Starting phenix.real_space_refine on Wed Jul 24 04:30:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juy_36666/07_2024/8juy_36666_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juy_36666/07_2024/8juy_36666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juy_36666/07_2024/8juy_36666.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juy_36666/07_2024/8juy_36666.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juy_36666/07_2024/8juy_36666_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juy_36666/07_2024/8juy_36666_neut.cif" } resolution = 4.34 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= 0.001 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 P 17 5.49 5 S 107 5.16 5 C 15675 2.51 5 N 4234 2.21 5 O 4521 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 415": "OD1" <-> "OD2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 606": "OE1" <-> "OE2" Residue "A PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 803": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 840": "OE1" <-> "OE2" Residue "B GLU 867": "OE1" <-> "OE2" Residue "B GLU 905": "OE1" <-> "OE2" Residue "B PHE 919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 934": "OE1" <-> "OE2" Residue "C PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 545": "OD1" <-> "OD2" Residue "C ASP 581": "OD1" <-> "OD2" Residue "C TYR 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 877": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 915": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 933": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1371": "OD1" <-> "OD2" Residue "D ASP 420": "OD1" <-> "OD2" Residue "D ASP 426": "OD1" <-> "OD2" Residue "D PHE 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 534": "OD1" <-> "OD2" Residue "D ASP 600": "OD1" <-> "OD2" Residue "D GLU 602": "OE1" <-> "OE2" Residue "D GLU 663": "OE1" <-> "OE2" Residue "D GLU 680": "OE1" <-> "OE2" Residue "D GLU 718": "OE1" <-> "OE2" Residue "D GLU 840": "OE1" <-> "OE2" Residue "D GLU 848": "OE1" <-> "OE2" Residue "D PHE 877": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 518": "OD1" <-> "OD2" Residue "E PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 714": "OD1" <-> "OD2" Residue "E GLU 728": "OE1" <-> "OE2" Residue "E TYR 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 510": "OE1" <-> "OE2" Residue "F PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 606": "OE1" <-> "OE2" Residue "F TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 668": "OD1" <-> "OD2" Residue "F GLU 905": "OE1" <-> "OE2" Residue "F PHE 1350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 1369": "OD1" <-> "OD2" Residue "F GLU 1384": "OE1" <-> "OE2" Residue "F PHE 1386": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 24554 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3472 Classifications: {'peptide': 442} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 30, 'TRANS': 406} Chain breaks: 3 Chain: "B" Number of atoms: 4197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4197 Classifications: {'peptide': 527} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 32, 'TRANS': 489} Chain breaks: 3 Chain: "C" Number of atoms: 4190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4190 Classifications: {'peptide': 527} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 492} Chain breaks: 3 Chain: "D" Number of atoms: 4206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4206 Classifications: {'peptide': 529} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 494} Chain breaks: 3 Chain: "E" Number of atoms: 4188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4188 Classifications: {'peptide': 526} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 32, 'TRANS': 489} Chain breaks: 3 Chain: "F" Number of atoms: 4119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4119 Classifications: {'peptide': 518} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 30, 'TRANS': 483} Chain breaks: 4 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.30, per 1000 atoms: 0.54 Number of scatterers: 24554 At special positions: 0 Unit cell: (141.9, 158.4, 139.7, 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) S 107 16.00 P 17 15.00 O 4521 8.00 N 4234 7.00 C 15675 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 - 3.50 Amino acid : False - 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.76 Conformation dependent library (CDL) restraints added in 4.7 seconds 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5850 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 13 sheets defined 51.9% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'A' and resid 432 through 448 removed outlier: 3.579A pdb=" N LEU A 438 " --> pdb=" O HIS A 434 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 474 through 484 Processing helix chain 'A' and resid 507 through 524 removed outlier: 3.846A pdb=" N ARG A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 Processing helix chain 'A' and resid 600 through 611 removed outlier: 3.566A pdb=" N ARG A 604 " --> pdb=" O ASP A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 631 removed outlier: 3.728A pdb=" N LEU A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 655 removed outlier: 3.791A pdb=" N LEU A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 684 removed outlier: 3.674A pdb=" N ALA A 682 " --> pdb=" O ASP A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 720 removed outlier: 5.285A pdb=" N ASN A 711 " --> pdb=" O PRO A 707 