Starting phenix.real_space_refine on Sun Sep 13 01:50:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6cg0_7470/09_2026/6cg0_7470.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cg0_7470/09_2026/6cg0_7470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6cg0_7470/09_2026/6cg0_7470.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6cg0_7470/09_2026/6cg0_7470.cif" model { file = "/net/cci-nas-00/data/ceres_data/6cg0_7470/09_2026/6cg0_7470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cg0_7470/09_2026/6cg0_7470.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6cg0_7470/09_2026/6cg0_7470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cg0_7470/09_2026/6cg0_7470.map" } resolution = 3.17 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= 0.000 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 Ca 2 9.91 5 Zn 2 6.06 5 P 209 5.49 5 S 109 5.16 5 C 12030 2.51 5 N 3547 2.21 5 O 4181 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 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: 20080 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4921 Classifications: {'peptide': 614} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 25, 'TRANS': 588} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 4944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4944 Classifications: {'peptide': 616} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 25, 'TRANS': 590} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 2664 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 342, 2649 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 19, 'TRANS': 322} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 342, 2649 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 19, 'TRANS': 322} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 2698 Chain: "B" Number of atoms: 2672 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 342, 2662 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 19, 'TRANS': 322} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 342, 2662 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 19, 'TRANS': 322} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 2717 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: "I" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 323 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "J" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 387 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "G" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1225 Classifications: {'DNA': 60} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 59} Chain: "L" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 610 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "M" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 845 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "N" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 538 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 70} Chain breaks: 2 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 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: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2590 SG CYS A 727 97.086 23.425 71.510 1.00 75.71 S ATOM 2611 SG CYS A 730 98.249 20.598 69.684 1.00 74.45 S ATOM 7542 SG CYS C 727 61.203 83.048 69.025 1.00 71.59 S ATOM 7563 SG CYS C 730 60.014 85.872 67.139 1.00 74.40 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AHIS D 47 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS D 47 " occ=0.50 residue: pdb=" N AHIS B 47 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 47 " occ=0.50 Time building chain proxies: 5.72, per 1000 atoms: 0.28 Number of scatterers: 20080 At special positions: 0 Unit cell: (159.43, 109.14, 182.97, 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 Ca 2 19.99 S 109 16.00 P 209 15.00 O 4181 8.00 N 3547 7.00 C 12030 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 856.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 727 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 730 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 937 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 727 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 730 " Number of angles added : 4 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3730 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 22 sheets defined 40.2% alpha, 18.7% beta 90 base pairs and 154 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'A' and resid 404 through 422 removed outlier: 3.582A pdb=" N LEU A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU A 410 " --> pdb=" O HIS A 406 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU A 411 " --> pdb=" O ARG A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 442 removed outlier: 3.573A pdb=" N VAL A 430 " --> pdb=" O ASP A 426 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 455 Processing helix chain 'A' and resid 463 through 473 Processing helix chain 'A' and resid 477 through 493 Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.878A pdb=" N LYS A 508 " --> pdb=" O ARG A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 removed outlier: 3.509A pdb=" N MET A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'A' and resid 648 through 652 removed outlier: 3.819A pdb=" N CYS A 651 " --> pdb=" O SER A 648 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS A 652 " --> pdb=" O GLU A 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 648 through 652' Processing helix chain 'A' and resid 664 through 683 Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 708 through 717 removed outlier: 3.522A pdb=" N GLY A 717 " --> pdb=" O ARG A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'A' and resid 768 through 777 Processing helix chain 'A' and resid 792 through 813 Processing helix chain 'A' and resid 822 through 841 removed outlier: 3.672A pdb=" N ARG A 826 " --> pdb=" O SER A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 858 Processing helix chain 'A' and resid 859 through 867 Processing helix chain 'A' and resid 873 through 895 removed outlier: 3.640A pdb=" N GLU A 877 " --> pdb=" O GLU A 873 " (cutoff:3.500A) Proline residue: A 891 - end of