Starting phenix.real_space_refine on Tue Jun 17 06:08:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oem_20030/06_2025/6oem_20030.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oem_20030/06_2025/6oem_20030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6oem_20030/06_2025/6oem_20030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oem_20030/06_2025/6oem_20030.map" model { file = "/net/cci-nas-00/data/ceres_data/6oem_20030/06_2025/6oem_20030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oem_20030/06_2025/6oem_20030.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 204 5.49 5 Mg 2 5.21 5 S 106 5.16 5 C 11819 2.51 5 N 3476 2.21 5 O 4098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19707 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4774 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 580} Chain breaks: 1 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 90 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 7, 'ARG:plan': 4, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "C" Number of atoms: 4843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4843 Classifications: {'peptide': 611} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 585} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 68 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 2668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2668 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2671 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1163 Classifications: {'DNA': 57} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 56} Chain: "I" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 936 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain: "F" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 947 Classifications: {'DNA': 46} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 45} Chain: "J" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1171 Classifications: {'DNA': 57} Link IDs: {'rna3p': 56} Chain: "N" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 242 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 33} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 288 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 3, 'TRANS': 51} Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 97 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2544 SG CYS A 727 88.110 24.912 57.634 1.00 91.74 S ATOM 2565 SG CYS A 730 88.645 22.480 57.782 1.00 90.71 S ATOM 7353 SG CYS C 727 61.828 106.636 58.091 1.00 82.68 S ATOM 7374 SG CYS C 730 61.375 108.925 56.753 1.00 82.68 S Time building chain proxies: 11.34, per 1000 atoms: 0.58 Number of scatterers: 19707 At special positions: 0 Unit cell: (150.87, 132.68, 157.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 106 16.00 P 204 15.00 Mg 2 11.99 O 4098 8.00 N 3476 7.00 C 11819 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: 4.87 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1102 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 727 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 730 " pdb=" ZN C1102 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 727 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 730 " Number of angles added : 4 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3738 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 22 sheets defined 39.2% alpha, 19.2% beta 102 base pairs and 164 stacking pairs defined. Time for finding SS restraints: 8.10 Creating SS restraints... Processing helix chain 'A' and resid 400 through 423 removed outlier: 5.608A pdb=" N GLU A 410 " --> pdb=" O HIS A 406 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LEU A 411 " --> pdb=" O ARG A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 442 Processing helix chain 'A' and resid 444 through 457 removed outlier: 3.501A pdb=" N ALA A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 478 through 493 Processing helix chain 'A' and resid 499 through 511 Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'A' and resid 664 through 683 Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 749 through 763 removed outlier: 3.712A pdb=" N ASN A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 777 Processing helix chain 'A' and resid 792 through 812 removed outlier: 3.804A pdb=" N ASN A 800 " --> pdb=" O CYS A 796 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU A 803 " --> pdb=" O GLY A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 841 Processing helix chain 'A' and resid 850 through 858 removed outlier: 3.647A pdb=" N ALA A 854 " --> pdb=" O ASN A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 868 removed outlier: 3.586A pdb=" N VAL A 863 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 894 removed outlier: 4.075A pdb=" N ALA A 878 " --> pdb=" O GLU A 874 " (cutoff:3.500A) Proline residue: A 891 - end of helix Processing helix chain 'A' and resid 902 through 907 removed outlier: 3.556A pdb=" N LEU A 906 " --> pdb=" O CYS A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 923 removed outlier: 3.547A pdb=" N LEU A 920 " --> pdb=" O PHE A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 941 Processing helix chain 'A' and resid 942 through 950 removed