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N THR A 712 " --> pdb=" O LEU A 708 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 717 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU A 718 " --> pdb=" O ASP A 714 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA A 719 " --> pdb=" O LYS A 715 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU A 720 " --> pdb=" O ILE A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 817 Processing helix chain 'A' and resid 826 through 831 removed outlier: 3.730A pdb=" N PHE A 831 " --> pdb=" O ILE A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 852 removed outlier: 3.651A pdb=" N THR A 841 " --> pdb=" O SER A 837 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A 843 " --> pdb=" O GLU A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 868 removed outlier: 3.799A pdb=" N ILE A 868 " --> pdb=" O TRP A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 880 Processing helix chain 'A' and resid 899 through 903 removed outlier: 3.783A pdb=" N ALA A 902 " --> pdb=" O PRO A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 909 removed outlier: 3.981A pdb=" N GLN A 908 " --> pdb=" O PRO A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 911 No H-bonds generated for 'chain 'A' and resid 910 through 911' Processing helix chain 'A' and resid 912 through 916 Processing helix chain 'B' and resid 432 through 448 removed outlier: 3.625A pdb=" N VAL B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N PHE B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) Proline residue: B 445 - end of helix Processing helix chain 'B' and resid 450 through 456 Processing helix chain 'B' and resid 472 through 485 removed outlier: 4.171A pdb=" N VAL B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA B 477 " --> pdb=" O LYS B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 510 removed outlier: 4.288A pdb=" N GLU B 510 " --> pdb=" O VAL B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 523 removed outlier: 4.205A pdb=" N ARG B 514 " --> pdb=" O GLU B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 536 Processing helix chain 'B' and resid 545 through 560 removed outlier: 4.122A pdb=" N SER B 549 " --> pdb=" O ASP B 545 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET B 559 " --> pdb=" O LEU B 555 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP B 560 " --> pdb=" O LEU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 580 Processing helix chain 'B' and resid 600 through 612 Processing helix chain 'B' and resid 620 through 629 Processing helix chain 'B' and resid 637 through 646 removed outlier: 3.624A pdb=" N ALA B 644 " --> pdb=" O LYS B 640 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 655 removed outlier: 3.508A pdb=" N TYR B 655 " --> pdb=" O LEU B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 686 removed outlier: 4.269A pdb=" N PHE B 679 " --> pdb=" O SER B 675 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU B 680 " --> pdb=" O ALA B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 694 removed outlier: 4.392A pdb=" N ALA B 693 " --> pdb=" O ALA B 689 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL B 694 " --> pdb=" O SER B 690 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 689 through 694' Processing helix chain 'B' and resid 705 through 724 removed outlier: 5.735A pdb=" N ASN B 711 " --> pdb=" O PRO B 707 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N THR B 712 " --> pdb=" O LEU B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 728 Processing helix chain 'B' and resid 808 through 817 removed outlier: 3.882A pdb=" N ALA B 812 " --> pdb=" O HIS B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 831 Processing helix chain 'B' and resid 837 through 852 Processing helix chain 'B' and resid 861 through 866 removed outlier: 3.534A pdb=" N TRP B 865 " --> pdb=" O HIS B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 869 No H-bonds generated for 'chain 'B' and resid 867 through 869' Processing helix chain 'B' and resid 870 through 881 removed outlier: 3.878A pdb=" N LEU B 881 " --> pdb=" O PHE B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 903 Processing helix chain 'B' and resid 904 through 909 Processing helix chain 'B' and resid 912 through 916 Processing helix chain 'B' and resid 925 through 935 removed outlier: 4.026A pdb=" N ASP B 935 " --> pdb=" O LYS B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 1331 through 1344 removed outlier: 4.154A pdb=" N ASN B1335 " --> pdb=" O GLU B1331 " (cutoff:3.500A) Processing helix chain 'B' and resid 1348 through 1365 removed outlier: 3.888A pdb=" N TYR B1356 " --> pdb=" O LEU B1352 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ALA B1357 " --> pdb=" O GLU B1353 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL B1358 " --> pdb=" O ASN B1354 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE B1359 " --> pdb=" O LEU B1355 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B1360 " --> pdb=" O TYR B1356 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N CYS B1362 " --> pdb=" O VAL B1358 " (cutoff:3.500A) Processing helix chain 'B' and resid 1375 through 1385 Processing helix chain 'C' and resid 432 through 443 removed outlier: 4.012A pdb=" N GLU C 440 " --> pdb=" O ALA C 436 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N MET C 441 " --> pdb=" O ALA C 437 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL C 442 " --> pdb=" O LEU C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 448 Processing helix chain 