Starting phenix.real_space_refine on Thu Jul 31 10:37:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jn9_61620/07_2025/9jn9_61620.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jn9_61620/07_2025/9jn9_61620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jn9_61620/07_2025/9jn9_61620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jn9_61620/07_2025/9jn9_61620.map" model { file = "/net/cci-nas-00/data/ceres_data/9jn9_61620/07_2025/9jn9_61620.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jn9_61620/07_2025/9jn9_61620.cif" } resolution = 3.36 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= 1.000 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 Zn 2 6.06 5 S 100 5.16 5 C 8670 2.51 5 N 2306 2.21 5 O 2474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13552 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 846, 6775 Classifications: {'peptide': 846} Link IDs: {'PTRANS': 38, 'TRANS': 807} Chain breaks: 3 Chain: "B" Number of atoms: 6775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 846, 6775 Classifications: {'peptide': 846} Link IDs: {'PTRANS': 38, 'TRANS': 807} Chain breaks: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2072 SG CYS A 284 53.528 75.596 52.688 1.00 65.80 S ATOM 2346 SG CYS A 318 53.295 76.925 49.259 1.00 65.43 S ATOM 8847 SG CYS B 284 75.034 30.675 53.232 1.00 69.68 S ATOM 9121 SG CYS B 318 74.985 29.394 49.527 1.00 67.45 S Time building chain proxies: 8.08, per 1000 atoms: 0.60 Number of scatterers: 13552 At special positions: 0 Unit cell: (129.105, 106.875, 127.395, 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) Zn 2 29.99 S 100 16.00 O 2474 8.00 N 2306 7.00 C 8670 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: 2.98 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 282 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 318 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 284 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 284 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 318 " pdb="ZN ZN B1001 " - pdb=" ND1 HIS B 282 " 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3216 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 17 sheets defined 38.2% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 25 through 32 removed outlier: 3.543A pdb=" N MET A 32 " --> pdb=" O ASN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 56 removed outlier: 3.628A pdb=" N LYS A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.501A pdb=" N HIS A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 88 Processing helix chain 'A' and resid 142 through 160 removed outlier: 3.590A pdb=" N GLY A 160 " --> pdb=" O ARG A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 187 removed outlier: 4.187A pdb=" N ILE A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 220 through 238 removed outlier: 3.642A pdb=" N ILE A 224 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Proline residue: A 229 - end of helix removed outlier: 3.524A pdb=" N ASN A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 275 removed outlier: 4.111A pdb=" N GLU A 272 " --> pdb=" O LYS A 268 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ASN A 273 " --> pdb=" O LYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 349 removed outlier: 4.047A pdb=" N VAL A 346 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N MET A 347 " --> pdb=" O GLN A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 395 removed outlier: 5.884A pdb=" N GLU A 388 " --> pdb=" O HIS A 384 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ALA A 389 " --> pdb=" O LYS A 385 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 417 removed outlier: 3.630A pdb=" N CYS A 410 " --> pdb=" O PRO A 406 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A 414 " --> pdb=" O CYS A 410 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER A 415 " --> pdb=" O LYS A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 429 removed outlier: 4.595A pdb=" N HIS A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 447 Processing helix chain 'A' and resid 478 through 492 removed outlier: 4.018A pdb=" N LEU A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU A 483 " --> pdb=" O PRO A 479 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR A 484 " --> pdb=" O GLY A 480 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A 488 " --> pdb=" O TYR A 484 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N HIS A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 497 Processing helix chain 'A' and resid 537 through 553 removed outlier: 3.553A pdb=" N MET A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 581 removed outlier: 4.120A pdb=" N CYS A 565 " --> pdb=" O ASP A 561 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLU A 566 " --> pdb=" O GLN A 