helix Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 902 through 908 Processing helix chain 'A' and resid 908 through 924 Processing helix chain 'A' and resid 924 through 929 Processing helix chain 'A' and resid 934 through 942 Processing helix chain 'A' and resid 942 through 951 Processing helix chain 'A' and resid 958 through 975 removed outlier: 3.659A pdb=" N GLN A 962 " --> pdb=" O SER A 958 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS A 966 " --> pdb=" O GLN A 962 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 967 " --> pdb=" O SER A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.584A pdb=" N ASP A 986 " --> pdb=" O TYR A 982 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 995 " --> pdb=" O HIS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1004 removed outlier: 3.900A pdb=" N PHE A1002 " --> pdb=" O TYR A 998 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET A1003 " --> pdb=" O LEU A 999 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN A1004 " --> pdb=" O GLN A1000 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 420 removed outlier: 5.413A pdb=" N GLU C 410 " --> pdb=" O HIS C 406 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU C 411 " --> pdb=" O ARG C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 442 removed outlier: 3.758A pdb=" N VAL C 430 " --> pdb=" O ASP C 426 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 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 511 removed outlier: 3.509A pdb=" N LEU C 503 " --> pdb=" O PRO C 499 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS C 508 " --> pdb=" O ARG C 504 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL C 509 " --> pdb=" O ASN C 505 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU C 510 " --> pdb=" O ALA C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 581 removed outlier: 5.288A pdb=" N GLU C 572 " --> pdb=" O MET C 568 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ASP C 573 " --> pdb=" O ASP C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 652 removed outlier: 3.678A pdb=" N CYS C 651 " --> pdb=" O SER C 648 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N CYS C 652 " --> pdb=" O GLU C 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 648 through 652' Processing helix chain 'C' and resid 664 through 683 Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 733 through 738 removed outlier: 3.523A pdb=" N SER C 738 " --> pdb=" O ARG C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 763 Processing helix chain 'C' and resid 768 through 777 Processing helix chain 'C' and resid 792 through 812 Processing helix chain 'C' and resid 822 through 842 removed outlier: 3.756A pdb=" N ARG C 826 " --> pdb=" O SER C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 858 Processing helix chain 'C' and resid 859 through 868 Processing helix chain 'C' and resid 873 through 895 Proline residue: C 891 - end of helix Processing helix chain 'C' and resid 897 through 902 removed outlier: 3.532A pdb=" N CYS C 902 " --> pdb=" O PRO C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 908 Processing helix chain 'C' and resid 908 through 923 Processing helix chain 'C' and resid 924 through 927 Processing helix chain 'C' and resid 933 through 942 removed outlier: 3.813A pdb=" N HIS C 937 " --> pdb=" O THR C 933 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS C 942 " --> pdb=" O LYS C 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 950 Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 958 through 975 removed outlier: 3.611A pdb=" N LYS C 973 " --> pdb=" O ARG C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 996 Processing helix chain 'C' and resid 999 through 1004 Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.742A pdb=" N LEU D 14 " --> pdb=" O ASN D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 removed outlier: 3.735A pdb=" N TRP D 172 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 15 removed outlier: 3.559A pdb=" N LEU B 14 " --> pdb=" O ASN B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 308 through 314 removed outlier: 3.508A pdb=" N LYS B 312 " --> pdb=" O THR B 308 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS B 313 " --> pdb=" O SER B 309 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 27 Processing helix chain 'N' and resid 41 through 48 removed outlier: 4.199A pdb=" N CYS N 45 " --> pdb=" O SER N 42 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER N 46 " --> pdb=" O LYS N 43 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU N 47 " --> pdb=" O LYS N 44 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG N 48 " --> pdb=" O CYS N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 117 Proline residue: N 111 - end of helix Processing helix chain 'N' and resid 121 through 136 removed outlier: 3.773A pdb=" N VAL N 125 " --> pdb=" O SER N 121 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 518 through 519 removed outlier: 3.771A pdb=" N GLU A 518 " --> pdb=" O THR A 688 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 688 " --> pdb=" O GLU A 518 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 535 through 536 removed outlier: 5.661A pdb=" N PHE A 624 " --> pdb=" O PRO A 654 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N MET A 627 " --> pdb=" O GLU A 642 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU A 642 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A 629 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 535 through 536 removed outlier: 5.661A pdb=" N PHE A 624 " --> pdb=" O PRO A 654 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 621 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A 705 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N CYS A 599 " --> pdb=" O THR A 705 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 690 through 691 Processing sheet with id=AA5, first strand: chain 'C' and resid 518 through 519 removed outlier: 3.677A pdb=" N GLU C 518 " --> pdb=" O THR C 688 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG C 703 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR C 705 " --> pdb=" O GLU C 597 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N