Starting phenix.real_space_refine on Sun Sep 13 00:28:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6oem_20030/09_2026/6oem_20030.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oem_20030/09_2026/6oem_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 { model { file = "/net/cci-nas-00/data/ceres_data/6oem_20030/09_2026/6oem_20030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oem_20030/09_2026/6oem_20030.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6oem_20030/09_2026/6oem_20030.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6oem_20030/09_2026/6oem_20030.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6oem_20030/09_2026/6oem_20030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oem_20030/09_2026/6oem_20030.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'ARG:plan': 4, 'GLN:plan1': 2, 'GLU:plan': 7, '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: {'ARG:plan': 4, 'GLN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 2, 'TRP:plan': 1, 'ASN:plan1': 1} 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: {'ASN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 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: {'ASN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 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, 'ASP:plan': 1, 'ASN:plan1': 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: {'PHE:plan': 3, 'GLU:plan': 5, 'TYR:plan': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASP:plan': 3, 'TRP:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 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: 3.93, per 1000 atoms: 0.20 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: 1.56 Conformation dependent library (CDL) restraints added in 658.7 milliseconds 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: 2.66 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: 4.95 Time building geometry restraints manager: 2.02 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=" C3' DG G 15 " pdb=" C2' DG G 15 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" C3' DT G 29 " pdb=" C2' DT G 29 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" C3' DC F 41 " pdb=" C2' DC F 41 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.30e+00 bond pdb=" C3' DT J 14 " pdb=" C2' DT J 14 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.17e+00 bond pdb=" C3' DT F 12 " pdb=" C2' DT F 12 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.52e+00 ... (remaining 20553 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 27126 1.21 - 2.42: 1276 2.42 - 3.63: 271 3.63 - 4.84: 28 4.84 - 6.05: 7 Bond angle restraints: 28708 Sorted by residual: angle pdb=" O4' DT G 24 " pdb=" C1' DT G 24 " pdb=" N1 DT G 24 " ideal model delta sigma weight residual 108.00 111.27 -3.27 7.00e-01 2.04e+00 2.18e+01 angle pdb=" N3 DT G 17 " pdb=" C4 DT G 17 " pdb=" O4 DT G 17 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT I 22 " pdb=" C4 DT I 22 " pdb=" O4 DT I 22 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT I 12 " pdb=" C4 DT I 12 " pdb=" O4 DT I 12 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT G 13 " pdb=" C4 DT G 13 " pdb=" O4 DT G 13 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 ... (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 - 0.034: 2087 0.034 - 0.067: 719 0.067 - 0.101: 280 0.101 - 0.135: 93 0.135 - 0.168: 6 Chirality restraints: 3185 Sorted by residual: chirality pdb=" C3' DA F 32 " pdb=" C4' DA F 32 " pdb=" O3' DA F 32 " pdb=" C2' DA F 32 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.07e-01 chirality pdb=" C3' DA F 33 " pdb=" C4' DA F 33 " pdb=" O3' DA F 33 " pdb=" C2' DA F 33 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.75e-01 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 ... (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 11 \ 02)) 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 1102)) } 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 22.680 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.234 20566 Z= 0.343 Angle : 0.684 43.180 28712 Z= 0.489 Chirality : 0.041 0.168 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.001 0.000 ARG B 39 TYR 0.009 0.001 TYR C 998 PHE 0.012 0.001 PHE A 911 TRP 0.006 0.001 TRP C 893 HIS 0.002 0.000 HIS A 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.33 (20558) covalent geometry : angle 0.59589 / 0.48 (28708) hydrogen bonds : bond 0.14156 / 9.63 ( 955) hydrogen bonds : angle 5.39894 / 3.87 ( 2534) metal coordination : bond 0.15681 / 9.59 ( 8) metal coordination : angle 28.47946 / 17.98 ( 4) *********************** 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 : 0.612 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: 0.6004 (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: 0.1384 time to fit residues: 49.4359 Evaluate side-chains 122 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 98 optimal weight: 5.9990 chunk 194 optimal weight: 30.