Starting phenix.real_space_refine on Sun Jun 22 11:03:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xoe_33346/06_2025/7xoe_33346.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xoe_33346/06_2025/7xoe_33346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xoe_33346/06_2025/7xoe_33346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xoe_33346/06_2025/7xoe_33346.map" model { file = "/net/cci-nas-00/data/ceres_data/7xoe_33346/06_2025/7xoe_33346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xoe_33346/06_2025/7xoe_33346.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.039 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: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 16298 2.51 5 N 4202 2.21 5 O 4976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 127 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25587 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8137 Classifications: {'peptide': 1053} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 50, 'TRANS': 1002} Chain breaks: 6 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 70 Chain: "B" Number of atoms: 8420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8420 Classifications: {'peptide': 1079} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 52, 'TRANS': 1026} Chain breaks: 5 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 8400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1078, 8400 Classifications: {'peptide': 1078} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 52, 'TRANS': 1025} Chain breaks: 5 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 16.48, per 1000 atoms: 0.64 Number of scatterers: 25587 At special positions: 0 Unit cell: (143, 160.6, 187, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 4976 8.00 N 4202 7.00 C 16298 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 163 " distance=1.98 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.02 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.04 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.04 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.00 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.09 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.02 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.02 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.04 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.04 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.07 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.02 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.01 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.02 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.04 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 163 " distance=1.96 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.04 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.05 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.02 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.05 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.04 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.06 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.04 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.04 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 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 Atom "HETATM25557 O5 NAG C1304 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 162 " " NAG A1302 " - " ASN A 231 " " NAG A1303 " - " ASN A 613 " " NAG A1304 " - " ASN A 279 " " NAG A1305 " - " ASN A 654 " " NAG A1306 " - " ASN A 706 " " NAG A1307 " - " ASN A1071 " " NAG A1308 " - " ASN A 61 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 613 " " NAG B1303 " - " ASN B 279 " " NAG B1304 " - " ASN B 328 " " NAG B1305 " - " ASN B 654 " " NAG B1306 " - " ASN B 706 " " NAG B1307 " - " ASN B1071 " " NAG C1301 " - " ASN C 613 " " NAG C1302 " - " ASN C 714 " " NAG C1304 " - " ASN C 279 " " NAG C1305 " - " ASN C 706 " " NAG C1306 " - " ASN C1071 " Time building additional restraints: 6.46 Conformation dependent library (CDL) restraints added in 3.2 seconds 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6014 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 46 sheets defined 23.9% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.37 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 400 through 408 Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 735 through 740 Processing helix chain 'A' and resid 743 through 753 removed outlier: 4.118A pdb=" N TYR A 753 " --> pdb=" O LEU A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 780 removed outlier: 3.505A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 847 through 852 Processing helix chain 'A' and resid 863 through 879 Processing helix chain 'A' and resid 894 through 907 Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.772A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 Processing helix chain 'A' and resid 942 through 963 removed outlier: 3.725A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 979 Processing helix chain 'A' and resid 982 through 1030 Processing helix chain 'A' and resid 1113 through 1117 removed outlier: 3.606A pdb=" N THR A1117 " --> pdb=" O THR A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1143 Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 380 through 386 Processing helix chain 'B' and resid 402 through 407 Processing helix chain 'B' and resid 734 through 741 Processing helix chain 'B' and resid 743 through 753 removed outlier: 3.938A pdb=" N TYR B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 780 removed outlier: 3.577A pdb=" N THR B 775 " --> pdb=" O GLN B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 863 through 876 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.542A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 907 Processing helix chain 'B' and resid 910 through 916 Processing helix chain 'B' and resid 916 through 937 Processing helix chain 'B' and resid 943 through 963 removed outlier: 3.740A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 979 Processing helix chain 'B' and resid 982 through 1030 removed outlier: 3.511A pdb=" N VAL B 988 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1113 through 1115 No H-bonds generated for 'chain 'B' and resid 1113 through 1115' Processing helix chain 'B' and resid 1138 through 1143 Processing helix chain 'C' and resid 193 through 197 Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 340 Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 362 through 368 Processing helix chain 'C' and resid 380 through 387 removed outlier: 3.590A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 435 through 440 removed outlier: 3.739A pdb=" N ASP C 439 " --> pdb=" O SER C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 754 removed outlier: 3.530A pdb=" N SER C 747 " --> pdb=" O SER C 743 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU C 749 " --> pdb=" O GLU C 745 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR C 753 " --> pdb=" O LEU C 749 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY C 754 " --> pdb=" O LEU C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 780 Processing helix chain 'C' and resid 799 through 803 Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 846 through 852 Processing helix chain 'C' and resid 863 through 879 Processing helix chain 'C' and resid 894 through 907 Processing helix chain 'C' and resid 910 through 916 Processing helix chain 'C' and resid 916 through 937 removed outlier: 3.622A pdb=" N ILE C 920 " --> pdb=" O ASN C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 963 removed outlier: 3.764A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 979 Processing helix chain 'C' and resid 982 through 1029 removed outlier: 3.525A pdb=" N GLU C1014 " --> pdb=" O ILE C1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 1113 through 1115 No H-bonds generated for 'chain 'C' and resid 1113 through 1115' Processing helix chain 'C' and resid 1138 through 1143 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 7.722A pdb=" N THR A 271 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASP A 287 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A 273 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA A 285 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS A 275 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 93 Processing sheet with id=AA5, first strand: chain 'A' and resid 102 through 104 Processing sheet with id=AA6, first strand: chain 'A' and resid 102 through 104 removed outlier: 4.674A pdb=" N PHE A 131 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N THR A 112 " --> pdb=" O CYS A 129 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N CYS A 129 " --> pdb=" O THR A 112 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 190 through 191 Processing sheet with id=AA8, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.262A pdb=" N GLU A 306 " --> pdb=" O GLY A 598 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY A 598 " --> pdb=" O GLU A 306 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AB1, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.927A pdb=" N LEU A 510 " --> pdb=" O CYS A 429 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N CYS A 429 " --> pdb=" O LEU A 510 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 449 through 450 Processing sheet with id=AB3, first strand: chain 'A' and resid 661 through 664 removed outlier: 6.676A pdb=" N ILE A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 700 through 701 removed