CYS C 599 " --> pdb=" O THR C 705 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ILE C 631 " --> pdb=" O PRO C 590 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL C 620 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU C 657 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE C 622 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 518 through 519 removed outlier: 3.677A pdb=" N GLU C 518 " --> pdb=" O THR C 688 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG C 703 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR C 705 " --> pdb=" O GLU C 597 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N CYS C 599 " --> pdb=" O THR C 705 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ILE C 631 " --> pdb=" O PRO C 590 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N MET C 627 " --> pdb=" O GLU C 642 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU C 642 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE C 629 " --> pdb=" O VAL C 640 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 2 through 5 removed outlier: 3.607A pdb=" N ARG D 349 " --> pdb=" O SER D 2 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE D 328 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE D 318 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 22 through 24 removed outlier: 4.131A pdb=" N VAL D 28 " --> pdb=" O PHE D 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 61 through 62 removed outlier: 7.654A pdb=" N ILE D 61 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LYS D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS D 115 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR D 121 " --> pdb=" O ALA D 113 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 78 through 81 removed outlier: 3.697A pdb=" N CYS D 78 " --> pdb=" O ILE D 92 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.033A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N SER D 194 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AB4, first strand: chain 'D' and resid 208 through 211 removed outlier: 4.259A pdb=" N LEU D 233 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 263 through 267 removed outlier: 7.256A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 2 through 5 removed outlier: 3.735A pdb=" N SER B 2 " --> pdb=" O ARG B 349 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 7 through 8 removed outlier: 6.477A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS B 56 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP B 49 " --> pdb=" O LYS B 56 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS B 58 " --> pdb=" O AHIS B 47 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL B 28 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 61 through 62 removed outlier: 7.489A pdb=" N ILE B 61 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LYS B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS B 115 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR B 121 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 78 through 80 removed outlier: 4.218A pdb=" N ILE B 107 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.831A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N SER B 194 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS B 191 " --> pdb=" O ASP B 186 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AC3, first strand: chain 'B' and resid 208 through 211 removed outlier: 3.526A pdb=" N ILE B 218 " --> pdb=" O TYR B 234 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU B 233 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN B 248 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 262 through 267 removed outlier: 3.679A pdb=" N VAL B 272 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR B 266 " --> pdb=" O GLU B 270 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) 711 hydrogen bonds defined for protein. 2002 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 224 hydrogen bonds 444 hydrogen bond angles 0 basepair planarities 90 basepair parallelities 154 stacking parallelities Total time for adding SS restraints: 5.09 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3060 1.32 - 1.45: 6618 1.45 - 1.57: 10699 1.57 - 1.69: 415 1.69 - 1.81: 165 Bond restraints: 20957 Sorted by residual: bond pdb=" N9 DA L 35 " pdb=" C4 DA L 35 " ideal model delta sigma weight residual 1.374 1.401 -0.027 6.00e-03 2.78e+04 2.04e+01 bond pdb=" C3' DA L 35 " pdb=" C2' DA L 35 " ideal model delta sigma weight residual 1.516 1.550 -0.034 8.00e-03 1.56e+04 1.80e+01 bond pdb=" C1' DT F 12 " pdb=" N1 DT F 12 " ideal model delta sigma weight residual 1.468 1.526 -0.058 1.40e-02 5.10e+03 1.71e+01 bond pdb=" C3' DT G 24 " pdb=" C2' DT G 24 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.29e+01 bond pdb=" C3' DA M 33 " pdb=" C2' DA M 33 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.29e+01 ... (remaining 20952 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 28199 1.76 - 3.51: 968 3.51 - 5.27: 54 5.27 - 7.02: 10 7.02 - 8.78: 5 Bond angle restraints: 29236 Sorted by residual: angle pdb=" C PRO C 521 " pdb=" N PRO C 522 " pdb=" CA PRO C 522 " ideal model delta sigma weight residual 119.84 127.93 -8.09 1.25e+00 6.40e-01 4.19e+01 angle pdb=" N TYR A 559 " pdb=" CA TYR A 559 " pdb=" C TYR A 559 " ideal model delta sigma weight residual 111.07 117.84 -6.77 1.07e+00 8.73e-01 4.00e+01 angle pdb=" O4' DG M 35 " pdb=" C4' DG M 35 " pdb=" C3' DG M 35 " ideal model delta sigma weight residual 106.00 102.53 3.47 6.00e-01 2.78e+00 3.34e+01 angle pdb=" N TYR C 725 " pdb=" CA TYR C 725 " pdb=" C TYR C 725 " ideal model delta sigma weight residual 109.25 100.47 8.78 1.53e+00 4.27e-01 3.29e+01 angle pdb=" O4' DG F 10 " pdb=" C4' DG F 10 " pdb=" C3' DG F 10 " ideal model delta sigma weight residual 106.00 102.81 3.19 6.00e-01 2.78e+00 2.83e+01 ... (remaining 29231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.69: 11004 34.69 - 69.38: 1017 69.38 - 104.07: 22 104.07 - 138.76: 0 138.76 - 173.45: 2 Dihedral angle restraints: 12045 sinusoidal: 6261 harmonic: 5784 Sorted by residual: dihedral pdb=" C4' DC J 9 " pdb=" C3' DC J 9 " pdb=" O3' DC J 9 " pdb=" P DT J 10 " ideal model delta