562 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN A 569 " --> pdb=" O CYS A 565 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET A 573 " --> pdb=" O ASN A 569 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 584 No H-bonds generated for 'chain 'A' and resid 582 through 584' Processing helix chain 'A' and resid 598 through 603 Processing helix chain 'A' and resid 604 through 615 removed outlier: 4.134A pdb=" N GLU A 608 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS A 609 " --> pdb=" O LYS A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 632 Processing helix chain 'A' and resid 644 through 649 removed outlier: 3.574A pdb=" N MET A 649 " --> pdb=" O ARG A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 682 removed outlier: 3.757A pdb=" N THR A 682 " --> pdb=" O ALA A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 708 removed outlier: 3.766A pdb=" N ILE A 708 " --> pdb=" O PRO A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 750 removed outlier: 3.675A pdb=" N VAL A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS A 747 " --> pdb=" O LYS A 743 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ARG A 748 " --> pdb=" O GLU A 744 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE A 749 " --> pdb=" O GLU A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 764 removed outlier: 3.892A pdb=" N THR A 761 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 762 " --> pdb=" O PRO A 759 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA A 763 " --> pdb=" O ASP A 760 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU A 764 " --> pdb=" O THR A 761 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 758 through 764' Processing helix chain 'A' and resid 793 through 798 removed outlier: 3.921A pdb=" N TYR A 797 " --> pdb=" O GLN A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 804 removed outlier: 3.778A pdb=" N HIS A 803 " --> pdb=" O ALA A 799 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER A 804 " --> pdb=" O ARG A 800 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 799 through 804' Processing helix chain 'A' and resid 824 through 829 Processing helix chain 'A' and resid 832 through 837 Processing helix chain 'A' and resid 889 through 894 removed outlier: 3.668A pdb=" N PHE A 894 " --> pdb=" O LYS A 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 32 Processing helix chain 'B' and resid 34 through 56 removed outlier: 3.777A pdb=" N LYS B 38 " --> pdb=" O ASN B 34 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 removed outlier: 3.520A pdb=" N HIS B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 88 Processing helix chain 'B' and resid 142 through 160 Processing helix chain 'B' and resid 183 through 185 No H-bonds generated for 'chain 'B' and resid 183 through 185' Processing helix chain 'B' and resid 186 through 192 removed outlier: 3.892A pdb=" N PHE B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 238 removed outlier: 3.852A pdb=" N ILE B 224 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) Proline residue: B 229 - end of helix removed outlier: 3.666A pdb=" N SER B 233 " --> pdb=" O PRO B 229 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 275 removed outlier: 4.002A pdb=" N GLU B 272 " --> pdb=" O LYS B 268 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASN B 273 " --> pdb=" O LYS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 349 removed outlier: 3.975A pdb=" N VAL B 346 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N MET B 347 " --> pdb=" O GLN B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 395 removed outlier: 5.812A pdb=" N GLU B 388 " --> pdb=" O HIS B 384 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ALA B 389 " --> pdb=" O LYS B 385 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS B 393 " --> pdb=" O ALA B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 417 removed outlier: 3.786A pdb=" N CYS B 410 " --> pdb=" O PRO B 406 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 415 " --> pdb=" O LYS B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 429 removed outlier: 3.729A pdb=" N ILE B 428 " --> pdb=" O MET B 424 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N HIS B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 447 Processing helix chain 'B' and resid 477 through 492 removed outlier: 3.954A pdb=" N LEU B 482 " --> pdb=" O TRP B 478 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU B 483 " --> pdb=" O PRO B 479 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N TYR B 484 " --> pdb=" O GLY B 480 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS B 490 " --> pdb=" O ARG B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 497 Processing helix chain 'B' and resid 537 through 553 removed outlier: 3.511A pdb=" N