outlier: 3.569A pdb=" N ILE A 946 " --> pdb=" O HIS A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 975 Processing helix chain 'A' and resid 981 through 995 removed outlier: 4.274A pdb=" N GLU A 985 " --> pdb=" O CYS A 981 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A 995 " --> pdb=" O HIS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1004 Processing helix chain 'A' and resid 1005 through 1007 No H-bonds generated for 'chain 'A' and resid 1005 through 1007' Processing helix chain 'C' and resid 395 through 399 Processing helix chain 'C' and resid 400 through 423 removed outlier: 5.733A pdb=" N GLU C 410 " --> pdb=" O HIS C 406 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU C 411 " --> pdb=" O ARG C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 441 Processing helix chain 'C' and resid 444 through 457 Processing helix chain 'C' and resid 463 through 474 Processing helix chain 'C' and resid 477 through 493 Processing helix chain 'C' and resid 499 through 509 Processing helix chain 'C' and resid 558 through 570 Processing helix chain 'C' and resid 570 through 581 Processing helix chain 'C' and resid 664 through 683 removed outlier: 3.503A pdb=" N LEU C 668 " --> pdb=" O ASP C 664 " (cutoff:3.500A) Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 708 through 713 Processing helix chain 'C' and resid 733 through 740 removed outlier: 3.772A pdb=" N GLN C 739 " --> pdb=" O LEU C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 763 Processing helix chain 'C' and resid 768 through 776 Processing helix chain 'C' and resid 792 through 813 removed outlier: 3.744A pdb=" N CYS C 796 " --> pdb=" O ASP C 792 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS C 806 " --> pdb=" O ALA C 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 841 Processing helix chain 'C' and resid 850 through 858 Processing helix chain 'C' and resid 859 through 868 Processing helix chain 'C' and resid 872 through 894 removed outlier: 3.965A pdb=" N HIS C 876 " --> pdb=" O SER C 872 " (cutoff:3.500A) Proline residue: C 891 - end of helix Processing helix chain 'C' and resid 902 through 907 Processing helix chain 'C' and resid 908 through 923 Processing helix chain 'C' and resid 933 through 941 Processing helix chain 'C' and resid 942 through 950 Processing helix chain 'C' and resid 963 through 974 removed outlier: 3.894A pdb=" N LEU C 967 " --> pdb=" O SER C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 995 removed outlier: 4.158A pdb=" N GLU C 985 " --> pdb=" O CYS C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1004 Processing helix chain 'C' and resid 1005 through 1008 removed outlier: 3.583A pdb=" N ALA C1008 " --> pdb=" O ALA C1005 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1005 through 1008' Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'D' and resid 308 through 314 Processing helix chain 'N' and resid 100 through 117 Proline residue: N 111 - end of helix Processing helix chain 'N' and resid 123 through 136 Processing helix chain 'H' and resid 102 through 117 Proline residue: H 111 - end of helix Processing helix chain 'H' and resid 121 through 136 Processing helix chain 'H' and resid 137 through 140 Processing helix chain 'H' and resid 141 through 155 Processing sheet with id=AA1, first strand: chain 'A' and resid 518 through 519 removed outlier: 6.124A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 621 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ALA A 619 " --> pdb=" O MET A 602 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A 620 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU A 657 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N PHE A 622 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 518 through 519 removed outlier: 6.124A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 621 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ALA A 619 " --> pdb=" O MET A 602 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE A 631 " --> pdb=" O LYS A 639 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N LYS A 639 " --> pdb=" O ILE A 631 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 518 through 519 removed outlier: 9.880A pdb=" N PHE C 591 " --> pdb=" O PHE C 700 " (cutoff:3.500A) removed outlier: 10.573A pdb=" N PHE C 702 " --> pdb=" O PHE C 591 " (cutoff:3.500A) removed outlier: 10.517A pdb=" N VAL C 593 " --> pdb=" O PHE C 702 " (cutoff:3.500A) removed outlier: 10.916A pdb=" N GLY C 704 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 11.092A pdb=" N VAL C 595 " --> pdb=" O GLY C 704 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N GLY C 706 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU C 597 " --> pdb=" O GLY C 706 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ALA C 619 " --> pdb=" O MET C 602 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 535 through 536 removed outlier: 6.666A pdb=" N PHE C 622 " --> pdb=" O LEU C 655 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU C 657 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL C 620 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE C 631 " --> pdb=" O LYS C 639 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LYS C 639 " --> pdb=" O ILE C 631 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N HIS C 633 " --> pdb=" O ASN C 637 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASN C 637 " --> pdb=" O HIS C 633 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 5 removed outlier: 3.505A pdb=" N PHE B 318 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 20 through 24 removed outlier: 3.819A pdb=" N LYS B 58 " --> pdb=" O HIS B 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 50 through 51 Processing sheet with id=AA8, first strand: chain 'B' and resid 75 through 80 removed outlier: 3.595A pdb=" N CYS B 78 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 92 " --> pdb=" O CYS B 78 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 107 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 112 through 116 removed outlier: 7.031A pdb=" N THR B 121 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS B 115 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LYS B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.630A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N SER B 194 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 141 " --> pdb=" O PHE B 156 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AB3, first strand: chain 'B' and resid 208 through 211 removed outlier: 3.617A pdb=" N LEU B 233 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 252 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 263 through 267 removed outlier: 3.713A pdb=" N THR B 264 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 3 through 5 Processing sheet with id=AB6, first strand: chain 'D' and resid 20 through 24 removed outlier: 3.789A pdb=" N LYS D 58 " --> pdb=" O HIS D 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 50 through 51 Processing sheet with id=AB8, first strand: chain 'D' and resid 75 through 80 Processing sheet with id=AB9, first strand: chain 'D' and resid 112 through 116 removed outlier: 6.784A pdb=" N THR D 121 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS D 115 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LYS D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.048A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N SER D 194 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER D 141 " --> pdb=" O PHE D 156 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AC3, first strand: chain 'D' and resid 208 through 211 removed outlier: 3.813A pdb=" N LEU D 233 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU D 252 " --> pdb=" O LEU D 233 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 263 through 267 removed outlier: 3.780A pdb=" N THR D 264 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) 715 hydrogen bonds defined for protein. 2028 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 253 hydrogen bonds 506 hydrogen bond angles 0 basepair planarities 102 basepair parallelities 164 stacking parallelities Total time for adding SS restraints: 9.87 Time building geometry restraints manager: 5.80 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: 5238 1.34 - 1.45: 4567 1.45 - 1.57: 10187 1.57 - 1.69: 406 1.69 - 1.81: 160 Bond restraints: 20558 Sorted by residual: bond pdb=" N GLU A 983 " pdb=" CA GLU A 983 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.15e+00 bond pdb=" N HIS C 609 " pdb=" CA HIS C 609 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.18e-02 7.18e+03 6.11e+00 bond pdb=" N ARG C 972 " pdb=" CA ARG C 972 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.33e-02 5.65e+03 5.97e+00 bond pdb=" N GLU C 983 " pdb=" CA GLU C 983 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.84e+00 bond pdb=" N GLU A 607 " pdb=" CA GLU A 607 " ideal model delta sigma weight residual 1.463 1.488 -0.025 1.24e-02 6.50e+03 4.08e+00 ... (remaining 20553 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 27795 1.21 - 2.42: 728 2.42 - 3.63: 158 3.63 - 4.84: 20 4.84 - 6.05: 7 Bond angle restraints: 28708 Sorted by residual: angle pdb=" N VAL A 742 " pdb=" CA VAL A 742 " pdb=" C VAL A 742 " ideal model delta sigma weight residual 106.21 110.09 -3.88 1.07e+00 8.73e-01 1.32e+01 angle pdb=" CA GLU A 607 " pdb=" C GLU A 607 " pdb=" O GLU A 607 " ideal model delta sigma weight residual 122.38 118.44 3.94 1.49e+00 4.50e-01 6.98e+00 angle pdb=" C3' DT G 25 " pdb=" O3' DT G 25 " pdb=" P DG G 26 " ideal model delta sigma weight residual 120.20 124.09 -3.89 1.50e+00 4.44e-01 6.71e+00 angle pdb=" CA GLU A 983 " pdb=" C GLU A 983 " pdb=" O GLU A 983 " ideal model delta sigma weight residual 120.82 118.16 2.66 1.05e+00 9.07e-01 6.42e+00 angle pdb=" CA HIS C 609 " pdb=" C HIS C 609 " pdb=" O HIS C 609 " ideal model delta sigma weight residual 120.90 118.31 2.59 1.03e+00 9.43e-01 6.30e+00 ... (remaining 28703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 10890 35.92 - 71.84: 883 71.84 - 107.76: 8 107.76 - 143.68: 7 143.68 - 179.60: 5 Dihedral angle restraints: 11793 sinusoidal: 5998 harmonic: 5795 Sorted by residual: dihedral pdb=" C4' DT J 14 " pdb=" C3' DT J 14 " pdb=" O3' DT J 14 " pdb=" P DT J 15 " ideal model delta sinusoidal sigma weight residual 220.00 40.40 179.60 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT G 29 " pdb=" C3' DT G 