sinusoidal sigma weight residual 220.00 46.55 173.45 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA GLN A 520 " pdb=" C GLN A 520 " pdb=" N PRO A 521 " pdb=" CA PRO A 521 " ideal model delta harmonic sigma weight residual 180.00 160.71 19.29 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" C4' DC I 9 " pdb=" C3' DC I 9 " pdb=" O3' DC I 9 " pdb=" P DT I 10 " ideal model delta sinusoidal sigma weight residual 220.00 72.06 147.94 1 3.50e+01 8.16e-04 1.45e+01 ... (remaining 12042 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2616 0.056 - 0.112: 512 0.112 - 0.167: 70 0.167 - 0.223: 6 0.223 - 0.279: 5 Chirality restraints: 3209 Sorted by residual: chirality pdb=" CA TYR C 935 " pdb=" N TYR C 935 " pdb=" C TYR C 935 " pdb=" CB TYR C 935 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA TYR A 559 " pdb=" N TYR A 559 " pdb=" C TYR A 559 " pdb=" CB TYR A 559 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA TRP A 893 " pdb=" N TRP A 893 " pdb=" C TRP A 893 " pdb=" CB TRP A 893 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 3206 not shown) Planarity restraints: 3027 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 46 " 0.020 2.00e-02 2.50e+03 4.03e-02 1.63e+01 pdb=" C PHE D 46 " -0.070 2.00e-02 2.50e+03 pdb=" O PHE D 46 " 0.027 2.00e-02 2.50e+03 pdb=" N AHIS D 47 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 46 " 0.018 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C PHE D 46 " -0.064 2.00e-02 2.50e+03 pdb=" O PHE D 46 " 0.024 2.00e-02 2.50e+03 pdb=" N BHIS D 47 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT F 12 " 0.021 2.00e-02 2.50e+03 1.99e-02 9.95e+00 pdb=" N1 DT F 12 " -0.010 2.00e-02 2.50e+03 pdb=" C2 DT F 12 " -0.021 2.00e-02 2.50e+03 pdb=" O2 DT F 12 " -0.024 2.00e-02 2.50e+03 pdb=" N3 DT F 12 " 0.045 2.00e-02 2.50e+03 pdb=" C4 DT F 12 " -0.007 2.00e-02 2.50e+03 pdb=" O4 DT F 12 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DT F 12 " 0.007 2.00e-02 2.50e+03 pdb=" C7 DT F 12 " -0.017 2.00e-02 2.50e+03 pdb=" C6 DT F 12 " 0.003 2.00e-02 2.50e+03 ... (remaining 3024 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1888 2.74 - 3.28: 18847 3.28 - 3.82: 34484 3.82 - 4.36: 40314 4.36 - 4.90: 65304 Nonbonded interactions: 160837 Sorted by model distance: nonbonded pdb=" OG1 THR D 308 " pdb=" OD1 ASP D 310 " model vdw 2.205 3.040 nonbonded pdb=" OE2 GLU C 811 " pdb=" OH TYR C 926 " model vdw 2.206 3.040 nonbonded pdb=" O LEU C 462 " pdb=" NE2 GLN C 498 " model vdw 2.224 3.120 nonbonded pdb=" OE2 GLU A 547 " pdb=" NH1 ARG B 159 " model vdw 2.226 3.120 nonbonded pdb=" NZ LYS B 97 " pdb=" OH TYR B 161 " model vdw 2.244 3.120 ... (remaining 160832 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 395 through 417 or (resid 418 through 419 and (name N or n \ ame CA or name C or name O or name CB )) or resid 420 through 439 or (resid 440 \ through 441 and (name N or name CA or name C or name O or name CB )) or resid 44 \ 2 through 1006 or (resid 1007 and (name N or name CA or name C or name O or name \ CB )) or resid 1101 through 1102)) selection = (chain 'C' and ((resid 395 and (name N or name CA or name C or name O or name CB \ )) or resid 396 or (resid 397 and (name N or name CA or name C or name O or nam \ e CB )) or resid 398 through 523 or (resid 524 and (name N or name CA or name C \ or name O or name CB )) or resid 525 through 689 or (resid 690 and (name N or na \ me CA or name C or name O or name CB )) or resid 691 through 1102)) } ncs_group { reference = (chain 'B' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 46 or resid 48 through 118 or (resid 119 and (name N or nam \ e CA or name C or name O or name CB )) or resid 120 through 187 or (resid 188 an \ d (name N or name CA or name C or name O or name CB )) or resid 189 through 247 \ or resid 249 through 334 or (resid 335 and (name N or name CA or name C or name \ O or name CB )) or resid 341 through 351)) selection = (chain 'D' and (resid 1 through 46 or resid 48 through 81 or resid 88 through 24 \ 7 or resid 249 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 24.640 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 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: 28.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 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 0.438 20965 Z= 0.383 Angle : 0.699 20.442 29240 Z= 0.557 Chirality : 0.046 0.279 3209 Planarity : 0.004 0.056 3027 Dihedral : 20.180 173.451 8315 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.49 % Favored : 97.41 % Rotamer: Outliers : 4.08 % Allowed : 3.44 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.47 (0.17), residues: 1974 helix: -0.47 (0.18), residues: 687 sheet: -1.89 (0.26), residues: 361 loop : -2.45 (0.18), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 773 TYR 0.015 0.001 TYR A 805 PHE 0.015 0.001 PHE D 29 TRP 0.011 0.001 TRP D 36 HIS 0.003 0.001 HIS N 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.37 (20957) covalent geometry : angle 0.68150 / 0.56 (29236) hydrogen bonds : bond 0.17140 / 11.62 ( 907) hydrogen bonds : angle 6.82911 / 4.82 ( 2446) metal coordination : bond 0.18385 / 10.03 ( 8) metal coordination : angle 13.22514 / 7.30 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 153 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 401 ARG cc_start: 0.3076 (OUTLIER) cc_final: 0.2725 (mtt90) REVERT: A 409 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.6763 (ptp-110) REVERT: A 748 ARG cc_start: 0.9305 (OUTLIER) cc_final: 0.8737 (mtt-85) REVERT: A 756 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7846 (mmt180) REVERT: A 890 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.8954 (tttt) REVERT: C 504 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8355 (mtm180) REVERT: C 734 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8199 (ttm170) REVERT: D 285 MET cc_start: 0.7955 (mmm) cc_final: 0.6929 (mmm) REVERT: B 138 TYR cc_start: 0.9276 (OUTLIER) cc_final: 0.8867 (p90) REVERT: B 317 TRP cc_start: 0.8827 (OUTLIER) cc_final: 0.8384 (p90) outliers start: 68 outliers final: 28 residues processed: 216 average time/residue: 0.2273 time to fit residues: 66.9159 Evaluate side-chains 112 