MET B 541 " --> pdb=" O ASP B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 584 removed outlier: 4.508A pdb=" N CYS B 565 " --> pdb=" O ASP B 561 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N GLU B 566 " --> pdb=" O GLN B 562 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU B 574 " --> pdb=" O LEU B 570 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 582 " --> pdb=" O LEU B 578 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 615 removed outlier: 3.993A pdb=" N ILE B 604 " --> pdb=" O THR B 600 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS B 605 " --> pdb=" O ALA B 601 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE B 606 " --> pdb=" O LEU B 602 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N MET B 607 " --> pdb=" O ALA B 603 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU B 608 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS B 609 " --> pdb=" O LYS B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 632 Processing helix chain 'B' and resid 644 through 649 Processing helix chain 'B' and resid 674 through 682 removed outlier: 3.654A pdb=" N THR B 682 " --> pdb=" O ALA B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 708 Processing helix chain 'B' and resid 735 through 750 removed outlier: 3.763A pdb=" N LYS B 747 " --> pdb=" O LYS B 743 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG B 748 " --> pdb=" O GLU B 744 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE B 749 " --> pdb=" O GLU B 745 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 750 " --> pdb=" O MET B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 763 removed outlier: 3.734A pdb=" N THR B 761 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA B 763 " --> pdb=" O ASP B 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 758 through 763' Processing helix chain 'B' and resid 772 through 778 Processing helix chain 'B' and resid 792 through 796 removed outlier: 3.619A pdb=" N ALA B 795 " --> pdb=" O GLU B 792 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN B 796 " --> pdb=" O GLN B 793 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 792 through 796' Processing helix chain 'B' and resid 799 through 803 removed outlier: 3.748A pdb=" N CYS B 802 " --> pdb=" O ALA B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 809 removed outlier: 3.632A pdb=" N GLY B 809 " --> pdb=" O PHE B 806 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 825 removed outlier: 3.615A pdb=" N ARG B 825 " --> pdb=" O GLY B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 841 removed outlier: 3.577A pdb=" N THR B 841 " --> pdb=" O GLU B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 895 removed outlier: 3.645A pdb=" N PHE B 894 " --> pdb=" O HIS B 890 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA B 895 " --> pdb=" O LYS B 891 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 890 through 895' Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 62 removed outlier: 3.512A pdb=" N ASP A 97 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 245 removed outlier: 3.808A pdb=" N VAL A 309 " --> pdb=" O LEU A 297 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 403 through 404 removed outlier: 6.229A pdb=" N GLN A 403 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N PHE A 438 " --> pdb=" O GLN A 403 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 439 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP A 457 " --> pdb=" O SER A 439 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N CYS A 456 " --> pdb=" O ILE A 472 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 403 through 404 removed outlier: 6.229A pdb=" N GLN A 403 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N PHE A 438 " --> pdb=" O GLN A 403 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 439 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP A 457 " --> pdb=" O SER A 439 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 460 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 468 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 659 through 660 removed outlier: 7.147A pdb=" N ILE A 659 " --> pdb=" O TRP A 700 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N PHE A 702 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU A 589 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N LEU A 703 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ILE A 591 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LYS A 726 " --> pdb=" O GLU A 588 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE A 590 " --> pdb=" O LYS A 726 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 622 through 624 Processing sheet with id=AA8, first strand: chain 'A' and resid 734 through 735 removed outlier: 7.006A pdb=" N CYS A 734 " --> pdb=" O LEU A 779 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 782 through 784 removed outlier: 6.161A pdb=" N VAL A 782 " --> pdb=" O LEU A 902 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR A 874 " --> pdb=" O HIS A 901 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N TYR A 903 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N VAL A 876 " --> pdb=" O TYR A 903 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 816 through 819 removed outlier: 5.963A pdb=" N ILE A 817 " --> pdb=" O ASP A 863 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 59 through 62 removed outlier: 3.567A pdb=" N ASP B 97 " --> pdb=" O PHE B 108 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 132 through 133 Processing sheet with id=AB4, first strand: chain 'B' and resid 243 through 245 removed outlier: 3.709A pdb=" N VAL B 309 " --> pdb=" O LEU B 297 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 403 through 404 removed outlier: 6.371A pdb=" N GLN B 403 " --> pdb=" O VAL B 436 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N PHE B 438 " --> pdb=" O GLN B 403 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N CYS B 456 " --> pdb=" O ILE B 472 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA B 458 " --> pdb=" O TYR B 470 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 468 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 659 through 660 removed outlier: 7.141A pdb=" N ILE B 659 " --> pdb=" O TRP B 700 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N PHE B 702 " --> pdb=" O ILE B 659 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU B 589 " --> pdb=" O LEU B 701 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU B 703 " --> pdb=" O LEU B 589 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE B 591 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LYS B 726 " --> pdb=" O GLU B 588 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE B 590 " --> pdb=" O LYS B 726 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 622 through 624 Processing sheet with id=AB8, first strand: chain 'B' and resid 782 through 784 removed outlier: 6.279A pdb=" N VAL B 782 " --> pdb=" O LEU B 902 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR B 874 " --> pdb=" O HIS B 901 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N TYR B 903 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N VAL B 876 " --> pdb=" O TYR B 903 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE B 815 " --> pdb=" O VAL B 861 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ASP B 863 " --> pdb=" O ILE B 815 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ILE B 817 " --> pdb=" O ASP B 863 " (cutoff:3.500A) 350 hydrogen bonds defined for protein. 1002 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: 4.14 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3287 1.33 - 1.45: 2621 1.45 - 1.57: 7788 1.57 - 1.69: 0 1.69 - 1.82: 142 Bond restraints: 13838 Sorted by residual: bond pdb=" N MET B 183 " pdb=" CA MET B 183 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.63e+00 bond pdb=" N LEU B 228 " pdb=" CA LEU B 228 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.41e-02 5.03e+03 8.25e+00 bond pdb=" N LEU A 228 " pdb=" CA LEU A 228 " ideal model delta sigma weight residual 1.457 1.495 -0.039 1.41e-02 5.03e+03 7.46e+00 bond pdb=" N GLU A 421 " pdb=" CA GLU A 421 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 6.90e+00 bond pdb=" N GLU B 421 " pdb=" CA GLU B 421 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.25e-02 6.40e+03 6.40e+00 ... (remaining 13833 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 17834 2.12 - 4.24: 665 4.24 - 6.36: 124 6.36 - 8.48: 36 8.48 - 10.60: 13 Bond angle restraints: 18672 Sorted by residual: angle pdb=" N ASP B 182 " pdb=" CA ASP B 182 " pdb=" C ASP B 182 " ideal model delta sigma weight residual 110.53 100.98 9.55 1.29e+00 6.01e-01 5.48e+01 angle pdb=" N PRO B 229 " pdb=" CA PRO B 229 " pdb=" C PRO B 229 " ideal model delta sigma weight residual 113.81 105.23 8.58 1.45e+00 4.76e-01 3.50e+01 angle pdb=" N GLU A 772 " pdb=" CA GLU A 772 " pdb=" C GLU A 772 " ideal model delta sigma weight residual 114.39 105.94 8.45 1.45e+00 4.76e-01 3.40e+01 angle pdb=" CA ASP B 182 " pdb=" C ASP B 182 " pdb=" O ASP B 182 " ideal model delta sigma weight residual 121.94 115.53 6.41 1.15e+00 7.56e-01 3.11e+01 angle pdb=" C TYR B 770 " pdb=" N GLU B 771 " pdb=" CA GLU B 771 " ideal model delta sigma weight residual 121.54 132.14 -10.60 1.91e+00 2.74e-01 3.08e+01 ... (remaining 18667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 7280 17.77 - 35.54: 914 35.54 - 53.31: 194 53.31 - 71.09: 45 71.09 - 88.86: 17 Dihedral angle restraints: 8450 sinusoidal: 3496 harmonic: 4954 Sorted by residual: dihedral pdb=" C LEU A 228 " pdb=" N