29 " pdb=" O3' DT G 29 " pdb=" P DT G 30 " ideal model delta sinusoidal sigma weight residual 220.00 40.97 179.03 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA F 33 " pdb=" C3' DA F 33 " pdb=" O3' DA F 33 " pdb=" P DG F 34 " ideal model delta sinusoidal sigma weight residual 220.00 42.48 177.52 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 11790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2228 0.029 - 0.059: 655 0.059 - 0.088: 159 0.088 - 0.118: 131 0.118 - 0.147: 12 Chirality restraints: 3185 Sorted by residual: chirality pdb=" CA ILE C 631 " pdb=" N ILE C 631 " pdb=" C ILE C 631 " pdb=" CB ILE C 631 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CA ILE B 331 " pdb=" N ILE B 331 " pdb=" C ILE B 331 " pdb=" CB ILE B 331 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA ILE D 331 " pdb=" N ILE D 331 " pdb=" C ILE D 331 " pdb=" CB ILE D 331 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 3182 not shown) Planarity restraints: 2980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT G 24 " -0.018 2.00e-02 2.50e+03 9.54e-03 2.27e+00 pdb=" N1 DT G 24 " 0.023 2.00e-02 2.50e+03 pdb=" C2 DT G 24 " 0.000 2.00e-02 2.50e+03 pdb=" O2 DT G 24 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DT G 24 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT G 24 " -0.002 2.00e-02 2.50e+03 pdb=" O4 DT G 24 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DT G 24 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT G 24 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DT G 24 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 870 " -0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO A 871 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 871 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 871 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 520 " -0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO A 521 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " -0.016 5.00e-02 4.00e+02 ... (remaining 2977 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 69 2.50 - 3.10: 13244 3.10 - 3.70: 31187 3.70 - 4.30: 43109 4.30 - 4.90: 67157 Nonbonded interactions: 154766 Sorted by model distance: nonbonded pdb=" OD2 ASP C 708 " pdb="MG MG C1101 " model vdw 1.897 2.170 nonbonded pdb=" OD1 ASP C 600 " pdb="MG MG C1101 " model vdw 1.901 2.170 nonbonded pdb=" OD2 ASP A 708 " pdb="MG MG A1101 " model vdw 1.901 2.170 nonbonded pdb=" OD1 ASP A 600 " pdb="MG MG A1101 " model vdw 1.906 2.170 nonbonded pdb=" OD1 ASP A 546 " pdb=" OG SER B 260 " model vdw 2.210 3.040 ... (remaining 154761 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 400 through 406 or (resid 407 and (name N or name CA or na \ me C or name O or name CB )) or resid 408 through 427 or (resid 428 through 429 \ and (name N or name CA or name C or name O or name CB )) or resid 430 through 45 \ 7 or (resid 458 and (name N or name CA or name C or name O or name CB )) or resi \ d 459 through 584 or (resid 585 and (name N or name CA or name C or name O or na \ me CB )) or resid 586 through 847 or (resid 848 and (name N or name CA or name C \ or name O or name CB )) or resid 849 through 903 or (resid 904 and (name N or n \ ame CA or name C or name O or name CB )) or resid 905 through 955 or (resid 956 \ and (name N or name CA or name C or name O or name CB )) or resid 961 through 10 \ 08 or resid 1101 through 1102)) selection = (chain 'C' and (resid 400 through 408 or (resid 409 and (name N or name CA or na \ me C or name O or name CB )) or resid 410 through 631 or (resid 632 and (name N \ or name CA or name C or name O or name CB )) or resid 633 through 638 or (resid \ 639 and (name N or name CA or name C or name O or name CB )) or resid 640 throug \ h 751 or (resid 752 and (name N or name CA or name C or name O or name CB )) or \ resid 753 through 757 or (resid 758 and (name N or name CA or name C or name O o \ r name CB )) or resid 759 through 810 or (resid 811 and (name N or name CA or na \ me C or name O or name CB )) or resid 812 through 819 or (resid 820 through 821 \ and (name N or name CA or name C or name O or name CB )) or resid 822 or (resid \ 823 and (name N or name CA or name C or name O or name CB )) or resid 824 throug \ h 834 or (resid 835 and (name N or name CA or name C or name O or name CB )) or \ resid 836 through 837 or (resid 838 through 839 and (name N or name CA or name C \ or name O or name CB )) or resid 840 through 860 or (resid 861 and (name N or n \ ame CA or name C or name O or name CB )) or resid 862 through 926 or (resid 927 \ through 928 and (name N or name CA or name C or name O or name CB )) or resid 92 \ 9 through 947 or (resid 948 and (name N or name CA or name C or name O or name C \ B )) or resid 949 through 956 or resid 961 through 1008 or resid 1101 through 11 \ 02)) } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 1 through 338 or (resid 339 and (name N or name CA or name \ C or name O or name CB )) or resid 340 through 351)) } 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 56.720 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.080 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 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 : 0.004 0.234 