residues: 341.8064 Evaluate side-chains 235 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 598 PHE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 506 PHE Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 506 PHE Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 414 TRP Chi-restraints excluded: chain D residue 477 GLU Chi-restraints excluded: chain D residue 485 PHE Chi-restraints excluded: chain D residue 545 PHE Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 611 TYR Chi-restraints excluded: chain D residue 676 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 58.21 > 50: distance: 45 - 49: 12.907 distance: 49 - 50: 4.953 distance: 50 - 51: 6.239 distance: 50 - 53: 21.288 distance: 51 - 52: 6.984 distance: 51 - 56: 8.480 distance: 53 - 54: 25.635 distance: 53 - 55: 22.903 distance: 56 - 57: 13.676 distance: 57 - 58: 9.288 distance: 57 - 60: 28.748 distance: 58 - 59: 37.016 distance: 58 - 62: 14.591 distance: 60 - 61: 6.068 distance: 62 - 63: 31.159 distance: 63 - 64: 36.964 distance: 63 - 66: 16.584 distance: 64 - 65: 6.585 distance: 64 - 68: 51.806 distance: 66 - 67: 32.355 distance: 68 - 69: 10.720 distance: 69 - 70: 12.550 distance: 69 - 72: 12.481 distance: 70 - 71: 22.405 distance: 70 - 77: 32.808 distance: 72 - 73: 12.467 distance: 73 - 74: 7.673 distance: 74 - 75: 6.224 distance: 74 - 76: 9.601 distance: 77 - 78: 16.315 distance: 78 - 79: 22.706 distance: 78 - 81: 21.886 distance: 79 - 80: 20.235 distance: 79 - 85: 7.891 distance: 81 - 82: 22.298 distance: 82 - 83: 5.686 distance: 82 - 84: 24.286 distance: 85 - 86: 8.212 distance: 86 - 87: 14.935 distance: 86 - 89: 30.836 distance: 87 - 88: 28.547 distance: 87 - 96: 37.917 distance: 89 - 90: 15.471 distance: 90 - 91: 12.791 distance: 91 - 92: 16.129 distance: 92 - 93: 8.089 distance: 93 - 94: 5.122 distance: 93 - 95: 5.093 distance: 96 - 97: 30.195 distance: 97 - 98: 30.387 distance: 97 - 100: 15.301 distance: 98 - 99: 36.285 distance: 98 - 101: 20.713 distance: 101 - 102: 22.680 distance: 101 - 107: 39.111 distance: 102 - 103: 17.709 distance: 102 - 105: 18.455 distance: 103 - 104: 40.962 distance: 103 - 108: 49.771 distance: 105 - 106: 23.696 distance: 106 - 107: 29.727 distance: 108 - 109: 7.674 distance: 109 - 110: 8.158 distance: 109 - 112: 6.635 distance: 110 - 111: 7.566 distance: 110 - 119: 17.877 distance: 112 - 113: 10.268 distance: 113 - 114: 7.230 distance: 113 - 115: 12.834 distance: 114 - 116: 7.501 distance: 115 - 117: 19.850 distance: 116 - 118: 10.406 distance: 117 - 118: 9.459 distance: 119 - 120: 15.427 distance: 120 - 121: 34.063 distance: 121 - 122: 8.911 distance: 121 - 123: 21.268