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 20.0000 chunk 212 optimal weight: 30.0000 chunk 77 optimal weight: 6.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 473 ASN A 480 GLN A 498 GLN A 581 GLN A 744 HIS 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 637 ASN C 739 GLN B 89 HIS ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN B 201 GLN B 282 GLN 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.066831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.052165 restraints weight = 126807.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.053090 restraints weight = 65863.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.053611 restraints weight = 42347.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.054038 restraints weight = 32124.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.054197 restraints weight = 26932.738| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20566 Z= 0.212 Angle : 0.673 10.933 28712 Z= 0.359 Chirality : 0.044 0.344 3185 Planarity : 0.005 0.051 2980 Dihedral : 25.214 176.492 4439 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.98 % Allowed : 10.54 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.18), residues: 1978 helix: 0.30 (0.18), residues: 750 sheet: -1.12 (0.29), residues: 303 loop : -2.52 (0.18), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 446 TYR 0.017 0.002 TYR D 68 PHE 0.032 0.002 PHE A 808 TRP 0.012 0.001 TRP C 893 HIS 0.007 0.001 HIS C 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.21 (20558) covalent geometry : angle 0.67157 / 0.36 (28708) hydrogen bonds : bond 0.04508 / 3.03 ( 955) hydrogen bonds : angle 4.28973 / 3.04 ( 2534) metal coordination : bond 0.02411 / 1.20 ( 8) metal coordination : angle 4.31554 / 2.63 ( 4) *********************** 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 159 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 110 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 ARG cc_start: 0.6467 (tpt90) cc_final: 0.6266 (ttp80) REVERT: A 408 LEU cc_start: 0.9130 (mt) cc_final: 0.8560 (pp) REVERT: C 858 MET cc_start: 0.7643 (mmm) cc_final: 0.7304 (mmm) REVERT: C 887 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8620 (mm) REVERT: B 232 ASN cc_start: 0.7026 (m-40) cc_final: 0.6782 (t0) REVERT: B 263 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7866 (pt) REVERT: D 189 PHE cc_start: 0.8150 (m-80) cc_final: 0.7705 (t80) REVERT: D 285 MET cc_start: 0.8504 (mmt) cc_final: 0.8147 (mmm) outliers start: 49 outliers final: 26 residues processed: 154 average time/residue: 0.1160 time to fit residues: 30.1971 Evaluate side-chains 120 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 638 VAL Chi-restraints excluded: chain A residue 658 MET Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 876 HIS 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 598 SER Chi-restraints excluded: chain C residue 633 HIS 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 C residue 921 SER Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 287 CYS 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 0 optimal weight: 30.0000 chunk 16 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 70 optimal weight: 0.0270 chunk 50 optimal weight: 9.9990 chunk 169 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 480 GLN C 414 GLN ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.067340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.052604 restraints weight = 127288.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.053503 restraints weight = 64735.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.054138 restraints weight = 41617.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.054500 restraints weight = 30543.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.054659 restraints weight = 25819.994| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20566 Z= 0.123 Angle : 0.568 7.457 28712 Z= 0.307 Chirality : 0.042 0.349 3185 Planarity : 0.004 0.046 2980 Dihedral : 25.255 177.524 4437 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.50 % Allowed : 10.90 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.19), residues: 1978 helix: 0.82 (0.19), residues: 753 sheet: -0.93 (0.28), residues: 325 loop : -2.29 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 529 TYR 0.013 0.001 TYR A 586 PHE 0.014 0.001 PHE A 853 TRP 0.008 0.001 TRP C 893 HIS 0.004 0.001 HIS C 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.12 (20558) covalent geometry : angle 0.56621 / 0.31 (28708) hydrogen bonds : bond 0.03657 / 2.41 ( 955) hydrogen bonds : angle 3.94714 / 2.82 ( 2534) metal coordination : bond 0.00816 / 0.49 ( 8) metal coordination : angle 