outlier: 7.487A pdb=" N ASN A 700 " --> pdb=" O LYS B 787 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 715 through 725 removed outlier: 3.855A pdb=" N ALA A1053 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET A1047 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 732 through 733 removed outlier: 3.725A pdb=" N SER A 732 " --> pdb=" O THR A 856 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 785 through 787 removed outlier: 6.330A pdb=" N ILE A 785 " --> pdb=" O ASN C 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1073 through 1074 Processing sheet with id=AB9, first strand: chain 'A' and resid 1077 through 1079 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 6.555A pdb=" N LEU B 273 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA B 285 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS B 275 " --> pdb=" O THR B 283 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 124 through 129 Processing sheet with id=AC4, first strand: chain 'B' and resid 308 through 315 removed outlier: 4.958A pdb=" N ASN B 314 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLY B 590 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 607 " --> pdb=" O ILE B 648 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 351 through 355 removed outlier: 3.677A pdb=" N VAL B 392 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL B 430 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS B 375 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC7, first strand: chain 'B' and resid 536 through 540 removed outlier: 3.708A pdb=" N GLY B 545 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 661 through 664 removed outlier: 6.637A pdb=" N ILE B 667 " --> pdb=" O ILE B 663 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 708 through 709 removed outlier: 3.562A pdb=" N THR B1073 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR B1102 " --> pdb=" O VAL B1091 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 715 through 719 Processing sheet with id=AD2, first strand: chain 'B' and resid 715 through 719 removed outlier: 3.646A pdb=" N MET B1047 " --> pdb=" O VAL B1062 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 731 through 732 Processing sheet with id=AD4, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.141A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AD6, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.062A pdb=" N VAL C 36 " --> pdb=" O LEU C 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.685A pdb=" N GLN C 268 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N THR C 271 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ASP C 287 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU C 273 " --> pdb=" O ALA C 285 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA C 285 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LYS C 275 " --> pdb=" O THR C 283 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 82 through 83 Processing sheet with id=AD9, first strand: chain 'C' and resid 154 through 155 removed outlier: 7.370A pdb=" N LEU C 139 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ARG C 243 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL C 141 " --> pdb=" O ARG C 243 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 308 through 315 removed outlier: 5.579A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASN C 314 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLY C 590 " --> pdb=" O ASN C 314 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 353 through 355 Processing sheet with id=AE3, first strand: chain 'C' and resid 358 through 359 removed outlier: 7.569A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AE5, first strand: chain 'C' and resid 536 through 540 Processing sheet with id=AE6, first strand: chain 'C' and resid 661 through 664 removed outlier: 6.910A pdb=" N ILE C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C 692 " --> pdb=" O CYS C 668 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 709 through 712 removed outlier: 3.657A pdb=" N THR C1102 " --> pdb=" O VAL C1091 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 715 through 725 removed outlier: 3.695A pdb=" N VAL C1065 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET C1047 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 731 through 733 Processing sheet with id=AF1, first strand: chain 'C' and resid 1078 through 1079 881 hydrogen bonds defined for protein. 2343 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.12 Time building geometry restraints manager: 7.