'C' and resid 448 through 453 removed outlier: 4.427A pdb=" N PHE C 452 " --> pdb=" O TYR C 448 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU C 453 " --> pdb=" O PRO C 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 448 through 453' Processing helix chain 'C' and resid 473 through 486 removed outlier: 4.009A pdb=" N ALA C 477 " --> pdb=" O LYS C 473 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN C 486 " --> pdb=" O ASN C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 509 Processing helix chain 'C' and resid 510 through 523 removed outlier: 3.510A pdb=" N ARG C 514 " --> pdb=" O GLU C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 536 removed outlier: 3.629A pdb=" N GLY C 535 " --> pdb=" O GLN C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 560 removed outlier: 4.298A pdb=" N SER C 549 " --> pdb=" O ASP C 545 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP C 560 " --> pdb=" O LEU C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 580 removed outlier: 3.617A pdb=" N SER C 579 " --> pdb=" O ARG C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 612 Processing helix chain 'C' and resid 620 through 630 removed outlier: 4.240A pdb=" N GLU C 629 " --> pdb=" O GLU C 625 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASN C 630 " --> pdb=" O GLU C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 655 removed outlier: 4.186A pdb=" N ALA C 647 " --> pdb=" O CYS C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 removed outlier: 3.728A pdb=" N TYR C 659 " --> pdb=" O PRO C 656 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR C 661 " --> pdb=" O ILE C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 705 through 708 Processing helix chain 'C' and resid 709 through 724 Processing helix chain 'C' and resid 809 through 817 Processing helix chain 'C' and resid 826 through 831 Processing helix chain 'C' and resid 837 through 852 removed outlier: 3.607A pdb=" N THR C 841 " --> pdb=" O SER C 837 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE C 846 " --> pdb=" O CYS C 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 866 Processing helix chain 'C' and resid 870 through 881 removed outlier: 3.581A pdb=" N LEU C 881 " --> pdb=" O PHE C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 911 removed outlier: 3.537A pdb=" N PHE C 911 " --> pdb=" O GLN C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 916 Processing helix chain 'C' and resid 925 through 939 removed outlier: 3.598A pdb=" N PHE C 933 " --> pdb=" O ARG C 929 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASP C 935 " --> pdb=" O LYS C 931 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU C 936 " --> pdb=" O PHE C 932 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS C 939 " --> pdb=" O ASP C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 1331 through 1344 removed outlier: 3.928A pdb=" N ASN C1335 " --> pdb=" O GLU C1331 " (cutoff:3.500A) Processing helix chain 'C' and resid 1348 through 1366 removed outlier: 3.556A pdb=" N CYS C1362 " --> pdb=" O VAL C1358 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C1363 " --> pdb=" O ILE C1359 " (cutoff:3.500A) Processing helix chain 'C' and resid 1374 through 1386 removed outlier: 4.207A pdb=" N LYS C1378 " --> pdb=" O SER C1374 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 440 removed outlier: 3.799A pdb=" N GLU D 440 " --> pdb=" O ALA D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 448 Processing helix chain 'D' and resid 472 through 486 removed outlier: 3.677A pdb=" N ALA D 477 " --> pdb=" O LYS D 473 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN D 486 " --> pdb=" O ASN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 523 removed outlier: 3.985A pdb=" N ARG D 511 " --> pdb=" O GLY D 507 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU D 513 " --> pdb=" O SER D 509 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET D 523 " --> pdb=" O GLN D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 536 Processing helix chain 'D' and resid 545 through 560 removed outlier: 4.379A pdb=" N SER D 549 " --> pdb=" O ASP D 545 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER D 553 " --> pdb=" O SER D 549 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU D 558 " --> pdb=" O THR D 554 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP D 560 " --> pdb=" O LEU D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 585 Processing helix chain 'D' and resid 600 through 612 removed outlier: 3.589A pdb=" N THR D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 631 removed outlier: 3.886A pdb=" N ASN D 630 " --> pdb=" O GLU D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 655 removed outlier: 3.646A pdb=" N CYS D 643 " --> pdb=" O ILE D 639 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA D 644 " --> pdb=" O LYS D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 659 removed outlier: 3.550A pdb=" N TYR D 659 " --> pdb=" O PRO D 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 656 through 659' Processing helix chain 'D' and resid 677 through 685 removed outlier: 3.805A pdb=" N LYS D 685 " --> pdb=" O VAL D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 693 removed outlier: 3.739A pdb=" N ARG D 692 " --> pdb=" O ALA D 689 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA D 693 " --> pdb=" O SER D 690 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 689 through 693' Processing helix chain 'D' and resid 705 through 724 removed outlier: 6.089A pdb=" N ASN