3.52178 / 2.20 ( 4) *********************** 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 144 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 103 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 ARG cc_start: 0.6419 (tpt90) cc_final: 0.6163 (ttp80) REVERT: A 726 ILE cc_start: 0.7072 (OUTLIER) cc_final: 0.6789 (pp) REVERT: C 658 MET cc_start: 0.8656 (pmm) cc_final: 0.8244 (pmm) REVERT: B 232 ASN cc_start: 0.7022 (m-40) cc_final: 0.6769 (t0) REVERT: D 189 PHE cc_start: 0.8173 (m-80) cc_final: 0.7770 (t80) REVERT: D 348 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8637 (mt) outliers start: 41 outliers final: 19 residues processed: 136 average time/residue: 0.1180 time to fit residues: 26.8739 Evaluate side-chains 115 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LEU 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 627 MET Chi-restraints excluded: chain A residue 638 VAL 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 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 726 ILE 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 348 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 158 optimal weight: 10.0000 chunk 74 optimal weight: 0.0770 chunk 174 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 23 optimal weight: 0.0770 chunk 88 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 214 optimal weight: 9.9990 chunk 198 optimal weight: 40.0000 overall best weight: 1.4300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN ** 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 = 0.3788 r_free = 0.3788 target = 0.066802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.051914 restraints weight = 126628.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.052912 restraints weight = 65101.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.053460 restraints weight = 41555.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.053868 restraints weight = 31375.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.054058 restraints weight = 26111.869| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20566 Z= 0.120 Angle : 0.567 10.123 28712 Z= 0.303 Chirality : 0.042 0.345 3185 Planarity : 0.003 0.045 2980 Dihedral : 25.284 178.037 4432 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.56 % Allowed : 11.94 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.19), residues: 1978 helix: 1.04 (0.19), residues: 754 sheet: -0.82 (0.28), residues: 321 loop : -2.14 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 529 TYR 0.010 0.001 TYR C 998 PHE 0.015 0.001 PHE C 641 TRP 0.007 0.001 TRP B 317 HIS 0.012 0.001 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.12 (20558) covalent geometry : angle 0.56660 / 0.30 (28708) hydrogen bonds : bond 0.03501 / 2.30 ( 955) hydrogen bonds : angle 3.79575 / 2.73 ( 2534) metal coordination : bond 0.00941 / 0.49 ( 8) metal coordination : angle 2.33248 / 1.47 ( 4) *********************** 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 143 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 101 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 ARG cc_start: 0.6389 (tpt90) cc_final: 0.6166 (ttp80) REVERT: A 408 LEU cc_start: 0.9155 (mt) cc_final: 0.8557 (tt) REVERT: A 726 ILE cc_start: 0.7101 (OUTLIER) cc_final: 0.6821 (pp) REVERT: C 658 MET cc_start: 0.8670 (pmm) cc_final: 0.8174 (pmm) REVERT: B 232 ASN cc_start: 0.7050 (m-40) cc_final: 0.6801 (t0) REVERT: B 285 MET cc_start: 0.7510 (mpp) cc_final: 0.7306 (mpp) REVERT: D 189 PHE cc_start: 0.8166 (m-80) cc_final: 0.7748 (t80) REVERT: D 348 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8644 (mt) REVERT: N 109 TYR cc_start: 0.4549 (m-10) cc_final: 0.4340 (t80) outliers start: 42 outliers final: 24 residues processed: 134 average time/residue: 0.1217 time to fit residues: 27.6411 Evaluate side-chains 117 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 627 MET Chi-restraints excluded: chain A residue 638 VAL 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 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 726 ILE Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 921 SER Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 287 CYS 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 348 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 119 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 168 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 153 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 750 HIS B 47 HIS ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.065848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.051223 restraints weight = 124164.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.052167 restraints weight = 63811.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.052762 restraints weight = 40643.