LEU A 228 " pdb=" CA LEU A 228 " pdb=" CB LEU A 228 " ideal model delta harmonic sigma weight residual -122.60 -142.13 19.53 0 2.50e+00 1.60e-01 6.10e+01 dihedral pdb=" N LEU A 228 " pdb=" C LEU A 228 " pdb=" CA LEU A 228 " pdb=" CB LEU A 228 " ideal model delta harmonic sigma weight residual 122.80 142.16 -19.36 0 2.50e+00 1.60e-01 6.00e+01 dihedral pdb=" C LEU B 228 " pdb=" N LEU B 228 " pdb=" CA LEU B 228 " pdb=" CB LEU B 228 " ideal model delta harmonic sigma weight residual -122.60 -137.82 15.22 0 2.50e+00 1.60e-01 3.71e+01 ... (remaining 8447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.159: 2067 0.159 - 0.318: 19 0.318 - 0.477: 0 0.477 - 0.636: 1 0.636 - 0.795: 1 Chirality restraints: 2088 Sorted by residual: chirality pdb=" CA LEU A 228 " pdb=" N LEU A 228 " pdb=" C LEU A 228 " pdb=" CB LEU A 228 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.58e+01 chirality pdb=" CA LEU B 228 " pdb=" N LEU B 228 " pdb=" C LEU B 228 " pdb=" CB LEU B 228 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.58e+00 chirality pdb=" CB ILE A 732 " pdb=" CA ILE A 732 " pdb=" CG1 ILE A 732 " pdb=" CG2 ILE A 732 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 2085 not shown) Planarity restraints: 2368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 227 " 0.021 2.00e-02 2.50e+03 4.26e-02 1.81e+01 pdb=" C MET A 227 " -0.074 2.00e-02 2.50e+03 pdb=" O MET A 227 " 0.027 2.00e-02 2.50e+03 pdb=" N LEU A 228 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 718 " 0.052 5.00e-02 4.00e+02 7.74e-02 9.59e+00 pdb=" N PRO B 719 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 719 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 719 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 683 " -0.049 5.00e-02 4.00e+02 7.40e-02 8.77e+00 pdb=" N PRO B 684 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 684 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 684 " -0.042 5.00e-02 4.00e+02 ... (remaining 2365 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3497 2.80 - 3.33: 11514 3.33 - 3.85: 21360 3.85 - 4.38: 23684 4.38 - 4.90: 40611 Nonbonded interactions: 100666 Sorted by model distance: nonbonded pdb=" O ILE A 330 " pdb=" OG1 THR A 337 " model vdw 2.280 3.040 nonbonded pdb=" OG SER B 669 " pdb=" O VAL B 713 " model vdw 2.280 3.040 nonbonded pdb=" O ILE B 330 " pdb=" OG1 THR B 337 " model vdw 2.290 3.040 nonbonded pdb=" O SER B 720 " pdb=" OG SER B 720 " model vdw 2.314 3.040 nonbonded pdb=" OG SER A 441 " pdb=" OH TYR A 484 " model vdw 2.318 3.040 ... (remaining 100661 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.860 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: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.640 Find NCS groups from input model: 0.440 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: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6103 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 : 0.010 0.693 13844 Z= 0.375 Angle : 1.019 10.597 18672 Z= 0.570 Chirality : 0.058 0.795 2088 Planarity : 0.008 0.077 2368 Dihedral : 16.719 88.856 5234 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.44 % Favored : 89.44 % Rotamer: Outliers : 0.99 % Allowed : 8.83 % Favored : 90.18 % Cbeta Deviations : 0.12 % 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: -4.81 (0.16), residues: 1676 helix: -3.45 (0.14), residues: 536 sheet: -2.67 (0.28), residues: 250 loop : -3.23 (0.18), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 674 HIS 0.008 0.001 HIS A 803 PHE 0.030 0.002 PHE A 215 TYR 0.016 0.002 TYR A 623 ARG 0.007 0.001 ARG B 843 Details of bonding type rmsd hydrogen bonds : bond 0.20279 ( 346) hydrogen bonds : angle 8.32888 ( 1002) metal coordination : bond 0.40651 ( 6) covalent geometry : bond 0.00479 (13838) covalent geometry : angle 1.01930 (18672) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 278 time to evaluate : 2.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 SER cc_start: 0.7805 (m) cc_final: 0.7564 (p) REVERT: A 268 LYS cc_start: 0.7938 (tptp) cc_final: 0.7546 (ttpp) REVERT: A 385 LYS cc_start: 0.8035 (tttt) cc_final: 0.7817 (tttt) REVERT: A 391 GLN cc_start: 0.8234 (tm-30) cc_final: 0.7624 (tm-30) REVERT: A 648 PHE cc_start: 0.4959 (t80) cc_final: 0.4174 (t80) REVERT: A 723 PHE cc_start: 0.6125 (OUTLIER) cc_final: 0.5862 (m-10) REVERT: A 770 TYR cc_start: 0.7611 (m-10) cc_final: 0.7404 (m-80) REVERT: A 836 MET cc_start: 0.5331 (mmt) cc_final: 0.4904 (mmt) REVERT: A 861 VAL cc_start: 0.7949 (t) cc_final: 0.7695 (t) REVERT: A 877 PHE cc_start: 0.6804 (m-80) cc_final: 0.6442 (m-80) REVERT: B 183 MET cc_start: 0.4600 (OUTLIER) cc_final: 0.4276 (ttp) REVERT: B 207 SER cc_start: 0.7921 (p) cc_final: 0.7381 (m) REVERT: B 288 PRO cc_start: 0.8639 (Cg_endo) cc_final: 0.8418 (Cg_exo) REVERT: B 437 ILE cc_start: 