D 711 " --> pdb=" O PRO D 707 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N THR D 712 " --> pdb=" O LEU D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 817 Processing helix chain 'D' and resid 826 through 831 Processing helix chain 'D' and resid 837 through 852 Processing helix chain 'D' and resid 861 through 869 removed outlier: 5.287A pdb=" N GLU D 867 " --> pdb=" O HIS D 863 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE D 868 " --> pdb=" O VAL D 864 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL D 869 " --> pdb=" O TRP D 865 " (cutoff:3.500A) Processing helix chain 'D' and resid 870 through 882 removed outlier: 4.051A pdb=" N GLN D 882 " --> pdb=" O THR D 878 " (cutoff:3.500A) Processing helix chain 'D' and resid 899 through 903 Processing helix chain 'D' and resid 904 through 910 Processing helix chain 'D' and resid 912 through 916 Processing helix chain 'D' and resid 925 through 938 removed outlier: 4.561A pdb=" N ASP D 935 " --> pdb=" O LYS D 931 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LEU D 936 " --> pdb=" O PHE D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 1332 through 1344 Processing helix chain 'D' and resid 1348 through 1366 removed outlier: 3.995A pdb=" N HIS D1366 " --> pdb=" O CYS D1362 " (cutoff:3.500A) Processing helix chain 'D' and resid 1375 through 1386 Processing helix chain 'E' and resid 433 through 448 removed outlier: 3.840A pdb=" N MET E 441 " --> pdb=" O ALA E 437 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N PHE E 444 " --> pdb=" O GLU E 440 " (cutoff:3.500A) Proline residue: E 445 - end of helix Processing helix chain 'E' and resid 450 through 455 removed outlier: 3.707A pdb=" N LYS E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE E 455 " --> pdb=" O VAL E 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 450 through 455' Processing helix chain 'E' and resid 474 through 486 Processing helix chain 'E' and resid 505 through 523 removed outlier: 4.405A pdb=" N GLU E 510 " --> pdb=" O VAL E 506 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU E 513 " --> pdb=" O SER E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 536 Processing helix chain 'E' and resid 545 through 561 removed outlier: 3.972A pdb=" N SER E 549 " --> pdb=" O ASP E 545 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU E 558 " --> pdb=" O THR E 554 " (cutoff:3.500A) Processing helix chain 'E' and resid 562 through 565 Processing helix chain 'E' and resid 600 through 612 Processing helix chain 'E' and resid 620 through 631 removed outlier: 4.293A pdb=" N ASN E 630 " --> pdb=" O GLU E 626 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS E 631 " --> pdb=" O LEU E 627 " (cutoff:3.500A) Processing helix chain 'E' and resid 635 through 655 removed outlier: 3.640A pdb=" N ALA E 644 " --> pdb=" O LYS E 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 675 through 686 Processing helix chain 'E' and resid 705 through 723 removed outlier: 6.228A pdb=" N ASN E 711 " --> pdb=" O PRO E 707 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N THR E 712 " --> pdb=" O LEU E 708 " (cutoff:3.500A) Processing helix chain 'E' and resid 800 through 804 removed outlier: 4.108A pdb=" N GLY E 804 " --> pdb=" O PRO E 801 " (cutoff:3.500A) Processing helix chain 'E' and resid 808 through 817 Processing helix chain 'E' and resid 826 through 831 Processing helix chain 'E' and resid 837 through 852 removed outlier: 3.558A pdb=" N THR E 841 " --> pdb=" O SER E 837 " (cutoff:3.500A) Processing helix chain 'E' and resid 861 through 866 Processing helix chain 'E' and resid 870 through 881 removed outlier: 3.523A pdb=" N LEU E 881 " --> pdb=" O PHE E 877 " (cutoff:3.500A) Processing helix chain 'E' and resid 904 through 909 removed outlier: 3.761A pdb=" N GLU E 909 " --> pdb=" O GLU E 905 " (cutoff:3.500A) Processing helix chain 'E' and resid 910 through 911 No H-bonds generated for 'chain 'E' and resid 910 through 911' Processing helix chain 'E' and resid 912 through 916 Processing helix chain 'E' and resid 925 through 935 removed outlier: 4.085A pdb=" N ASP E 935 " --> pdb=" O LYS E 931 " (cutoff:3.500A) Processing helix chain 'E' and resid 939 through 943 removed outlier: 3.837A pdb=" N LYS E 943 " --> pdb=" O GLN E 940 " (cutoff:3.500A) Processing helix chain 'E' and resid 1331 through 1344 Processing helix chain 'E' and resid 1348 through 1366 Processing helix chain 'E' and resid 1375 through 1385 Processing helix chain 'F' and resid 431 through 441 removed outlier: 3.527A pdb=" N ALA F 436 " --> pdb=" O SER F 432 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA F 437 " --> pdb=" O ASN F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 485 Processing helix chain 'F' and resid 507 through 523 removed outlier: 4.042A pdb=" N MET F 523 " --> pdb=" O GLN F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 537 Processing helix chain 'F' and resid 545 through 559 Processing helix chain 'F' and resid 560 through 562 No H-bonds generated for 'chain 'F' and resid 560 through 562' Processing helix chain 'F' and resid 576 through 580 removed outlier: 3.759A pdb=" N ILE F 580 " --> pdb=" O LEU F 577 " (cutoff:3.500A) Processing helix chain 'F' and resid 602 through 612 removed outlier: 4.173A pdb=" N GLU F 606 " --> pdb=" O GLU F 602 " (cutoff:3.500A) Processing helix chain 'F' and resid 620 through 631 Processing helix chain 'F' and resid 637 through 654 Processing helix chain 'F' and resid 655 through 659 removed outlier: 3.762A pdb=" N ILE F 658 " --> pdb=" O