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.053151 restraints weight = 30130.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.053325 restraints weight = 25024.324| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20566 Z= 0.142 Angle : 0.584 10.995 28712 Z= 0.313 Chirality : 0.042 0.345 3185 Planarity : 0.004 0.045 2980 Dihedral : 25.363 177.724 4432 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.25 % Allowed : 12.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.19), residues: 1978 helix: 1.14 (0.19), residues: 754 sheet: -0.82 (0.28), residues: 333 loop : -2.01 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 927 TYR 0.011 0.001 TYR D 346 PHE 0.015 0.001 PHE A 911 TRP 0.009 0.001 TRP C 893 HIS 0.012 0.001 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (20558) covalent geometry : angle 0.58342 / 0.31 (28708) hydrogen bonds : bond 0.03699 / 2.45 ( 955) hydrogen bonds : angle 3.76585 / 2.72 ( 2534) metal coordination : bond 0.01420 / 0.72 ( 8) metal coordination : angle 2.24499 / 1.39 ( 4) *********************** 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 130 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 93 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 726 ILE cc_start: 0.7312 (OUTLIER) cc_final: 0.7021 (pp) REVERT: C 658 MET cc_start: 0.8700 (pmm) cc_final: 0.8172 (pmm) REVERT: B 162 MET cc_start: 0.8135 (mmm) cc_final: 0.7830 (mmm) REVERT: D 189 PHE cc_start: 0.8196 (m-80) cc_final: 0.7791 (t80) REVERT: D 348 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8662 (mt) REVERT: N 109 TYR cc_start: 0.4760 (m-10) cc_final: 0.4373 (t80) outliers start: 37 outliers final: 27 residues processed: 121 average time/residue: 0.1216 time to fit residues: 25.0390 Evaluate side-chains 115 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 568 MET Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 638 VAL 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 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 726 ILE Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 921 SER Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 287 CYS 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 348 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 79 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 176 optimal weight: 0.3980 chunk 180 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN ** 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 = 0.3771 r_free = 0.3771 target = 0.066469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.051612 restraints weight = 125143.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.052536 restraints weight = 64246.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.053173 restraints weight = 41604.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.053455 restraints weight = 30936.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.053717 restraints weight = 26383.925| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20566 Z= 0.115 Angle : 0.559 8.105 28712 Z= 0.300 Chirality : 0.042 0.345 3185 Planarity : 0.003 0.046 2980 Dihedral : 25.365 179.292 4432 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.56 % Allowed : 12.55 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.19), residues: 1978 helix: 1.25 (0.19), residues: 754 sheet: -0.70 (0.28), residues: 333 loop : -1.92 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 402 TYR 0.012 0.001 TYR C 998 PHE 0.015 0.001 PHE A 911 TRP 0.008 0.001 TRP B 317 HIS 0.004 0.001 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.12 (20558) covalent geometry : angle 0.55873 / 0.30 (28708) hydrogen bonds : bond 0.03382 / 2.24 ( 955) hydrogen bonds : angle 3.65880 / 2.65 ( 2534) metal coordination : bond 0.00802 / 0.42 ( 8) metal coordination : angle 1.87531 / 1.18 ( 4) *********************** 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 137 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 95 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 726 ILE cc_start: 0.7348 (OUTLIER) cc_final: 0.7072 (pp) REVERT: C 658 MET cc_start: 0.8645 (pmm) cc_final: 0.8150 (pmm) REVERT: C 887 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8558 (mm) REVERT: B 162 MET cc_start: 0.8100 (mmm) cc_final: 0.7782 (mmt) REVERT: D 189 PHE cc_start: 0.8212 (m-80) cc_final: 0.7803 (t80) REVERT: D 240 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.6779 (tt) REVERT: D 348 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8675 (mt) REVERT: N 109 TYR cc_start: 0.4744 (m-10) cc_final: 0.4335 (t80) outliers start: 42 outliers final: 25 residues processed: 130 average time/residue: 0.1147 time to fit residues: 25.9037 Evaluate side-chains 118 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 568 MET 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 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 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 C residue 921 SER Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 287 CYS 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 Chi-restraints excluded: chain D residue 348 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 11 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 123 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 744 HIS ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3718 r_free = 0.3718 target = 0.064200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.049249 restraints weight = 126758.