20566 Z= 0.160 Angle : 0.596 43.180 28712 Z= 0.299 Chirality : 0.036 0.147 3185 Planarity : 0.003 0.031 2980 Dihedral : 20.020 179.604 8055 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.19 % Allowed : 7.49 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: -2.82 (0.16), residues: 1978 helix: -0.65 (0.17), residues: 736 sheet: -1.80 (0.25), residues: 349 loop : -2.98 (0.17), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 893 HIS 0.002 0.000 HIS A 836 PHE 0.012 0.001 PHE A 911 TYR 0.009 0.001 TYR C 998 ARG 0.001 0.000 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.14156 ( 955) hydrogen bonds : angle 5.39894 ( 2534) metal coordination : bond 0.15681 ( 8) metal coordination : angle 28.47946 ( 4) covalent geometry : bond 0.00226 (20558) covalent geometry : angle 0.49259 (28708) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 199 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 ARG cc_start: 0.6252 (tpt90) cc_final: 0.6047 (ttp80) REVERT: A 408 LEU cc_start: 0.9084 (mt) cc_final: 0.8808 (tt) REVERT: A 726 ILE cc_start: 0.6513 (OUTLIER) cc_final: 0.6286 (pp) REVERT: A 919 LEU cc_start: 0.8506 (mt) cc_final: 0.8008 (mm) REVERT: C 858 MET cc_start: 0.7452 (mmm) cc_final: 0.7103 (mmm) REVERT: B 152 MET cc_start: 0.6971 (tpp) cc_final: 0.6276 (tpp) REVERT: B 232 ASN cc_start: 0.6573 (m-40) cc_final: 0.6283 (t0) REVERT: D 189 PHE cc_start: 0.8006 (m-80) cc_final: 0.7596 (t80) REVERT: D 285 MET cc_start: 0.8388 (mmt) cc_final: 0.8017 (mmm) outliers start: 36 outliers final: 6 residues processed: 228 average time/residue: 0.3093 time to fit residues: 109.0583 Evaluate side-chains 121 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 658 MET Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 726 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 10.0000 chunk 162 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 109 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 195 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN A 480 GLN A 498 GLN A 581 GLN A 739 GLN A 744 HIS ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 GLN A 991 HIS C 456 GLN C 463 GLN C 473 ASN C 495 GLN C 515 HIS C 636 GLN C 739 GLN C 744 HIS C 852 ASN B 47 HIS B 89 HIS ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN B 201 GLN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN D 89 HIS D 94 HIS D 101 ASN ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.063665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.048904 restraints weight = 127991.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.049769 restraints weight = 66917.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.050259 restraints weight = 43415.456| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 20566 Z= 0.333 Angle : 0.787 9.483 28712 Z= 0.418 Chirality : 0.046 0.241 3185 Planarity : 0.006 0.062 2980 Dihedral : 25.362 176.529 4439 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 3.23 % Allowed : 11.69 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: -2.00 (0.18), residues: 1978 helix: 0.07 (0.18), residues: 747 sheet: -1.23 (0.28), residues: 329 loop : -2.64 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 893 HIS 0.011 0.002 HIS D 313 PHE 0.029 0.003 PHE D 62 TYR 0.023 0.003 TYR B 108 ARG 0.007 0.001 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.05567 ( 955) hydrogen bonds : angle 4.53892 ( 2534) metal coordination : bond 0.03656 ( 8) metal coordination : angle 3.48144 ( 4) covalent geometry : bond 0.00735 (20558) covalent geometry : angle 0.78557 (28708) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 97 time to evaluate : 1.916 Fit side-chains revert: symmetry clash REVERT: A 402 ARG cc_start: 0.6335 (tpt90) cc_final: 0.6028 (ttp80) REVERT: C 858 MET cc_start: 0.7660 (mmm) cc_final: 0.7163 (mmm) REVERT: C 883 MET cc_start: 0.8357 (tpp) cc_final: 0.7950 (tpp) REVERT: D 189 PHE cc_start: 0.8304 (m-80) cc_final: 0.7746 (t80) REVERT: N 109 TYR cc_start: 0.5139 (m-10) cc_final: 0.4549 (t80) outliers start: 53 outliers final: 31 residues processed: 143 average time/residue: 0.2631 time to fit residues: 63.1033 Evaluate side-chains 115 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 921 SER Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 242 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 122 optimal weight: 4.9990 chunk 143 optimal weight: 9.9990 chunk 198 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 163 optimal weight: 0.0870 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 chunk 58 optimal weight: 0.5980 chunk 124 optimal weight: 0.1980 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN A 750 HIS ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 HIS C 800 ASN B 94 HIS ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.065429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.050339 restraints weight = 120021.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.051281 restraints weight = 62413.