TYR F 655 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TYR F 659 " --> pdb=" O PRO F 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 655 through 659' Processing helix chain 'F' and resid 676 through 681 removed outlier: 3.584A pdb=" N GLU F 680 " --> pdb=" O ALA F 676 " (cutoff:3.500A) Processing helix chain 'F' and resid 682 through 686 removed outlier: 3.680A pdb=" N MET F 686 " --> pdb=" O MET F 683 " (cutoff:3.500A) Processing helix chain 'F' and resid 705 through 724 removed outlier: 3.864A pdb=" N LEU F 709 " --> pdb=" O VAL F 705 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ASN F 711 " --> pdb=" O PRO F 707 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N THR F 712 " --> pdb=" O LEU F 708 " (cutoff:3.500A) Processing helix chain 'F' and resid 808 through 816 removed outlier: 4.155A pdb=" N ALA F 812 " --> pdb=" O HIS F 808 " (cutoff:3.500A) Processing helix chain 'F' and resid 840 through 852 removed outlier: 4.040A pdb=" N GLN F 844 " --> pdb=" O GLU F 840 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE F 846 " --> pdb=" O CYS F 842 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR F 852 " --> pdb=" O GLU F 848 " (cutoff:3.500A) Processing helix chain 'F' and resid 861 through 866 Processing helix chain 'F' and resid 867 through 869 No H-bonds generated for 'chain 'F' and resid 867 through 869' Processing helix chain 'F' and resid 871 through 883 removed outlier: 3.679A pdb=" N ALA F 875 " --> pdb=" O PRO F 871 " (cutoff:3.500A) Processing helix chain 'F' and resid 899 through 903 removed outlier: 3.682A pdb=" N LEU F 903 " --> pdb=" O HIS F 900 " (cutoff:3.500A) Processing helix chain 'F' and resid 904 through 909 Processing helix chain 'F' and resid 925 through 934 Processing helix chain 'F' and resid 1332 through 1344 Processing helix chain 'F' and resid 1348 through 1366 removed outlier: 4.115A pdb=" N HIS F1366 " --> pdb=" O CYS F1362 " (cutoff:3.500A) Processing helix chain 'F' and resid 1374 through 1386 removed outlier: 3.513A pdb=" N GLU F1384 " --> pdb=" O GLU F1380 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 462 through 464 removed outlier: 7.469A pdb=" N CYS A 463 " --> pdb=" O GLY A 572 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 796 through 798 removed outlier: 3.979A pdb=" N PHE A 919 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 822 through 824 removed outlier: 3.729A pdb=" N TYR A 858 " --> pdb=" O TYR A 823 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL A 857 " --> pdb=" O LEU A 893 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 494 through 496 removed outlier: 3.543A pdb=" N ALA B 573 " --> pdb=" O PHE B 530 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N PHE B 594 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU B 464 " --> pdb=" O PHE B 594 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 821 through 824 removed outlier: 6.881A pdb=" N SER B 855 " --> pdb=" O LEU B 891 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N LEU B 893 " --> pdb=" O SER B 855 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL B 857 " --> pdb=" O LEU B 893 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N THR B 895 " --> pdb=" O VAL B 857 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N VAL B 859 " --> pdb=" O THR B 895 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER B 896 " --> pdb=" O ILE B 797 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLY B 799 " --> pdb=" O SER B 896 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 494 through 496 removed outlier: 3.630A pdb=" N ALA C 573 " --> pdb=" O PHE C 530 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR C 466 " --> pdb=" O PHE C 594 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 822 through 824 removed outlier: 6.532A pdb=" N TYR C 823 " --> pdb=" O TYR C 858 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU C 891 " --> pdb=" O SER C 855 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR C 895 " --> pdb=" O VAL C 859 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA C 894 " --> pdb=" O ILE C 795 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N PHE C 919 " --> pdb=" O ARG C 794 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU C 796 " --> pdb=" O PHE C 919 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 527 through 531 removed outlier: 3.564A pdb=" N ALA D 573 " --> pdb=" O PHE D 530 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N PHE D 594 " --> pdb=" O GLY D 462 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU D 464 " --> pdb=" O PHE D 594 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 821 through 824 removed outlier: 7.197A pdb=" N THR D 821 " --> pdb=" O ILE D 856 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N TYR D 858 " --> pdb=" O THR D 821 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N TYR D 823 " --> pdb=" O TYR D 858 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU D 891 " --> pdb=" O SER D 855 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR D 895 " --> pdb=" O VAL D 859 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE D 795 " --> pdb=" O ALA D 894 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N SER D 896 " --> pdb=" O ILE D 795 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE D 797 " --> pdb=" O SER D 896 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 492 through 495 removed outlier: 6.393A pdb=" N ALA E 492 " --> pdb=" O ILE E 527 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N PHE E 529 " --> pdb=" O