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.050134 restraints weight = 66019.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.050642 restraints weight = 42762.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.051026 restraints weight = 32718.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.051204 restraints weight = 27812.109| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 20566 Z= 0.228 Angle : 0.673 7.266 28712 Z= 0.359 Chirality : 0.045 0.352 3185 Planarity : 0.005 0.045 2980 Dihedral : 25.530 177.179 4431 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.50 % Allowed : 13.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.19), residues: 1978 helix: 0.94 (0.19), residues: 760 sheet: -0.60 (0.29), residues: 321 loop : -2.05 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 927 TYR 0.019 0.002 TYR D 234 PHE 0.037 0.002 PHE A 808 TRP 0.016 0.002 TRP C 893 HIS 0.006 0.001 HIS A 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.23 (20558) covalent geometry : angle 0.67174 / 0.36 (28708) hydrogen bonds : bond 0.04666 / 3.13 ( 955) hydrogen bonds : angle 3.98085 / 2.89 ( 2534) metal coordination : bond 0.02802 / 1.41 ( 8) metal coordination : angle 3.12874 / 1.69 ( 4) *********************** 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 129 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 88 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: C 568 MET cc_start: 0.8698 (mmm) cc_final: 0.8016 (mmm) REVERT: C 887 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8600 (mm) REVERT: B 162 MET cc_start: 0.8236 (mmm) cc_final: 0.7862 (mmm) REVERT: B 294 ASP cc_start: 0.5953 (OUTLIER) cc_final: 0.5434 (m-30) REVERT: D 189 PHE cc_start: 0.8374 (m-80) cc_final: 0.7830 (t80) REVERT: N 109 TYR cc_start: 0.5029 (m-10) cc_final: 0.4567 (t80) REVERT: N 132 MET cc_start: 0.3113 (tmm) cc_final: 0.2829 (tmm) outliers start: 41 outliers final: 29 residues processed: 121 average time/residue: 0.1096 time to fit residues: 23.1611 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 : 0.632 ------------------------------------------------------------------------------- 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 638 VAL Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 759 VAL 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 620 VAL Chi-restraints excluded: chain C residue 633 HIS 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 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 146 TYR Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain D residue 8 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 71 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 129 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 181 optimal weight: 0.0370 chunk 151 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 191 optimal weight: 40.0000 chunk 169 optimal weight: 6.9990 overall best weight: 1.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 ASN ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 ASN ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.065018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.050481 restraints weight = 123233.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.051333 restraints weight = 62829.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.051865 restraints weight = 39972.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.052212 restraints weight = 29996.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.052434 restraints weight = 25203.874| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20566 Z= 0.129 Angle : 0.587 8.203 28712 Z= 0.316 Chirality : 0.042 0.345 3185 Planarity : 0.004 0.046 2980 Dihedral : 25.487 179.515 4431 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.31 % Allowed : 14.25 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.19), residues: 1978 helix: 1.17 (0.19), residues: 760 sheet: -0.54 (0.29), residues: 331 loop : -1.98 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 621 TYR 0.018 0.001 TYR D 217 PHE 0.015 0.001 PHE A 911 TRP 0.010 0.001 TRP B 317 HIS 0.005 0.001 HIS C 991 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 (20558) covalent geometry : angle 