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 75 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 486 ARG Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 748 ARG Chi-restraints excluded: chain A residue 756 ARG Chi-restraints excluded: chain A residue 806 LYS Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 890 LYS Chi-restraints excluded: chain A residue 923 LYS Chi-restraints excluded: chain A residue 977 ARG Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 447 GLN Chi-restraints excluded: chain C residue 455 MET Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 486 ARG Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain C residue 508 LYS Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 628 ARG Chi-restraints excluded: chain C residue 641 PHE Chi-restraints excluded: chain C residue 683 LYS Chi-restraints excluded: chain C residue 734 ARG Chi-restraints excluded: chain C residue 758 GLU Chi-restraints excluded: chain C residue 817 LYS Chi-restraints excluded: chain C residue 840 ARG Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 894 ARG Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 317 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 30.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.0670 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 chunk 212 optimal weight: 0.0060 chunk 77 optimal weight: 2.9990 overall best weight: 1.0136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 473 ASN A 495 GLN A 505 ASN A 850 ASN A 978 GLN A 990 HIS A1000 GLN C 406 HIS ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 809 GLN C 860 GLN ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 GLN C 978 GLN C 990 HIS C1000 GLN D 89 HIS ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN ** B 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.086705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.057599 restraints weight = 124352.497| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.39 r_work: 0.2969 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 20965 Z= 0.147 Angle : 0.603 11.927 29240 Z= 0.343 Chirality : 0.042 0.242 3209 Planarity : 0.005 0.048 3027 Dihedral : 24.201 175.614 4611 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.92 % Allowed : 6.24 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.25 (0.18), residues: 1974 helix: 0.79 (0.20), residues: 698 sheet: -1.27 (0.26), residues: 353 loop : -1.95 (0.19), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 407 TYR 0.020 0.001 TYR A 586 PHE 0.019 0.001 PHE D 29 TRP 0.010 0.001 TRP D 317 HIS 0.016 0.001 HIS A1006 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.15 (20957) covalent geometry : angle 0.60199 / 0.34 (29236) hydrogen bonds : bond 0.05049 / 3.30 ( 907) hydrogen bonds : angle 5.05641 / 3.58 ( 2446) metal coordination : bond 0.00760 / 0.50 ( 8) metal coordination : angle 2.77709 / 1.16 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 0.625 Fit side-chains REVERT: A 401 ARG cc_start: 0.2784 (OUTLIER) cc_final: 0.2441 (mtt180) REVERT: A 806 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8864 (tttt) REVERT: C 578 MET cc_start: 0.9285 (ttp) cc_final: 0.9019 (ttp) REVERT: D 285 MET cc_start: 0.8434 (mmm) cc_final: 0.7380 (mmm) REVERT: B 317 TRP cc_start: 0.9102 (OUTLIER) cc_final: 0.8477 (p90) REVERT: N 110 ARG cc_start: 0.2612 (mtt-85) cc_final: 0.2174 (mtp85) outliers start: 31 outliers final: 16 residues processed: 109 average time/residue: 0.1773 time to fit residues: 28.7103 Evaluate side-chains 95 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 486 ARG Chi-restraints excluded: chain A residue 658 MET Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 806 LYS Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 447 GLN Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 486 ARG Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 683 LYS Chi-restraints excluded: chain C residue 840 ARG Chi-restraints excluded: chain C residue 894 ARG Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 317 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 25 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 188 optimal weight: 6.9990 chunk 83 optimal weight: 0.0060 chunk 120 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 205 optimal weight: 10.0000 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 860 GLN C 961 ASN ** C 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 HIS ** 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 = 0.3744 r_free = 0.3744 target = 0.085067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.055698 restraints weight = 115820.324| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.27 r_work: 0.2903 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20965 Z= 0.169 Angle : 0.568 7.421 29240 Z= 0.326 Chirality : 0.042 0.255 3209 Planarity : 0.004 0.048 3027 Dihedral : 24.129 174.944 4525 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.57 % Allowed : 6.12 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.58 (0.19), residues: 1974 helix: 1.34 (0.20), residues: 700 sheet: -0.85 (0.27), residues: 353 loop : -1.58 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 504 TYR 0.016 0.002 TYR D 161 PHE 0.018 0.002 PHE D 29 TRP 0.011 0.001 TRP C 893 HIS 0.009 0.001 HIS A1006 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (20957) covalent geometry : angle 0.56750 / 0.33 (29236) hydrogen bonds : bond 0.04872 / 3.15 ( 907) hydrogen bonds : angle 4.60229 / 3.25 ( 2446) metal coordination : bond 0.01134 / 0.76 ( 8) metal coordination : angle 2.17298 / 1.25 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.675 Fit side-chains REVERT: A 401 ARG cc_start: 0.2992 (OUTLIER) cc_final: 0.2571 (mtt180) REVERT: A 894 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.7356 (tmt170) REVERT: C 683 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8962 (ttmm) REVERT: C 756 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8729 (mtt90) REVERT: D 285 MET cc_start: 0.8418 (mmm) cc_final: 0.7353 (mmm) REVERT: N 110 ARG cc_start: 0.2320 (mtt-85) cc_final: 0.0412 (ttm-80) outliers start: 25 outliers final: 12 residues processed: 99 average time/residue: 0.1675 time to fit residues: 