ALA E 492 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE E 494 " --> pdb=" O PHE E 529 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL E 569 " --> pdb=" O SER E 526 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY E 572 " --> pdb=" O CYS E 463 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N PHE E 594 " --> pdb=" O GLY E 462 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LEU E 464 " --> pdb=" O PHE E 594 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 821 through 824 removed outlier: 3.667A pdb=" N THR E 895 " --> pdb=" O VAL E 859 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA E 894 " --> pdb=" O ILE E 795 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE E 919 " --> pdb=" O LEU E 796 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 570 through 573 removed outlier: 7.279A pdb=" N PHE F 594 " --> pdb=" O GLY F 462 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU F 464 " --> pdb=" O PHE F 594 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 855 through 859 removed outlier: 6.774A pdb=" N SER F 855 " --> pdb=" O LEU F 891 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LEU F 893 " --> pdb=" O SER F 855 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL F 857 " --> pdb=" O LEU F 893 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N THR F 895 " --> pdb=" O VAL F 857 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL F 859 " --> pdb=" O THR F 895 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE F 797 " --> pdb=" O SER F 896 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU F 796 " --> pdb=" O PHE F 919 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 940 hydrogen bonds defined for protein. 2694 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: 7.55 Time building geometry restraints manager: 10.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7828 1.34 - 1.46: 3872 1.46 - 1.58: 13223 1.58 - 1.70: 19 1.70 - 1.81: 155 Bond restraints: 25097 Sorted by residual: bond pdb=" CA ASP D 614 " pdb=" CB ASP D 614 " ideal model delta sigma weight residual 1.527 1.472 0.055 2.48e-02 1.63e+03 5.00e+00 bond pdb=" CG GLU B 626 " pdb=" CD GLU B 626 " ideal model delta sigma weight residual 1.516 1.470 0.046 2.50e-02 1.60e+03 3.46e+00 bond pdb=" CA ARG C 585 " pdb=" CB ARG C 585 " ideal model delta sigma weight residual 1.523 1.500 0.023 1.27e-02 6.20e+03 3.33e+00 bond pdb=" C LYS D 605 " pdb=" N GLU D 606 " ideal model delta sigma weight residual 1.334 1.308 0.026 1.43e-02 4.89e+03 3.27e+00 bond pdb=" O3B ATP C1401 " pdb=" PB ATP C1401 " ideal model delta sigma weight residual 1.592 1.539 0.053 3.00e-02 1.11e+03 3.14e+00 ... (remaining 25092 not shown) Histogram of bond angle deviations from ideal: 98.85 - 106.99: 1023 106.99 - 115.12: 15167 115.12 - 123.26: 16724 123.26 - 131.40: 1066 131.40 - 139.54: 48 Bond angle restraints: 34028 Sorted by residual: angle pdb=" N VAL C 907 " pdb=" CA VAL C 907 " pdb=" C VAL C 907 " ideal model delta sigma weight residual 111.90 107.88 4.02 8.10e-01 1.52e+00 2.47e+01 angle pdb=" N VAL B 864 " pdb=" CA VAL B 864 " pdb=" C VAL B 864 " ideal model delta sigma weight residual 113.42 108.12 5.30 1.17e+00 7.31e-01 2.05e+01 angle pdb=" N THR C1373 " pdb=" CA THR C1373 " pdb=" C THR C1373 " ideal model delta sigma weight residual 113.38 108.18 5.20 1.17e+00 7.31e-01 1.98e+01 angle pdb=" N LEU F 431 " pdb=" CA LEU F 431 " pdb=" C LEU F 431 " ideal model delta sigma weight residual 113.21 108.37 4.84 1.15e+00 7.56e-01 1.77e+01 angle pdb=" N THR E 474 " pdb=" CA THR E 474 " pdb=" C THR E 474 " ideal model delta sigma weight residual 113.18 107.65 5.53 1.33e+00 5.65e-01 1.73e+01 ... (remaining 34023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.40: 14579 26.40 - 52.81: 759 52.81 - 79.21: 92 79.21 - 105.61: 14 105.61 - 132.02: 3 Dihedral angle restraints: 15447 sinusoidal: 6479 harmonic: 8968 Sorted by residual: dihedral pdb=" O2A ADP A1301 " pdb=" O3A ADP A1301 " pdb=" PA ADP A1301 " pdb=" PB ADP A1301 " ideal model delta sinusoidal sigma weight residual -60.00 72.02 -132.02 1 2.00e+01 2.50e-03 4.01e+01 dihedral pdb=" C5' ADP A1301 " pdb=" O5' ADP A1301 " pdb=" PA ADP A1301 " pdb=" O2A ADP A1301 " ideal model delta sinusoidal sigma weight residual -60.00 61.87 -121.87 1 2.00e+01 2.50e-03 3.67e+01 dihedral pdb=" O1B ADP A1301 " pdb=" O3A ADP A1301 " pdb=" PB ADP A1301 " pdb=" PA ADP A1301 " ideal model delta sinusoidal sigma weight residual -60.00 -176.58 116.58 1 2.00e+01 2.50e-03 3.47e+01 ... (remaining 15444 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2875 0.051 - 0.103: 801 0.103 - 0.154: 145 0.154 - 0.206: 11 0.206 - 0.257: 4 Chirality restraints: 3836 Sorted by residual: chirality pdb=" CA GLU B 625 " pdb=" N GLU B 625 " pdb=" C GLU B 625 " pdb=" CB GLU B 625 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CG LEU F 910 " pdb=" CB LEU F 910 " pdb=" CD1 LEU F 910 " pdb=" CD2 LEU F 910 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CB ILE A 912 " pdb=" CA ILE A 912 " pdb=" CG1 ILE A 912 " pdb=" CG2 ILE A 912 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 3833 not shown) Planarity restraints: 4361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 586 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO D 587 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO D 587 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO D 587 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 524 " -0.055 5.00e-02 4.00e+02 8.45e-02 1.14e+01 pdb=" N PRO A 525 