0.58634 / 0.32 (28708) hydrogen bonds : bond 0.03697 / 2.48 ( 955) hydrogen bonds : angle 3.77263 / 2.74 ( 2534) metal coordination : bond 0.00855 / 0.46 ( 8) metal coordination : angle 2.02041 / 1.27 ( 4) *********************** 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 127 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 89 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: C 568 MET cc_start: 0.8672 (mmm) cc_final: 0.8015 (mmm) REVERT: C 887 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8560 (mm) REVERT: C 889 MET cc_start: 0.8084 (mmt) cc_final: 0.7826 (mmp) REVERT: B 162 MET cc_start: 0.8203 (mmm) cc_final: 0.7821 (mmm) REVERT: D 189 PHE cc_start: 0.8256 (m-80) cc_final: 0.7731 (t80) REVERT: D 217 TYR cc_start: 0.7955 (m-10) cc_final: 0.7485 (m-10) REVERT: N 109 TYR cc_start: 0.5114 (m-10) cc_final: 0.4635 (t80) REVERT: N 132 MET cc_start: 0.3302 (tmm) cc_final: 0.3060 (tmm) outliers start: 38 outliers final: 29 residues processed: 119 average time/residue: 0.1202 time to fit residues: 24.6241 Evaluate side-chains 116 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 86 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 568 MET Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 759 VAL 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 598 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 633 HIS 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 C residue 921 SER Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain D residue 8 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 45 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 196 optimal weight: 20.0000 chunk 153 optimal weight: 0.8980 chunk 85 optimal weight: 0.0970 chunk 119 optimal weight: 0.7980 chunk 188 optimal weight: 8.9990 chunk 18 optimal weight: 0.6980 chunk 154 optimal weight: 0.9990 chunk 177 optimal weight: 0.0270 chunk 30 optimal weight: 9.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 795 HIS ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3752 r_free = 0.3752 target = 0.065690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.051160 restraints weight = 122391.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.052068 restraints weight = 62336.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.052709 restraints weight = 39854.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.052985 restraints weight = 29419.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.053203 restraints weight = 25055.350| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20566 Z= 0.111 Angle : 0.573 7.854 28712 Z= 0.306 Chirality : 0.042 0.342 3185 Planarity : 0.003 0.046 2980 Dihedral : 25.415 177.970 4431 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.19 % Allowed : 14.56 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.19), residues: 1978 helix: 1.30 (0.19), residues: 761 sheet: -0.52 (0.29), residues: 333 loop : -1.84 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 621 TYR 0.014 0.001 TYR C 998 PHE 0.016 0.001 PHE A 911 TRP 0.008 0.001 TRP B 317 HIS 0.004 0.001 HIS C 991 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.11 (20558) covalent geometry : angle 0.57305 / 0.31 (28708) hydrogen bonds : bond 0.03361 / 2.23 ( 955) hydrogen bonds : angle 3.61862 / 2.62 ( 2534) metal coordination : bond 0.00460 / 0.22 ( 8) metal coordination : angle 1.61024 / 1.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 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 126 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 90 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: A 726 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7142 (pp) REVERT: C 658 MET cc_start: 0.8765 (pmm) cc_final: 0.8145 (pmm) REVERT: C 691 MET cc_start: 0.7942 (ppp) cc_final: 0.7518 (ptm) REVERT: C 887 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8552 (mm) REVERT: C 889 MET cc_start: 0.8087 (mmt) cc_final: 0.7828 (mmp) REVERT: B 303 GLU cc_start: 0.5817 (pm20) cc_final: 0.4686 (tp30) REVERT: D 189 PHE cc_start: 0.8207 (m-80) cc_final: 0.7675 (t80) REVERT: N 109 TYR cc_start: 0.5057 (m-10) cc_final: 0.4620 (t80) outliers start: 36 outliers final: 28 residues processed: 120 average time/residue: 0.1182 time to fit residues: 24.6194 Evaluate side-chains 117 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 87 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 568 MET Chi-restraints excluded: chain A residue 638 VAL 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 541 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 633 HIS 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 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 287 CYS Chi-restraints excluded: chain B residue 289 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 75 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 133 optimal weight: 0.0670 chunk 171 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 94 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 = 0.3722 r_free = 0.3722 target = 0.064613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.049722 restraints weight = 125638.