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 7990 1.34 - 1.48: 5503 1.48 - 1.62: 12522 1.62 - 1.76: 0 1.76 - 1.90: 140 Bond restraints: 26155 Sorted by residual: bond pdb=" N LYS A 525 " pdb=" CA LYS A 525 " ideal model delta sigma weight residual 1.458 1.491 -0.033 6.30e-03 2.52e+04 2.69e+01 bond pdb=" N THR A 19 " pdb=" CA THR A 19 " ideal model delta sigma weight residual 1.457 1.489 -0.032 6.40e-03 2.44e+04 2.57e+01 bond pdb=" N VAL C1065 " pdb=" CA VAL C1065 " ideal model delta sigma weight residual 1.454 1.493 -0.039 7.70e-03 1.69e+04 2.54e+01 bond pdb=" N VAL B1065 " pdb=" CA VAL B1065 " ideal model delta sigma weight residual 1.454 1.492 -0.038 7.70e-03 1.69e+04 2.42e+01 bond pdb=" N GLY A 697 " pdb=" CA GLY A 697 " ideal model delta sigma weight residual 1.445 1.482 -0.037 8.30e-03 1.45e+04 2.01e+01 ... (remaining 26150 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.13: 35355 5.13 - 10.26: 242 10.26 - 15.39: 7 15.39 - 20.52: 1 20.52 - 25.65: 1 Bond angle restraints: 35606 Sorted by residual: angle pdb=" C CYS C 129 " pdb=" CA CYS C 129 " pdb=" CB CYS C 129 " ideal model delta sigma weight residual 111.11 85.46 25.65 2.10e+00 2.27e-01 1.49e+02 angle pdb=" C CYS A 129 " pdb=" CA CYS A 129 " pdb=" CB CYS A 129 " ideal model delta sigma weight residual 109.66 93.30 16.36 1.94e+00 2.66e-01 7.11e+01 angle pdb=" CA ASN A 61 " pdb=" CB ASN A 61 " pdb=" CG ASN A 61 " ideal model delta sigma weight residual 112.60 120.65 -8.05 1.00e+00 1.00e+00 6.48e+01 angle pdb=" N MET C 150 " pdb=" CA MET C 150 " pdb=" C MET C 150 " ideal model delta sigma weight residual 108.38 119.12 -10.74 1.35e+00 5.49e-01 6.32e+01 angle pdb=" CA PHE A 183 " pdb=" C PHE A 183 " pdb=" O PHE A 183 " ideal model delta sigma weight residual 120.36 113.25 7.11 1.07e+00 8.73e-01 4.41e+01 ... (remaining 35601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.82: 14479 25.82 - 51.65: 1198 51.65 - 77.47: 369 77.47 - 103.30: 75 103.30 - 129.12: 23 Dihedral angle restraints: 16144 sinusoidal: 6800 harmonic: 9344 Sorted by residual: dihedral pdb=" C CYS C 129 " pdb=" N CYS C 129 " pdb=" CA CYS C 129 " pdb=" CB CYS C 129 " ideal model delta harmonic sigma weight residual -122.60 -94.52 -28.08 0 2.50e+00 1.60e-01 1.26e+02 dihedral pdb=" CB CYS A 659 " pdb=" SG CYS A 659 " pdb=" SG CYS A 668 " pdb=" CB CYS A 668 " ideal model delta sinusoidal sigma weight residual 93.00 12.05 80.95 1 1.00e+01 1.00e-02 8.09e+01 dihedral pdb=" CB CYS A 735 " pdb=" SG CYS A 735 " pdb=" SG CYS A 757 " pdb=" CB CYS A 757 " ideal model delta sinusoidal sigma weight residual 93.00 162.75 -69.75 1 1.00e+01 1.00e-02 6.28e+01 ... (remaining 16141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.242: 4129 0.242 - 0.484: 44 0.484 - 0.726: 6 0.726 - 0.967: 0 0.967 - 1.209: 3 Chirality restraints: 4182 Sorted by residual: chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 613 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -3.61 1.21 2.00e-01 2.50e+01 3.66e+01 chirality pdb=" C1 NAG C1306 " pdb=" ND2 ASN C1071 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.35 -1.05 2.00e-01 2.50e+01 2.78e+01 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 162 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.37 -1.03 2.00e-01 2.50e+01 2.64e+01 ... (remaining 4179 not shown) Planarity restraints: 4570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1302 " -0.332 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG B1302 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG B1302 " -0.034 2.00e-02 2.50e+03 pdb=" N2 NAG B1302 " 0.502 2.00e-02 2.50e+03 pdb=" O7 NAG B1302 " -0.210 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1308 " 0.282 2.00e-02 2.50e+03 2.41e-01 7.28e+02 pdb=" C7 NAG A1308 " -0.068 2.00e-02 2.50e+03 pdb=" C8 NAG A1308 " 0.167 2.00e-02 2.50e+03 pdb=" N2 NAG A1308 " -0.421 2.00e-02 2.50e+03 pdb=" O7 NAG A1308 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1303 " 0.224 2.00e-02 2.50e+03 1.87e-01 4.37e+02 pdb=" C7 NAG B1303 " -0.060 2.00e-02 2.50e+03 pdb=" C8 NAG B1303 " 0.159 2.00e-02 2.50e+03 pdb=" N2 NAG B1303 " -0.309 2.00e-02 2.50e+03 pdb=" O7 NAG B1303 " -0.013 2.00e-02 2.50e+03 ... (remaining 4567 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 22 2.26 - 2.92: 11638 2.92 - 3.58: 35765 3.58 - 4.24: 58918 4.24 - 4.90: 93625 Nonbonded interactions: 199968 Sorted by model distance: nonbonded pdb=" OG1 THR B 615 " pdb=" C1 NAG B1302 " model vdw 1.596 3.470 nonbonded pdb=" OD1 ASP B 212 " pdb=" OH TYR B 263 " model vdw 1.990 3.040 nonbonded pdb=" O THR B 390 " pdb=" O GLU B 513 " model vdw 2.027 2.432 nonbonded pdb=" O ASP C 291 " pdb=" OG SER C 294 " model vdw 2.074 3.040 nonbonded pdb=" OD1 ASP B 291 " pdb=" OG SER B 294 " model vdw 2.085 3.040 ... (remaining 199963 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 16 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 101 or (resid 102 and (name N or n \ ame CA or name C or name O or name CB )) or resid 103 through 174 or resid 183 t \ hrough 210 or (resid 211 and (name N or name CA or name C or name O or name CB ) \ ) or resid 212 through 615 or (resid 616 and (name N or name CA or name C or nam \ e O or name CB )) or resid 617 through 618 or resid 637 through 1143 or resid 13 \ 01 through 1306)) selection = (chain 'B' and (resid 16 through 81 or (resid 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 through 99 or (resid 100 and (name N or na \ me CA or name C or name O or name CB )) or resid 101 or (resid 102 and (name N o \ r name CA or name C or name O or name CB )) or resid 103 through 123 or (resid 1 \ 24 and (name N or name CA or name C or name O or name CB )) or resid 125 through \ 127 or (resid 128 and (name N or name CA or name C or name O or name CB )) or r \ esid 129 through 130 or (resid 131 through 132 and (name N or name CA or name C \ or name O or name CB )) or resid 133 through 140 or (resid 141 through 147 and ( \ name N or name CA or name C or name O or name CB )) or resid 148 or (resid 149 t \ hrough 151 and (name N or name CA or name C or name O or name CB )) or resid 152 \ or (resid 153 and (name N or name CA or name C or name O or name CB )) or resid \ 154 or (resid 155 and (name N or name CA or name C or name O or name CB )) or r \ esid 156 through 210 or (resid 211 and (name N or name CA or name C or name O or \ name CB )) or resid 212 through 314 or (resid 315 through 316 and (name N or na \ me CA or name C or name O or name CB )) or resid 317 or (resid 318 and (name N o \ r name CA or name C or name O or name CB )) or resid 319 through 464 or resid 48 \ 9 through 524 or (resid 525 through 526 and (name N or name CA or name C or name \ O or name CB )) or resid 527 through 618 or resid 634 or resid 638 through 1143 \ or resid 1301 through 1306)) selection = (chain 'C' and (resid 16 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 81 or (resid 82 and (name N or nam \ e CA or name C or name O or name CB )) or resid 83 through 99 or (resid 100 and \ (name N or name CA or name C or name O or name CB )) or resid 101 through 123 or \ (resid 124 and (name N or name CA or name C or name O or name CB )) or resid 12 \ 5 through 127 or (resid 128 and (name N or name CA or name C or name O or name C \ B )) or resid 129 through 130 or (resid 131 through 132 and (name N or name CA o \ r name C or name O or name CB )) or resid 133 through 140 or (resid 141 through \ 147 and (name N or name CA or name C or name O or name CB )) or resid 148 or (re \ sid 149 through 151 and (name N or name CA or name C or name O or name CB )) or \ resid 152 or (resid 153 and (name N or name CA or name C or name O or name CB )) \ or resid 154 or (resid 155 and (name N or name CA or name C or name O or name C \ B )) or resid 156 through 174 or resid 183 through 314 or (resid 315 through 316 \ and (name N or name CA or name C or name O or name CB )) or resid 317 or (resid \ 318 and (name N or name CA or name C or name O or name CB )) or resid 319 throu \ gh 464 or resid 489 through 524 or (resid 525 through 526 and (name N or name CA \ or name C or name O or name CB )) or resid 527 through 615 or (resid 616 and (n \ ame N or name CA or name C or name O or name CB )) or resid 617 through 618 or r \ esid 637 through 1143 or resid 1301 through 1306)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.060 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 59.640 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 : 0.012 0.430 26224 Z= 0.798 Angle : 1.604 54.303 35776 Z= 1.057 Chirality : 0.097 1.209 4182 Planarity : 0.009 0.287 4550 Dihedral : 21.159 129.123 10019 Min Nonbonded Distance : 1.596 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 1.10 % Allowed : 13.62 % Favored : 85.28 % Rotamer: Outliers : 15.63 % Allowed : 11.76 % Favored : 72.61 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.45 (0.12), residues: 3172 helix: -2.32 (0.15), residues: 663 sheet: -1.94 (0.22), residues: 521 loop : -3.70 (0.11), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 433 HIS 0.009 0.002 HIS C 242 PHE 0.044 0.003 PHE C 90 TYR 0.060 0.003 TYR A 450 ARG 0.009 0.001 ARG A 506 Details of bonding type rmsd link_NAG-ASN : bond 0.11509 ( 20) link_NAG-ASN : angle 13.81340 ( 60) link_BETA1-4 : bond 0.01438 ( 12) link_BETA1-4 : angle 2.33344 ( 36) hydrogen bonds : bond 0.23244 ( 873) hydrogen bonds : angle 9.72651 ( 2343) SS BOND : bond 0.02185 ( 37) SS BOND : angle 3.42506 ( 74) covalent geometry : bond 0.01122 (26155) covalent geometry : angle 1.49462 (35606) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 433 poor density : 270 time to evaluate : 2.