0.7548 (mm) cc_final: 0.7181 (mt) REVERT: B 499 VAL cc_start: 0.7997 (t) cc_final: 0.7730 (m) REVERT: B 543 ASP cc_start: 0.6994 (t0) cc_final: 0.6744 (t0) REVERT: B 648 PHE cc_start: 0.4726 (t80) cc_final: 0.3713 (t80) REVERT: B 653 PHE cc_start: 0.6726 (m-80) cc_final: 0.6526 (m-80) REVERT: B 836 MET cc_start: 0.5211 (mmt) cc_final: 0.4891 (mmt) outliers start: 15 outliers final: 4 residues processed: 292 average time/residue: 0.3290 time to fit residues: 136.8971 Evaluate side-chains 259 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 253 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 723 PHE Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 228 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 70 optimal weight: 0.0170 chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 131 optimal weight: 0.0980 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 0.0370 chunk 98 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 263 ASN A 282 HIS A 452 GLN A 487 ASN A 575 GLN A 641 GLN A 680 ASN B 28 ASN B 393 HIS B 417 HIS B 673 ASN B 680 ASN B 901 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.197709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.178340 restraints weight = 20731.990| |-----------------------------------------------------------------------------| r_work (start): 0.4253 rms_B_bonded: 2.87 r_work: 0.4152 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 2.331 13844 Z= 0.670 Angle : 0.623 12.015 18672 Z= 0.318 Chirality : 0.043 0.192 2088 Planarity : 0.006 0.065 2368 Dihedral : 5.776 56.200 1827 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.47 % Favored : 91.47 % Rotamer: Outliers : 1.98 % Allowed : 14.36 % Favored : 83.66 % 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: -3.62 (0.18), residues: 1676 helix: -2.09 (0.19), residues: 560 sheet: -2.26 (0.30), residues: 236 loop : -2.68 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 674 HIS 0.010 0.001 HIS B 393 PHE 0.018 0.001 PHE B 448 TYR 0.024 0.001 TYR B 484 ARG 0.007 0.001 ARG B 534 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 346) hydrogen bonds : angle 5.69542 ( 1002) metal coordination : bond 0.95172 ( 6) covalent geometry : bond 0.00254 (13838) covalent geometry : angle 0.62304 (18672) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 250 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ILE cc_start: 0.7865 (mm) cc_final: 0.7556 (mt) REVERT: A 133 ARG cc_start: 0.7242 (tpt90) cc_final: 0.6975 (tpt90) REVERT: A 207 SER cc_start: 0.7899 (m) cc_final: 0.7446 (p) REVERT: A 215 PHE cc_start: 0.6815 (p90) cc_final: 0.6590 (p90) REVERT: A 268 LYS cc_start: 0.8084 (tptp) cc_final: 0.7658 (ttpp) REVERT: A 449 ARG cc_start: 0.8235 (ttp80) cc_final: 0.7895 (ttp80) REVERT: A 452 GLN cc_start: 0.5987 (OUTLIER) cc_final: 0.5741 (pp30) REVERT: A 543 ASP cc_start: 0.7094 (t0) cc_final: 0.6879 (t0) REVERT: A 563 MET cc_start: 0.6963 (OUTLIER) cc_final: 0.5783 (mpp) REVERT: A 648 PHE cc_start: 0.5308 (t80) cc_final: 0.4407 (t80) REVERT: A 655 LYS cc_start: 0.6063 (tppt) cc_final: 0.5849 (tppt) REVERT: A 723 PHE cc_start: 0.6825 (OUTLIER) cc_final: 0.6490 (m-10) REVERT: A 742 MET cc_start: 0.6571 (mmt) cc_final: 0.6331 (mmt) REVERT: A 836 MET cc_start: 0.5512 (mmt) cc_final: 0.4935 (mmt) REVERT: A 837 GLU cc_start: 0.5865 (OUTLIER) cc_final: 0.5554 (mp0) REVERT: A 877 PHE cc_start: 0.6890 (m-80) cc_final: 0.6520 (m-80) REVERT: B 207 SER cc_start: 0.7776 (p) cc_final: 0.7447 (m) REVERT: B 534 ARG cc_start: 0.7419 (mtm110) cc_final: 0.7192 (mtm-85) REVERT: B 588 GLU cc_start: 0.6480 (mp0) cc_final: 0.6020 (pm20) REVERT: B 648 PHE cc_start: 0.4776 (t80) cc_final: 0.3601 (t80) REVERT: B 653 PHE cc_start: 0.6893 (m-80) cc_final: 0.6689 (m-80) outliers start: 30 outliers final: 13 residues processed: 271 average time/residue: 0.2782 time to fit residues: 107.5173 Evaluate side-chains 259 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 242 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 723 PHE Chi-restraints excluded: chain A residue 837 GLU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 723 PHE Chi-restraints excluded: chain B residue 817 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 109 optimal weight: 0.0970 chunk 5 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 101 GLN ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 GLN A 866 GLN B 54 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 GLN B 237 ASN B 393 HIS B 641 GLN B 696 HIS B 901 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.187663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.168317 restraints weight = 20622.069| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 2.75 r_work: 0.4048 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 13844 Z= 0.275 Angle : 0.782 16.295 18672 