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.051888 restraints weight = 40250.665| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20566 Z= 0.122 Angle : 0.566 9.904 28712 Z= 0.303 Chirality : 0.039 0.216 3185 Planarity : 0.004 0.051 2980 Dihedral : 25.185 177.195 4433 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.74 % Allowed : 12.18 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: -1.30 (0.19), residues: 1978 helix: 0.77 (0.19), residues: 749 sheet: -1.03 (0.27), residues: 355 loop : -2.30 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 317 HIS 0.004 0.001 HIS C 991 PHE 0.015 0.001 PHE A 808 TYR 0.013 0.001 TYR C 998 ARG 0.004 0.000 ARG C 761 Details of bonding type rmsd hydrogen bonds : bond 0.03421 ( 955) hydrogen bonds : angle 3.83881 ( 2534) metal coordination : bond 0.00569 ( 8) metal coordination : angle 3.29555 ( 4) covalent geometry : bond 0.00264 (20558) covalent geometry : angle 0.56505 (28708) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 105 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 LEU cc_start: 0.8920 (mt) cc_final: 0.8689 (pp) REVERT: A 726 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7208 (pp) REVERT: C 858 MET cc_start: 0.7558 (mmm) cc_final: 0.7269 (mmm) REVERT: D 189 PHE cc_start: 0.8298 (m-80) cc_final: 0.7764 (t80) REVERT: D 240 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.6986 (tt) REVERT: N 109 TYR cc_start: 0.5202 (m-10) cc_final: 0.4654 (t80) outliers start: 45 outliers final: 23 residues processed: 141 average time/residue: 0.2778 time to fit residues: 64.9596 Evaluate side-chains 113 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 2.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 240 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 164 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 160 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 chunk 199 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 chunk 93 optimal weight: 0.5980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 213 ASN ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.064679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.050138 restraints weight = 123817.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.051062 restraints weight = 63180.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.051606 restraints weight = 40401.242| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20566 Z= 0.149 Angle : 0.569 7.477 28712 Z= 0.307 Chirality : 0.039 0.199 3185 Planarity : 0.004 0.046 2980 Dihedral : 25.171 175.072 4433 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.17 % Allowed : 13.03 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: -1.01 (0.19), residues: 1978 helix: 0.93 (0.19), residues: 758 sheet: -0.71 (0.29), residues: 317 loop : -2.12 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 317 HIS 0.012 0.001 HIS A 876 PHE 0.024 0.001 PHE B 29 TYR 0.011 0.001 TYR C 998 ARG 0.003 0.000 ARG C 927 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 955) hydrogen bonds : angle 3.78062 ( 2534) metal coordination : bond 0.01341 ( 8) metal coordination : angle 2.60647 ( 4) covalent geometry : bond 0.00329 (20558) covalent geometry : angle 0.56853 (28708) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 87 time to evaluate : 1.893 Fit side-chains revert: symmetry clash REVERT: A 402 ARG cc_start: 0.6301 (OUTLIER) cc_final: 0.6037 (ttp80) REVERT: C 658 MET cc_start: 0.8843 (pmm) cc_final: 0.8326 (pmm) REVERT: B 219 LEU cc_start: 0.8662 (mm) cc_final: 0.7565 (tp) REVERT: B 294 ASP cc_start: 0.5781 (OUTLIER) cc_final: 0.5325 (m-30) REVERT: D 189 PHE cc_start: 0.8366 (m-80) cc_final: 0.7738 (t80) REVERT: N 109 TYR cc_start: 0.5117 (m-10) cc_final: 0.4580 (t80) outliers start: 52 outliers final: 30 residues processed: 133 average time/residue: 0.2518 time to fit residues: 57.1103 Evaluate side-chains 119 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 921 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 191 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 185 optimal weight: 0.8980 chunk 203 optimal weight: 8.9990 chunk 64 optimal weight: 8.9990 chunk 176 optimal weight: 7.9990 chunk 46 optimal weight: 0.1980 chunk 113 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.065089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.050223 restraints weight = 127113.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.051136 restraints weight = 64948.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.051660 restraints weight = 41769.949| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20566 Z= 0.132 Angle : 0.557 8.057 28712 Z= 0.300 Chirality : 0.039 0.167 3185 Planarity : 0.003 0.046 2980 Dihedral : 25.154 176.099 4433 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.11 % Allowed : 13.22 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.19), residues: 1978 helix: 1.13 (0.19), residues: 759 sheet: -0.63 (0.28), residues: 338 loop : -1.98 (0.20), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 317 HIS 0.005 0.001 HIS A 876 PHE 0.023 0.001 PHE B 29 TYR 0.012 0.001 TYR C 886 ARG 0.003 0.000 ARG D 123 Details of bonding type rmsd hydrogen bonds : bond 0.03270 ( 955) hydrogen bonds : angle 3.65815 ( 2534) metal coordination : bond 0.00936 ( 8) metal coordination : angle 2.03965 ( 4) covalent geometry : bond 0.00290 (20558) covalent geometry : angle 0.55605 (28708) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 88 time