25.4574 Evaluate side-chains 90 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 486 ARG Chi-restraints excluded: chain A residue 658 MET Chi-restraints excluded: chain A residue 894 ARG Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 447 GLN Chi-restraints excluded: chain C residue 486 ARG Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 683 LYS Chi-restraints excluded: chain C residue 756 ARG Chi-restraints excluded: chain C residue 840 ARG Chi-restraints excluded: chain C residue 894 ARG Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 201 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 8 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 208 optimal weight: 50.0000 chunk 169 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 89 optimal weight: 0.6980 chunk 174 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 GLN ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 ASN C1000 GLN ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 HIS ** 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 = 0.3705 r_free = 0.3705 target = 0.083508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.053588 restraints weight = 145889.173| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.73 r_work: 0.2832 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20965 Z= 0.200 Angle : 0.605 12.268 29240 Z= 0.340 Chirality : 0.043 0.249 3209 Planarity : 0.004 0.047 3027 Dihedral : 24.244 175.279 4515 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.52 % Allowed : 6.82 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.43 (0.19), residues: 1974 helix: 1.37 (0.20), residues: 710 sheet: -0.67 (0.27), residues: 353 loop : -1.48 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 409 TYR 0.043 0.002 TYR D 161 PHE 0.022 0.002 PHE D 29 TRP 0.013 0.001 TRP D 317 HIS 0.007 0.001 HIS A1006 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.20 (20957) covalent geometry : angle 0.60528 / 0.34 (29236) hydrogen bonds : bond 0.04908 / 3.21 ( 907) hydrogen bonds : angle 4.48448 / 3.16 ( 2446) metal coordination : bond 0.01651 / 1.03 ( 8) metal coordination : angle 1.37153 / 0.81 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.642 Fit side-chains REVERT: A 894 ARG cc_start: 0.9230 (OUTLIER) cc_final: 0.7500 (tmt170) REVERT: C 546 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.8257 (t70) REVERT: C 756 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8729 (mtt90) REVERT: D 285 MET cc_start: 0.8550 (mmm) cc_final: 0.7553 (mmm) REVERT: N 110 ARG cc_start: 0.2557 (mtt-85) cc_final: 0.0359 (ttm-80) outliers start: 24 outliers final: 13 residues processed: 90 average time/residue: 0.1588 time to fit residues: 22.1971 Evaluate side-chains 87 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 658 MET Chi-restraints excluded: chain A residue 894 ARG Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 447 GLN Chi-restraints excluded: chain C residue 486 ARG Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 756 ARG Chi-restraints excluded: chain C residue 840 ARG Chi-restraints excluded: chain C residue 894 ARG Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain B residue 201 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 45 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 128 optimal weight: 0.7980 chunk 194 optimal weight: 30.0000 chunk 174 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 204 optimal weight: 30.0000 chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 GLN C 443 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 HIS ** 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 = 0.3730 r_free = 0.3730 target = 0.084684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.054832 restraints weight = 142041.787| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.72 r_work: 0.2872 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 20965 Z= 0.122 Angle : 0.529 7.801 29240 Z= 0.303 Chirality : 0.041 0.267 3209 Planarity : 0.003 0.045 3027 Dihedral : 24.117 175.188 4503 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.40 % Allowed : 6.88 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.16 (0.19), residues: 1974 helix: 1.54 (0.20), residues: 711 sheet: -0.50 (0.27), residues: 353 loop : -1.29 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 407 TYR 0.014 0.001 TYR B 108 PHE 0.013 0.001 PHE D 29 TRP 0.010 0.001 TRP C 893 HIS 0.006 0.001 HIS A1006 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.12 (20957) covalent geometry : angle 0.52882 / 0.30 (29236) hydrogen bonds : bond 0.04238 / 2.70 ( 907) hydrogen bonds : angle 4.28297 / 3.02 ( 2446) metal coordination : bond 0.00596 / 0.37 ( 8) metal coordination : angle 2.26162 / 1.29 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.708 Fit side-chains REVERT: A 401 ARG cc_start: 0.2893 (OUTLIER) cc_final: 0.2553 (mtt180) REVERT: A 894 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.7368 (tmt170) REVERT: C 546 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8290 (t70) REVERT: C 578 MET cc_start: 0.9236 (ttp) cc_final: 0.8924 (ttp) REVERT: C 756 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8695 (mtt90) REVERT: D 5 MET cc_start: 0.8670 (mmm) cc_final: 0.8304 (tpt) REVERT: N 110 ARG cc_start: 0.2525 (mtt-85) cc_final: 0.0465 (ttm-80) outliers start: 22 outliers final: 11 residues processed: 92 average time/residue: 0.1744 time to fit residues: 24.4060 Evaluate side-chains 87 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 894 ARG Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 447 GLN Chi-restraints excluded: chain C residue 486 ARG Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 756 ARG Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 840 ARG Chi-restraints excluded: chain C residue 894 ARG Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain B residue 201 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 83 optimal weight: 10.0000 chunk 151 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 202 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.082674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.053002 restraints weight = 117378.067| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 