Z= 0.402 Chirality : 0.050 0.185 2088 Planarity : 0.007 0.073 2368 Dihedral : 6.311 39.194 1819 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.99 % Favored : 87.89 % Rotamer: Outliers : 3.36 % Allowed : 18.31 % Favored : 78.33 % 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: -3.57 (0.18), residues: 1676 helix: -2.00 (0.19), residues: 588 sheet: -2.34 (0.30), residues: 236 loop : -2.65 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 344 HIS 0.014 0.002 HIS A 282 PHE 0.025 0.002 PHE B 667 TYR 0.026 0.003 TYR A 623 ARG 0.007 0.001 ARG B 449 Details of bonding type rmsd hydrogen bonds : bond 0.05649 ( 346) hydrogen bonds : angle 5.98564 ( 1002) metal coordination : bond 0.04653 ( 6) covalent geometry : bond 0.00625 (13838) covalent geometry : angle 0.78173 (18672) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 250 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ILE cc_start: 0.7971 (mm) cc_final: 0.7708 (mt) REVERT: A 213 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.7040 (ttpt) REVERT: A 214 ARG cc_start: 0.7394 (ptt180) cc_final: 0.6835 (ptt180) REVERT: A 215 PHE cc_start: 0.7006 (p90) cc_final: 0.6750 (p90) REVERT: A 268 LYS cc_start: 0.8193 (tptp) cc_final: 0.7752 (ttpp) REVERT: A 306 ASP cc_start: 0.3940 (OUTLIER) cc_final: 0.0517 (m-30) REVERT: A 385 LYS cc_start: 0.8366 (tttt) cc_final: 0.8151 (tttt) REVERT: A 563 MET cc_start: 0.6965 (OUTLIER) cc_final: 0.6762 (tpp) REVERT: A 655 LYS cc_start: 0.6406 (tppt) cc_final: 0.6071 (tppt) REVERT: A 674 TRP cc_start: 0.6737 (t60) cc_final: 0.6528 (t60) REVERT: A 723 PHE cc_start: 0.6710 (OUTLIER) cc_final: 0.6341 (m-10) REVERT: A 788 ASN cc_start: 0.7610 (t0) cc_final: 0.7391 (t0) REVERT: A 836 MET cc_start: 0.5734 (mmt) cc_final: 0.5110 (mmt) REVERT: B 207 SER cc_start: 0.8216 (p) cc_final: 0.7859 (m) REVERT: B 577 GLN cc_start: 0.8191 (tp-100) cc_final: 0.7934 (tp40) REVERT: B 659 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7358 (pt) REVERT: B 836 MET cc_start: 0.5511 (mmt) cc_final: 0.4615 (mmp) REVERT: B 877 PHE cc_start: 0.7174 (m-80) cc_final: 0.6931 (m-80) outliers start: 51 outliers final: 26 residues processed: 280 average time/residue: 0.2701 time to fit residues: 108.7392 Evaluate side-chains 271 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 240 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 282 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 723 PHE Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 866 GLN Chi-restraints excluded: chain B residue 284 CYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 329 TRP Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 723 PHE Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 855 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 39 optimal weight: 0.2980 chunk 130 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN A 491 GLN A 866 GLN B 54 ASN B 93 GLN B 237 ASN B 393 HIS B 901 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.192028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.172093 restraints weight = 20603.449| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 2.98 r_work: 0.4093 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6435 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13844 Z= 0.134 Angle : 0.642 11.900 18672 Z= 0.324 Chirality : 0.044 0.210 2088 Planarity : 0.005 0.059 2368 Dihedral : 5.631 41.192 1818 Min Nonbonded Distance : 1.628 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.79 % Favored : 90.16 % Rotamer: Outliers : 3.16 % Allowed : 20.22 % Favored : 76.61 % 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: -3.13 (0.19), residues: 1676 helix: -1.51 (0.20), residues: 604 sheet: -2.16 (0.31), residues: 236 loop : -2.48 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 674 HIS 0.017 0.001 HIS A 282 PHE 0.021 0.001 PHE B 653 TYR 0.019 0.001 TYR B 484 ARG 0.008 0.000 ARG A 534 Details of bonding type rmsd hydrogen bonds : bond 0.03826 ( 346) hydrogen bonds : angle 5.35933 ( 1002) metal coordination : bond 0.02948 ( 6) covalent geometry : bond 0.00300 (13838) covalent geometry : angle 0.64189 (18672) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 246 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ILE cc_start: 0.7848 (mm) cc_final: 0.7545 (mp) REVERT: A 213 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.6978 (ttpt) REVERT: A 215 PHE cc_start: 0.6914 (p90) cc_final: 0.6637 (p90) REVERT: A 268 LYS cc_start: 0.8124 (tptp) cc_final: 0.7710 (ttpp) REVERT: A 385 LYS cc_start: 0.8311 (tttt) cc_final: 0.8108 (tttt) REVERT: A 397 VAL cc_start: 0.8310 (OUTLIER) cc_final: 0.8035 (m) REVERT: A 452 GLN cc_start: 0.6289 (OUTLIER) cc_final: 0.5804 (pp30) REVERT: A 543 ASP cc_start: 0.7130 (t0) cc_final: 0.6905 (t0) REVERT: A 563 MET cc_start: 0.6962 (OUTLIER) cc_final: 