to evaluate : 1.809 Fit side-chains revert: symmetry clash REVERT: A 402 ARG cc_start: 0.6117 (OUTLIER) cc_final: 0.5914 (ttp80) REVERT: A 726 ILE cc_start: 0.7633 (OUTLIER) cc_final: 0.7290 (pp) REVERT: C 658 MET cc_start: 0.8875 (pmm) cc_final: 0.8424 (pmm) REVERT: C 887 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8509 (mm) REVERT: B 219 LEU cc_start: 0.8684 (mm) cc_final: 0.7542 (tp) REVERT: D 189 PHE cc_start: 0.8411 (m-80) cc_final: 0.7730 (t80) REVERT: D 240 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6669 (tt) REVERT: N 109 TYR cc_start: 0.5108 (m-10) cc_final: 0.4644 (t80) outliers start: 51 outliers final: 32 residues processed: 131 average time/residue: 0.2528 time to fit residues: 55.6342 Evaluate side-chains 122 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 86 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 921 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 240 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 89 optimal weight: 8.9990 chunk 184 optimal weight: 0.8980 chunk 156 optimal weight: 0.0050 chunk 177 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 overall best weight: 3.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.063696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.049171 restraints weight = 123503.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.050059 restraints weight = 62741.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.050579 restraints weight = 39946.144| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20566 Z= 0.180 Angle : 0.594 7.656 28712 Z= 0.321 Chirality : 0.040 0.167 3185 Planarity : 0.004 0.045 2980 Dihedral : 25.265 175.651 4433 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.86 % Allowed : 14.49 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.19), residues: 1978 helix: 1.07 (0.19), residues: 758 sheet: -0.41 (0.30), residues: 318 loop : -2.02 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 317 HIS 0.006 0.001 HIS A 876 PHE 0.022 0.002 PHE B 29 TYR 0.011 0.001 TYR C 998 ARG 0.004 0.000 ARG C 927 Details of bonding type rmsd hydrogen bonds : bond 0.03926 ( 955) hydrogen bonds : angle 3.80804 ( 2534) metal coordination : bond 0.01671 ( 8) metal coordination : angle 2.41357 ( 4) covalent geometry : bond 0.00398 (20558) covalent geometry : angle 0.59360 (28708) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 85 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 ARG cc_start: 0.6292 (OUTLIER) cc_final: 0.6084 (ttp80) REVERT: A 602 MET cc_start: 0.7154 (mmm) cc_final: 0.6835 (mtt) REVERT: A 726 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7661 (pp) REVERT: C 484 MET cc_start: 0.8627 (tmm) cc_final: 0.8349 (ttt) REVERT: C 887 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8531 (mm) REVERT: C 1001 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.9082 (ttpp) REVERT: B 219 LEU cc_start: 0.8655 (mm) cc_final: 0.7531 (tp) REVERT: B 294 ASP cc_start: 0.6431 (OUTLIER) cc_final: 0.5520 (m-30) REVERT: D 189 PHE cc_start: 0.8407 (m-80) cc_final: 0.7760 (t80) REVERT: D 240 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6681 (tt) REVERT: N 109 TYR cc_start: 0.5128 (m-10) cc_final: 0.4601 (t80) outliers start: 47 outliers final: 34 residues processed: 124 average time/residue: 0.2601 time to fit residues: 54.5012 Evaluate side-chains 121 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 81 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 921 SER Chi-restraints excluded: chain C residue 1001 LYS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 240 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 163 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 147 optimal weight: 0.3980 chunk 87 optimal weight: 7.9990 chunk 182 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.065189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.050385 restraints weight = 123257.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.051280 restraints weight = 63175.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.051805 restraints weight = 40783.567| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20566 Z= 0.117 Angle : 0.549 8.111 28712 Z= 0.295 Chirality : 0.038 0.170 3185 Planarity : 0.003 0.048 2980 Dihedral : 25.150 178.210 4433 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.44 % Allowed : 14.98 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.19), residues: 1978 helix: 1.30 (0.19), residues: 757 sheet: -0.18 (0.29), residues: 316 loop : -1.92 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 317 HIS 0.003 0.001 HIS A 876 PHE 0.018 0.001 PHE B 29 TYR 0.012 0.001 TYR C 998 ARG 0.003 0.000 ARG C 761 Details of bonding type rmsd hydrogen bonds : bond 0.03140 ( 955) hydrogen bonds : angle 3.55184 ( 2534) metal coordination : bond 0.00617 ( 8) metal coordination : angle 1.54400 ( 4) covalent geometry : bond 0.00254 (20558) covalent geometry : angle 0.54899 (28708) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 92 time to evaluate : 1.