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO A 525 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 525 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 575 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.45e+00 pdb=" CG ASN D 575 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN D 575 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN D 575 " 0.018 2.00e-02 2.50e+03 ... (remaining 4358 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 2 2.06 - 2.77: 5178 2.77 - 3.48: 35684 3.48 - 4.19: 54000 4.19 - 4.90: 92160 Nonbonded interactions: 187024 Sorted by model distance: nonbonded pdb=" CD1 LEU F 717 " pdb=" N LEU F 817 " model vdw 1.353 3.540 nonbonded pdb=" CD1 LEU F 717 " pdb=" CA LEU F 817 " model vdw 2.052 3.890 nonbonded pdb=" OD2 ASP C 668 " pdb=" OG SER C 670 " model vdw 2.100 2.440 nonbonded pdb=" OG SER E 690 " pdb=" OE1 GLN E 691 " model vdw 2.114 2.440 nonbonded pdb=" OE2 GLU E 440 " pdb=" OH TYR F 659 " model vdw 2.126 2.440 ... (remaining 187019 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 422 through 598 or resid 601 through 688 or resid 696 thro \ ugh 727 or resid 787 through 923)) selection = (chain 'F' and (resid 422 through 539 or resid 546 through 659 or resid 666 thro \ ugh 727 or resid 787 through 923)) } ncs_group { reference = (chain 'B' and (resid 422 through 690 or resid 692 through 693 or resid 697 thro \ ugh 727 or resid 786 through 945 or resid 1330 through 1389)) selection = (chain 'C' and (resid 422 through 693 or resid 697 through 1389)) selection = (chain 'D' and (resid 422 through 690 or resid 692 through 693 or resid 697 thro \ ugh 727 or resid 786 through 1389)) selection = (chain 'E' and (resid 422 through 690 or resid 692 through 693 or resid 697 thro \ ugh 727 or resid 786 through 1389)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.680 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: 0.000 Extract box with map and model: 0.670 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 63.590 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 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 : 0.005 0.055 25097 Z= 0.348 Angle : 0.863 12.456 34028 Z= 0.477 Chirality : 0.048 0.257 3836 Planarity : 0.006 0.103 4361 Dihedral : 15.362 132.018 9597 Min Nonbonded Distance : 1.353 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.71 % Favored : 91.16 % Rotamer: Outliers : 0.15 % Allowed : 0.71 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % 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: -1.58 (0.15), residues: 3019 helix: -0.52 (0.14), residues: 1320 sheet: -0.54 (0.28), residues: 330 loop : -1.66 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 865 HIS 0.009 0.002 HIS A 815 PHE 0.049 0.002 PHE F 877 TYR 0.018 0.002 TYR C 634 ARG 0.013 0.001 ARG F 913 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 542 time to evaluate : 2.901 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: symmetry clash REVERT: A 523 MET cc_start: 0.2705 (tpp) cc_final: 0.0864 (mmt) REVERT: D 426 ASP cc_start: 0.8506 (p0) cc_final: 0.8237 (p0) REVERT: D 523 MET cc_start: 0.7300 (mpp) cc_final: 0.6979 (mtt) REVERT: D 530 PHE cc_start: 0.8345 (m-80) cc_final: 0.7980 (m-80) REVERT: D 559 MET cc_start: 0.7050 (ttm) cc_final: 0.6826 (mtp) REVERT: E 438 LEU cc_start: 0.8453 (pp) cc_final: 0.8250 (tt) REVERT: E 495 MET cc_start: 0.7396 (ppp) cc_final: 0.6865 (ppp) REVERT: F 615 TRP cc_start: 0.3799 (m-10) cc_final: 0.3314 (m-10) REVERT: F 721 GLN cc_start: 0.5393 (mp10) cc_final: 0.4722 (tp-100) REVERT: F 913 ARG cc_start: 0.0042 (tpt170) cc_final: -0.0184 (ptm-80) outliers start: 4 outliers final: 1 residues processed: 545 average time/residue: 0.4155 time to fit residues: 332.0364 Evaluate side-chains 259 residues out of total 2695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 2.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 255 optimal weight: 7.9990 chunk 229 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 237 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 275 optimal weight: 0.0980 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 HIS A 458 GLN A 512 GLN A 548 HIS A 908 GLN B 808 HIS C 512 GLN ** C1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1385 ASN D 691 GLN D 808 HIS ** D 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1330 HIS E 815 HIS E1366 HIS F 922 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25097 Z= 0.299 Angle : 0.761 10.464 34028 Z= 0.386 Chirality : 0.047 0.240 3836 Planarity : 0.006 0.086 4361 Dihedral : 10.096 111.522 3486 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.52 % Favored : 92.32 % Rotamer: Outliers : 0.41 % Allowed : 6.49 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % 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: -1.55 (0.15), residues: 3019 helix: -0.44 (0.14), residues: 1340 sheet: -0.54 (0.29), residues: 320 loop : -1.70 (0.17), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 505 HIS 0.008 0.001 HIS F 861 PHE 0.036 0.002 PHE F 877 TYR 0.024 0.002 TYR F 634 ARG 0.007 0.001 ARG B1332 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 340 time to evaluate : 2.935 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: symmetry clash revert: symmetry clash REVERT: A 441 MET cc_start: 0.5389 (OUTLIER) cc_final: 0.3884 (mmt) REVERT: A 523 MET cc_start: 0.3980 (tpp) cc_final: 0.1899 (mmt) REVERT: A 575 ASN cc_start: 0.0342 (OUTLIER) cc_final: 0.0077 (p0) REVERT: A 611 HIS cc_start: 0.1799 (t-90) cc_final: 0.1544 (t70) REVERT: A 686 MET cc_start: -0.1708 (mtp) cc_final: -0.2816 (tpp) REVERT: C 1379 MET cc_start: 0.7886 (tpp) cc_final: 0.7655 (mmm) REVERT: D 533 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8548 (mp) REVERT: E 438 LEU cc_start: 0.8386 (pp) cc_final: 0.8044 (tt) REVERT: E 680 GLU cc_start: 0.7389 (mt-10) cc_final: 0.7065 (mp0) REVERT: E 938 LEU cc_start: 0.6304 (OUTLIER) cc_final: 0.5931 (pp) REVERT: F 559 MET cc_start: 0.6384 (tpt) cc_final: 0.4146 (ptt) REVERT: F 615 TRP cc_start: 0.3964 (m-10) cc_final: 0.3593 (m-10) REVERT: F 721 GLN cc_start: 0.5213 (mp10) cc_final: 0.4494 (tp-100) REVERT: F 913 ARG cc_start: 0.0338 (tpt170) cc_final: -0.0104 (ptm-80) outliers start: 11 outliers final: 2 residues processed: 348 average time/residue: 0.3675 time to fit residues: 196.8400 Evaluate side-chains 242 residues out of total 2695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 236 time to evaluate : 2.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 152 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 229 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 275 optimal weight: 10.0000 chunk 297 optimal weight: 9.9990 chunk 245 optimal weight: 5.9990 chunk 273 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 221 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN B 861 HIS ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN ** D 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1345 GLN E 699 GLN ** E 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 815 HIS F1351 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25097 Z= 0.207 Angle : 0.688 10.447 34028 Z= 0.344 Chirality : 0.045 0.243 3836 Planarity : 0.005 0.082 4361 Dihedral : 9.605 101.637 3486 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.39 % Favored : 92.45 % Rotamer: Outliers : 0.15 % Allowed : 4.16 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % 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: -1.34 (0.15), residues: 3019 helix: -0.30 (0.14), residues: 1346 sheet: -0.31 (0.29), residues: 318 loop : -1.59 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 865 HIS 0.007 0.001 HIS F 611 PHE 0.035 0.001 PHE F 877 TYR 0.028 0.002 TYR F 858 ARG 0.005 0.000 ARG D 851 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 332 time to evaluate : 2.981 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 MET cc_start: 0.5583 (mtt) cc_final: 0.4592 (mmt) REVERT: A 523 MET cc_start: 0.5031 (tpp) cc_final: 0.2600 (mmt) REVERT: A 611 HIS cc_start: 0.1160 (t-90) cc_final: 0.0830 (t-90) REVERT: A 686 MET cc_start: -0.1200 (mtp) cc_final: -0.2561 (tpp) REVERT: A 789 MET cc_start: 0.1450 (ppp) cc_final: -0.1774 (mmt) REVERT: B 823 TYR cc_start: 0.6667 (m-80) cc_final: 0.6229 (m-80) REVERT: C 626 GLU cc_start: 0.6579 (tp30) cc_final: 0.6374 (tp30) REVERT: C 686 MET cc_start: 0.6931 (mmt) cc_final: 0.6571 (tpt) REVERT: D 426 ASP cc_start: 0.8000 (p0) cc_final: 0.7738 (p0) REVERT: E 438 LEU cc_start: 0.8310 (pp) cc_final: 0.8008 (tt) REVERT: E 820 PHE cc_start: 0.6267 (m-80) cc_final: 0.6054 (m-80) REVERT: E 851 ARG cc_start: 0.7283 (mmp80) cc_final: 0.6670 (mtm110) REVERT: F 559 MET cc_start: 0.5691 (tpt) cc_final: 0.3807 (ptt) REVERT: F 615 TRP cc_start: 0.4433 (m-10) cc_final: 0.4103 (m-10) REVERT: F 627 LEU cc_start: 0.7159 (tt) cc_final: 0.6846 (tt) REVERT: F 721 GLN cc_start: 0.5159 (mp10) cc_final: 0.4378 (tp-100) outliers start: 4 outliers final: 1 residues processed: 335 average time/residue: 0.3807 time to fit residues: 197.2887 Evaluate side-chains 229 residues out of total 2695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 228 time to evaluate : 2.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.5392 > 50: distance: 38 - 65: 8.591 distance: 45 - 50: 6.451 distance: 50 - 51: 4.917 distance: 51 - 54: 4.406 distance: 52 - 53: 8.186 distance: 54 - 55: 13.196 distance: 54 - 56: 4.490 distance: 58 - 59: 5.130 distance: 58 - 61: 6.551 distance: 59 - 60: 14.095 distance: 59 - 65: 3.734 distance: 61 - 62: 5.411 distance: 62 - 64: 4.115 distance: 65 - 66: 5.668 distance: 66 - 67: 3.999 distance: 66 - 69: 5.485 distance: 67 - 68: 3.118 distance: 67 - 76: 3.369 distance: 69 - 70: 7.701 distance: 70 - 71: 10.800 distance: 70 - 72: 11.422 distance: 71 - 73: 7.586 distance: 72 - 74: 5.387 distance: 73 - 75: 11.668 distance: 74 - 75: 9.879 distance: 76 - 77: 13.321 distance: 77 - 78: 30.266 distance: 78 - 79: 35.824 distance: 78 - 80: 10.115 distance: 80 - 81: 23.891 distance: 81 - 82: 14.404 distance: 81 - 84: 11.105 distance: 82 - 83: 12.690 distance: 82 - 87: 15.146 distance: 84 - 85: 4.259 distance: 84 - 86: 22.060 distance: 87 - 88: 7.417 distance: 88 - 89: 4.134 distance: 88 - 91: 13.159 distance: 89 - 90: 12.332 distance: 89 - 93: 15.487 distance: 91 - 92: 17.326 distance: 93 - 94: 16.235 distance: 94 - 95: 17.179 distance: 94 - 97: 30.017 distance: 95 - 96: 20.954 distance: 95 - 100: 8.348 distance: 97 - 98: 16.224 distance: 97 - 99: 4.882 distance: 100 - 101: 24.194 distance: 101 - 102: 21.628 distance: 101 - 104: 9.126 distance: 102 - 103: 14.763 distance: 102 - 107: 26.363 distance: 104 - 105: 14.069 distance: 104 - 106: 12.933 distance: 107 - 108: 28.236 distance: 108 - 109: 7.478 distance: 108 - 111: 21.366 distance: 109 - 110: 34.374 distance: 109 - 113: 28.843 distance: 111 - 112: 28.664 distance: 113 - 114: 20.932 distance: 113 - 119: 32.665 distance: 114 - 115: 17.434 distance: 114 - 117: 5.758 distance: 115 - 116: 13.022 distance: 115 - 120: 14.889 distance: 116 - 143: 29.144 distance: 117 - 118: 25.109 distance: 118 - 119: 10.361