0.6727 (mpp) REVERT: A 655 LYS cc_start: 0.6305 (tppt) cc_final: 0.5963 (tppt) REVERT: A 723 PHE cc_start: 0.6745 (OUTLIER) cc_final: 0.6353 (m-10) REVERT: A 751 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7451 (mp0) REVERT: A 788 ASN cc_start: 0.7619 (t0) cc_final: 0.7363 (t0) REVERT: A 836 MET cc_start: 0.5727 (mmt) cc_final: 0.5045 (mmt) REVERT: A 837 GLU cc_start: 0.5771 (OUTLIER) cc_final: 0.5500 (mp0) REVERT: A 866 GLN cc_start: 0.5601 (OUTLIER) cc_final: 0.4420 (tm-30) REVERT: A 877 PHE cc_start: 0.6990 (m-80) cc_final: 0.6608 (m-80) REVERT: B 427 LEU cc_start: 0.8412 (tp) cc_final: 0.8161 (tt) REVERT: B 836 MET cc_start: 0.5399 (mmt) cc_final: 0.4632 (mmp) REVERT: B 877 PHE cc_start: 0.7186 (m-80) cc_final: 0.6763 (m-80) outliers start: 48 outliers final: 26 residues processed: 272 average time/residue: 0.2718 time to fit residues: 103.9873 Evaluate side-chains 277 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 243 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 282 HIS Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 723 PHE Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 837 GLU Chi-restraints excluded: chain A residue 866 GLN Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 284 CYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 329 TRP Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 723 PHE Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 855 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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-5711/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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-5711/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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-5711/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-5711/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-5711/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-5711/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-5711/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-5711/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-5711/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-5711/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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-5711/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-5711/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-5711/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-5711/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: 69.8904 > 50: distance: 7 - 12: 7.196 distance: 12 - 13: 38.018 distance: 13 - 14: 23.309 distance: 13 - 16: 15.718 distance: 14 - 15: 8.222 distance: 14 - 20: 21.861 distance: 16 - 17: 18.145 distance: 17 - 19: 11.452 distance: 20 - 21: 49.702 distance: 21 - 22: 57.840 distance: 21 - 24: 25.129 distance: 22 - 23: 59.092 distance: 22 - 32: 58.373 distance: 24 - 25: 9.729 distance: 25 - 26: 38.511 distance: 25 - 27: 24.879 distance: 26 - 28: 38.663 distance: 27 - 29: 34.688 distance: 28 - 30: 27.434 distance: 29 - 30: 21.331 distance: 30 - 31: 42.693 distance: 32 - 33: 57.046 distance: 33 - 34: 43.884 distance: 33 - 36: 44.600 distance: 34 - 35: 35.051 distance: 34 - 38: 29.711 distance: 36 - 37: 39.110 distance: 38 - 39: 28.326 distance: 39 - 40: 41.286 distance: 39 - 42: 15.698 distance: 40 - 41: 39.551 distance: 40 - 49: 39.921 distance: 42 - 43: 21.309 distance: 43 - 44: 20.062 distance: 43 - 45: 7.409 distance: 44 - 46: 17.444 distance: 45 - 47: 20.566 distance: 46 - 48: 30.280 distance: 47 - 48: 17.023 distance: 49 - 50: 47.979 distance: 49 - 55: 14.915 distance: 50 - 51: 9.103 distance: 50 - 53: 19.965 distance: 51 - 52: 8.366 distance: 51 - 56: 33.715 distance: 53 - 54: 46.560 distance: 54 - 55: 59.239 distance: 56 - 57: 13.419 distance: 57 - 58: 37.502 distance: 58 - 59: 30.791 distance: 58 - 60: 33.546 distance: 60 - 61: 10.567 distance: 61 - 62: 27.683 distance: 61 - 64: 26.302 distance: 62 - 63: 51.793 distance: 62 - 67: 6.702 distance: 64 - 65: 36.510 distance: 64 - 66: 37.320 distance: 67 - 68: 21.620 distance: 68 - 69: 13.368 distance: 68 - 71: 11.993 distance: 69 - 70: 29.453 distance: 69 - 78: 33.256 distance: 70 - 99: 15.331 distance: 71 - 72: 23.960 distance: 72 - 73: 23.618 distance: 73 - 74: 22.159 distance: 74 - 75: 8.671 distance: 75 - 76: 13.464 distance: 75 - 77: 10.399 distance: 78 - 79: 22.857 distance: 79 - 80: 15.438 distance: 79 - 82: 19.041 distance: 80 - 81: 8.996 distance: 80 - 87: 24.226 distance: 81 - 105: 26.066 distance: 82 - 83: 30.659 distance: 83 - 84: 20.497 distance: 84 - 85: 41.660 distance: 85 - 86: 27.776 distance: 87 - 88: 20.110 distance: 88 - 89: 12.292 distance: 88 - 91: 23.413 distance: 89 - 90: 14.589 distance: 89 - 94: 28.711 distance: 91 - 92: 25.172 distance: 91 - 93: 10.156