3.29 r_work: 0.2823 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 20965 Z= 0.253 Angle : 0.624 14.916 29240 Z= 0.345 Chirality : 0.044 0.242 3209 Planarity : 0.004 0.051 3027 Dihedral : 24.308 175.228 4503 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.34 % Allowed : 7.46 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.20 (0.19), residues: 1974 helix: 1.53 (0.20), residues: 710 sheet: -0.51 (0.27), residues: 355 loop : -1.34 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 442 TYR 0.026 0.002 TYR D 161 PHE 0.024 0.002 PHE D 29 TRP 0.015 0.001 TRP C 893 HIS 0.006 0.002 HIS C 445 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.25 (20957) covalent geometry : angle 0.62329 / 0.35 (29236) hydrogen bonds : bond 0.05203 / 3.40 ( 907) hydrogen bonds : angle 4.39298 / 3.09 ( 2446) metal coordination : bond 0.02202 / 1.40 ( 8) metal coordination : angle 1.82115 / 1.06 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.677 Fit side-chains REVERT: A 401 ARG cc_start: 0.2797 (OUTLIER) cc_final: 0.2546 (mtt180) REVERT: A 894 ARG cc_start: 0.9246 (OUTLIER) cc_final: 0.7569 (tmt170) REVERT: C 546 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8352 (t70) REVERT: C 578 MET cc_start: 0.9250 (ttp) cc_final: 0.8887 (ttp) REVERT: C 894 ARG cc_start: 0.9260 (OUTLIER) cc_final: 0.7507 (tmt170) REVERT: D 5 MET cc_start: 0.8749 (mmm) cc_final: 0.8407 (tpt) REVERT: N 110 ARG cc_start: 0.2481 (mtt-85) cc_final: 0.0261 (ttm-80) outliers start: 21 outliers final: 9 residues processed: 88 average time/residue: 0.1659 time to fit residues: 22.5398 Evaluate side-chains 84 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 894 ARG Chi-restraints excluded: chain C residue 447 GLN Chi-restraints excluded: chain C residue 486 ARG Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 840 ARG Chi-restraints excluded: chain C residue 894 ARG Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain B residue 201 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 196 optimal weight: 50.0000 chunk 201 optimal weight: 40.0000 chunk 35 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 473 ASN A 495 GLN A 962 GLN C 443 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.083600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.053873 restraints weight = 143107.064| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.63 r_work: 0.2834 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20965 Z= 0.150 Angle : 0.553 9.163 29240 Z= 0.312 Chirality : 0.042 0.260 3209 Planarity : 0.004 0.052 3027 Dihedral : 24.243 175.275 4503 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.52 % Allowed : 7.41 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.03 (0.19), residues: 1974 helix: 1.63 (0.20), residues: 711 sheet: -0.37 (0.27), residues: 353 loop : -1.23 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 756 TYR 0.013 0.001 TYR C 805 PHE 0.019 0.001 PHE D 29 TRP 0.012 0.001 TRP C 893 HIS 0.003 0.001 HIS A1006 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (20957) covalent geometry : angle 0.55278 / 0.31 (29236) hydrogen bonds : bond 0.04422 / 2.85 ( 907) hydrogen bonds : angle 4.25819 / 3.00 ( 2446) metal coordination : bond 0.01075 / 0.67 ( 8) metal coordination : angle 2.25064 / 1.28 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.743 Fit side-chains REVERT: A 401 ARG cc_start: 0.2623 (OUTLIER) cc_final: 0.2373 (mtt180) REVERT: A 894 ARG cc_start: 0.9226 (OUTLIER) cc_final: 0.7469 (tmt170) REVERT: C 546 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.8403 (t70) REVERT: C 578 MET cc_start: 0.9201 (ttp) cc_final: 0.8817 (ttp) REVERT: C 894 ARG cc_start: 0.9216 (OUTLIER) cc_final: 0.7695 (tmt170) REVERT: C 974 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8946 (mmt) outliers start: 24 outliers final: 12 residues processed: 90 average time/residue: 0.1388 time to fit residues: 20.0116 Evaluate side-chains 88 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 894 ARG Chi-restraints excluded: chain C residue 447 GLN Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 486 ARG Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 840 ARG Chi-restraints excluded: chain C residue 894 ARG Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 233 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 131 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 147 optimal weight: 0.9990 chunk 38 optimal weight: 0.0020 chunk 94 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 186 optimal weight: 0.0980 chunk 145 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 991 HIS ** D 94 HIS ** 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 = 0.3733 r_free = 0.3733 target = 0.084767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.055193 restraints weight = 124989.252| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.45 r_work: 0.2882 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 20965 Z= 0.112 Angle : 0.539 16.249 29240 Z= 0.301 Chirality : 0.040 0.268 3209 Planarity : 0.003 0.042 3027 Dihedral : 24.112 175.121 4503 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.05 % Allowed : 8.16 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.13 (0.19), residues: 1974 helix: 1.75 (0.20), residues: 711 sheet: -0.23 (0.27), residues: 356 loop : -1.15 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 756 TYR 0.010 0.001 TYR C 805 PHE 0.012 0.001 PHE D 29 TRP 0.010 0.001 TRP C 893 HIS 0.003 0.000 HIS A1006 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.11 (20957) covalent geometry : angle 0.53816 / 0.30 (29236) hydrogen bonds : bond 0.03970 / 2.50 ( 907) hydrogen bonds : angle 4.10100 / 2.89 ( 2446) metal coordination : bond 0.00472 / 0.30 ( 8) metal coordination : angle 1.91144 / 1.07 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.672 Fit side-chains REVERT: A 401 ARG cc_start: 0.2657 (OUTLIER) cc_final: 0.2327 (mtt180) REVERT: A 894 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.7378 (tmt170) REVERT: C 546 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8363 (t70) REVERT: C 578 MET cc_start: 0.9140 (ttp) cc_final: 0.8808 (ttp) REVERT: D 285 MET cc_start: 0.8417 (mmm) cc_final: 0.7574 (mmm) outliers start: 