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.050593 restraints weight = 64933.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.051163 restraints weight = 42344.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.051459 restraints weight = 32195.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.051665 restraints weight = 27466.577| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20566 Z= 0.176 Angle : 0.618 9.258 28712 Z= 0.330 Chirality : 0.043 0.350 3185 Planarity : 0.004 0.046 2980 Dihedral : 25.492 179.984 4431 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 1.89 % Allowed : 15.29 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.19), residues: 1978 helix: 1.25 (0.19), residues: 759 sheet: -0.40 (0.29), residues: 340 loop : -1.92 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 927 TYR 0.017 0.001 TYR D 217 PHE 0.034 0.002 PHE B 29 TRP 0.015 0.001 TRP B 317 HIS 0.005 0.001 HIS C 991 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 (20558) covalent geometry : angle 0.61753 / 0.33 (28708) hydrogen bonds : bond 0.04018 / 2.70 ( 955) hydrogen bonds : angle 3.76143 / 2.72 ( 2534) metal coordination : bond 0.01936 / 0.98 ( 8) metal coordination : angle 2.40433 / 1.34 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 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 114 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 83 time to evaluate : 0.690 Fit side-chains REVERT: A 602 MET cc_start: 0.7373 (mmm) cc_final: 0.7160 (mtt) REVERT: A 658 MET cc_start: 0.8817 (pmm) cc_final: 0.8581 (pmm) REVERT: C 568 MET cc_start: 0.8715 (mmm) cc_final: 0.8107 (mmm) REVERT: C 658 MET cc_start: 0.8830 (pmm) cc_final: 0.8222 (pmm) REVERT: C 887 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8580 (mm) REVERT: C 889 MET cc_start: 0.8070 (mmt) cc_final: 0.7854 (mmp) REVERT: B 303 GLU cc_start: 0.6269 (pm20) cc_final: 0.5096 (tt0) REVERT: D 189 PHE cc_start: 0.8248 (m-80) cc_final: 0.7694 (t80) REVERT: N 109 TYR cc_start: 0.5069 (m-10) cc_final: 0.4535 (t80) outliers start: 31 outliers final: 28 residues processed: 108 average time/residue: 0.1059 time to fit residues: 20.2779 Evaluate side-chains 111 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 82 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 568 MET Chi-restraints excluded: chain A residue 638 VAL 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 598 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 633 HIS 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 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 287 CYS Chi-restraints excluded: chain B residue 289 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 132 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 86 optimal weight: 0.4980 chunk 211 optimal weight: 2.9990 chunk 25 optimal weight: 0.0010 chunk 156 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 213 optimal weight: 50.0000 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 94 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 = 0.3740 r_free = 0.3740 target = 0.065344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.050772 restraints weight = 122935.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.051708 restraints weight = 62589.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.052236 restraints weight = 39799.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.052614 restraints weight = 29831.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.052844 restraints weight = 24844.666| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20566 Z= 0.111 Angle : 0.588 16.136 28712 Z= 0.311 Chirality : 0.042 0.344 3185 Planarity : 0.003 0.046 2980 Dihedral : 25.456 177.121 4431 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.77 % Allowed : 15.41 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.19), residues: 1978 helix: 1.34 (0.19), residues: 758 sheet: -0.44 (0.29), residues: 333 loop : -1.84 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 402 TYR 0.016 0.001 TYR C 998 PHE 0.023 0.001 PHE B 29 TRP 0.009 0.001 TRP B 317 HIS 0.004 0.001 HIS C 991 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.11 (20558) covalent geometry : angle 0.58711 / 0.31 (28708) hydrogen bonds : bond 0.03442 / 2.30 ( 955) hydrogen bonds : angle 3.62630 / 2.63 ( 2534) metal coordination : bond 0.00504 / 0.26 ( 8) metal coordination : angle 1.92695 / 1.20 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3217.80 seconds wall clock time: 56 minutes 28.67 seconds (3388.67 seconds total)