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 645 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8814 (ptmm) REVERT: A 726 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7540 (pp) REVERT: C 568 MET cc_start: 0.8564 (mmm) cc_final: 0.7890 (mmm) REVERT: C 887 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8621 (mm) REVERT: B 219 LEU cc_start: 0.8648 (mm) cc_final: 0.7578 (tp) REVERT: D 189 PHE cc_start: 0.8371 (m-80) cc_final: 0.7670 (t80) REVERT: D 240 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6459 (tt) REVERT: N 109 TYR cc_start: 0.4971 (m-10) cc_final: 0.4524 (t80) outliers start: 40 outliers final: 26 residues processed: 125 average time/residue: 0.2635 time to fit residues: 55.0684 Evaluate side-chains 118 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 645 LYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 240 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 31 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 212 optimal weight: 20.0000 chunk 78 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 126 optimal weight: 0.0770 chunk 21 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.064476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.049756 restraints weight = 123725.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.050648 restraints weight = 63013.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.051166 restraints weight = 40120.614| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20566 Z= 0.146 Angle : 0.565 8.508 28712 Z= 0.304 Chirality : 0.039 0.168 3185 Planarity : 0.003 0.046 2980 Dihedral : 25.172 177.377 4433 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.07 % Allowed : 15.83 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.19), residues: 1978 helix: 1.36 (0.19), residues: 756 sheet: -0.10 (0.30), residues: 306 loop : -1.91 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 317 HIS 0.004 0.001 HIS C 501 PHE 0.022 0.001 PHE B 29 TYR 0.018 0.001 TYR D 217 ARG 0.003 0.000 ARG C 927 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 955) hydrogen bonds : angle 3.59490 ( 2534) metal coordination : bond 0.01308 ( 8) metal coordination : angle 1.98079 ( 4) covalent geometry : bond 0.00322 (20558) covalent geometry : angle 0.56484 (28708) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 88 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8648 (tt) REVERT: A 645 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8803 (ptmm) REVERT: A 726 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7661 (pp) REVERT: C 484 MET cc_start: 0.8599 (tmm) cc_final: 0.8255 (ttt) REVERT: C 658 MET cc_start: 0.8881 (pmm) cc_final: 0.8249 (pmm) REVERT: C 887 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8508 (mm) REVERT: B 219 LEU cc_start: 0.8560 (mm) cc_final: 0.7538 (tp) REVERT: D 189 PHE cc_start: 0.8384 (m-80) cc_final: 0.7555 (t80) REVERT: D 240 LEU cc_start: 0.6960 (OUTLIER) cc_final: 0.6565 (tt) REVERT: N 109 TYR cc_start: 0.5044 (m-10) cc_final: 0.4578 (t80) outliers start: 34 outliers final: 26 residues processed: 116 average time/residue: 0.2593 time to fit residues: 51.0259 Evaluate side-chains 117 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 645 LYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 921 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 240 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 69.3485 > 50: distance: 11 - 15: 26.156 distance: 15 - 16: 51.264 distance: 16 - 17: 10.213 distance: 16 - 19: 8.106 distance: 17 - 18: 5.810 distance: 17 - 21: 9.296 distance: 19 - 20: 15.348 distance: 21 - 22: 38.405 distance: 22 - 23: 18.601 distance: 22 - 25: 15.490 distance: 23 - 24: 16.103 distance: 23 - 28: 27.220 distance: 25 - 26: 16.200 distance: 25 - 27: 26.023 distance: 28 - 29: 7.798 distance: 29 - 30: 15.141 distance: 29 - 32: 16.030 distance: 30 - 31: 16.561 distance: 30 - 36: 8.531 distance: 32 - 33: 3.713 distance: 33 - 34: 13.136 distance: 33 - 35: 13.364 distance: 36 - 37: 4.891 distance: 37 - 38: 12.882 distance: 37 - 40: 6.111 distance: 38 - 39: 16.589 distance: 38 - 45: 27.967 distance: 40 - 41: 7.358 distance: 41 - 42: 16.350 distance: 42 - 43: 7.587 distance: 42 - 44: 24.512 distance: 45 - 46: 17.077 distance: 46 - 47: 35.191 distance: 46 - 49: 19.385 distance: 47 - 48: 6.686 distance: 47 - 57: 28.293 distance: 50 - 51: 21.584 distance: 50 - 52: 30.761 distance: 51 - 53: 12.345 distance: 52 - 54: 12.525 distance: 53 - 55: 29.938 distance: 54 - 55: 18.538 distance: 55 - 56: 10.107 distance: 57 - 58: 22.634 distance: 57 - 63: 27.709 distance: 58 - 59: 30.962 distance: 58 - 61: 25.277 distance: 59 - 60: 9.912 distance: 59 - 64: 33.870 distance: 61 - 62: 12.746 distance: 62 - 63: 8.348 distance: 64 - 65: 27.556 distance: 65 - 66: 10.618 distance: 65 - 68: 20.121 distance: 66 - 67: 5.417 distance: 66 - 71: 8.154 distance: 68 - 69: 13.302 distance: 68 - 70: 28.984 distance: 71 - 72: 14.347 distance: 72 - 73: 8.200 distance: 72 - 75: 32.528 distance: 73 - 79: 18.238 distance: 75 - 76: 25.231 distance: 76 - 77: 16.005 distance: 76 - 78: 21.970 distance: 80 - 81: 13.540 distance: 80 - 83: 31.137 distance: 81 - 82: 30.226 distance: 83 - 84: 43.285 distance: 83 - 85: 18.487 distance: 86 - 87: 13.234 distance: 87 - 88: 13.113 distance: 87 - 90: 40.027 distance: 88 - 89: 3.295 distance: 88 - 94: 32.378 distance: 90 - 91: 11.761 distance: 90 - 92: 17.536 distance: 91 - 93: 25.590