16 outliers final: 10 residues processed: 90 average time/residue: 0.1459 time to fit residues: 20.9483 Evaluate side-chains 83 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 894 ARG Chi-restraints excluded: chain C residue 447 GLN Chi-restraints excluded: chain C residue 486 ARG Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 840 ARG Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain B residue 201 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 153 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 191 optimal weight: 40.0000 chunk 110 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 169 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** 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 = 0.3704 r_free = 0.3704 target = 0.083448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.054014 restraints weight = 128165.142| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.25 r_work: 0.2834 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20965 Z= 0.180 Angle : 0.565 12.676 29240 Z= 0.315 Chirality : 0.042 0.254 3209 Planarity : 0.004 0.045 3027 Dihedral : 24.244 174.842 4499 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.82 % Allowed : 8.40 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.17 (0.19), residues: 1974 helix: 1.77 (0.20), residues: 711 sheet: -0.20 (0.27), residues: 356 loop : -1.12 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 848 TYR 0.016 0.002 TYR D 161 PHE 0.019 0.001 PHE D 29 TRP 0.014 0.001 TRP C 893 HIS 0.004 0.001 HIS A 795 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (20957) covalent geometry : angle 0.56512 / 0.31 (29236) hydrogen bonds : bond 0.04571 / 2.94 ( 907) hydrogen bonds : angle 4.17219 / 2.94 ( 2446) metal coordination : bond 0.01510 / 0.94 ( 8) metal coordination : angle 1.60344 / 0.93 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.672 Fit side-chains REVERT: A 401 ARG cc_start: 0.3358 (OUTLIER) cc_final: 0.2742 (mtt180) REVERT: A 894 ARG cc_start: 0.9180 (OUTLIER) cc_final: 0.7509 (tmt170) REVERT: C 546 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8409 (t70) REVERT: D 285 MET cc_start: 0.8512 (mmm) cc_final: 0.7633 (mmm) outliers start: 12 outliers final: 8 residues processed: 81 average time/residue: 0.1519 time to fit residues: 19.7865 Evaluate side-chains 81 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 894 ARG Chi-restraints excluded: chain C residue 486 ARG Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 840 ARG Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain B residue 201 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 113 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.0570 chunk 63 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** 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 = 0.3729 r_free = 0.3729 target = 0.084684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.054944 restraints weight = 151538.003| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.79 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 20965 Z= 0.113 Angle : 0.540 16.577 29240 Z= 0.300 Chirality : 0.040 0.271 3209 Planarity : 0.003 0.043 3027 Dihedral : 24.128 174.536 4496 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.82 % Allowed : 8.69 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.25 (0.19), residues: 1974 helix: 1.81 (0.20), residues: 711 sheet: -0.11 (0.27), residues: 356 loop : -1.06 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 407 TYR 0.012 0.001 TYR C 805 PHE 0.013 0.001 PHE D 29 TRP 0.010 0.001 TRP C 893 HIS 0.003 0.001 HIS A1006 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.11 (20957) covalent geometry : angle 0.53909 / 0.30 (29236) hydrogen bonds : bond 0.03973 / 2.52 ( 907) hydrogen bonds : angle 4.07960 / 2.87 ( 2446) metal coordination : bond 0.00515 / 0.32 ( 8) metal coordination : angle 2.05717 / 1.15 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.689 Fit side-chains REVERT: A 894 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.7323 (tmt170) REVERT: C 546 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8384 (t70) REVERT: D 285 MET cc_start: 0.8262 (mmm) cc_final: 0.7338 (mmm) outliers start: 12 outliers final: 8 residues processed: 81 average time/residue: 0.1474 time to fit residues: 19.3021 Evaluate side-chains 80 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 894 ARG Chi-restraints excluded: chain C residue 486 ARG Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 840 ARG Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain B residue 201 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 139 optimal weight: 2.9990 chunk 214 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 192 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 140 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 123 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 482 HIS ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN 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 = 0.084829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.055137 restraints weight = 153351.375| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.78 r_work: 0.2866 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 20965 Z= 0.113 Angle : 0.521 12.909 29240 Z= 0.293 Chirality : 0.040 0.269 3209 Planarity : 0.003 0.043 3027 Dihedral : 24.078 174.177 4496 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.82 % Allowed : 8.63 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.33 (0.19), residues: 1974 helix: 1.86 (0.20), residues: 711 sheet: -0.05 (0.27), residues: 356 loop : -1.00 (0.21), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 407 TYR 0.011 0.001 TYR D 161 PHE 0.013 0.001 PHE D 29 TRP 0.009 0.001 TRP C 893 HIS 0.003 0.001 HIS A1006 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.11 (20957) covalent geometry : angle 0.52057 / 0.29 (29236) hydrogen bonds : bond 0.03946 / 2.49 ( 907) hydrogen bonds : angle 4.02372 / 2.83 ( 2446) metal coordination : bond 0.00563 / 0.37 ( 8) metal coordination : angle 1.58365 / 0.89 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6193.13 seconds wall clock time: 106 minutes 22.21 seconds (6382.21 seconds total)