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASN cc_start: 0.1092 (OUTLIER) cc_final: 0.0667 (m-40) REVERT: A 223 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.7061 (tp) REVERT: A 399 ILE cc_start: 0.4624 (OUTLIER) cc_final: 0.4093 (pt) REVERT: A 584 ILE cc_start: 0.6996 (OUTLIER) cc_final: 0.6420 (pt) REVERT: A 655 ASN cc_start: 0.8612 (OUTLIER) cc_final: 0.8343 (p0) REVERT: A 657 TYR cc_start: 0.7484 (OUTLIER) cc_final: 0.6736 (m-80) REVERT: A 660 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.7456 (p0) REVERT: A 976 ASP cc_start: 0.8815 (t70) cc_final: 0.8423 (t0) REVERT: A 1033 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8699 (tt0) REVERT: A 1142 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7758 (mm) REVERT: B 86 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7844 (p0) REVERT: B 92 SER cc_start: 0.6819 (OUTLIER) cc_final: 0.6386 (p) REVERT: B 187 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7550 (mmm160) REVERT: B 189 PHE cc_start: 0.7738 (m-80) cc_final: 0.7439 (m-80) REVERT: B 202 SER cc_start: 0.6362 (OUTLIER) cc_final: 0.5062 (p) REVERT: B 690 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8850 (pp) REVERT: B 777 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7946 (mp0) REVERT: B 807 SER cc_start: 0.9048 (OUTLIER) cc_final: 0.8824 (p) REVERT: B 820 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.8399 (m-80) REVERT: B 850 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.7155 (pt0) REVERT: B 944 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8226 (mttp) REVERT: B 959 LEU cc_start: 0.9357 (tp) cc_final: 0.9068 (tp) REVERT: B 980 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7848 (ptp90) REVERT: C 164 THR cc_start: 0.7887 (OUTLIER) cc_final: 0.7507 (p) REVERT: C 199 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8457 (mptt) REVERT: C 502 TYR cc_start: 0.8223 (m-80) cc_final: 0.7941 (t80) REVERT: C 525 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8653 (mmtm) REVERT: C 743 SER cc_start: 0.8068 (OUTLIER) cc_final: 0.7696 (t) REVERT: C 988 VAL cc_start: 0.9488 (OUTLIER) cc_final: 0.9111 (p) REVERT: C 997 ARG cc_start: 0.9459 (OUTLIER) cc_final: 0.9258 (mtt180) outliers start: 433 outliers final: 53 residues processed: 626 average time/residue: 0.3773 time to fit residues: 362.8941 Evaluate side-chains 206 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 127 time to evaluate : 2.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 614 CYS Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 657 TYR Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 668 CYS Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 983 LYS Chi-restraints excluded: chain A residue 1033 GLN Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 187 ARG Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 618 PRO Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 772 ASP Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 827 ASP Chi-restraints excluded: chain B residue 850 GLN Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 944 LYS Chi-restraints excluded: chain B residue 980 ARG Chi-restraints excluded: chain B residue 1081 ASP Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 525 LYS Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 657 TYR Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 916 ASN Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 985 GLU Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 997 ARG Chi-restraints excluded: chain C residue 1014 GLU Chi-restraints excluded: chain C residue 1081 ASP Chi-restraints excluded: chain C residue 1129 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 269 optimal weight: 3.9990 chunk 241 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 82 optimal weight: 0.5980 chunk 163 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 250 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 186 optimal weight: 0.9990 chunk 289 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 85 ASN A 185 ASN A 204 HIS ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 434 ASN A 457 ASN A 490 GLN A 752 GLN A 781 GLN A 869 GLN A 922 ASN A 950 ASN A 952 ASN A 962 GLN A 989 GLN ** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1110 GLN B 97 ASN B 236 GLN B 391 ASN B 478 ASN B 850 GLN B 923 GLN B 962 GLN ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1033 GLN B1095 ASN B1110 GLN ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 119 ASN C 145 ASN C 162 ASN ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN C 391 ASN C 553 ASN C 910 GLN C 950 ASN C 951 GLN C1085 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.075097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.053314 restraints weight = 147858.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.055331 restraints weight = 81246.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.055788 restraints weight = 49747.955| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 26224 Z= 0.191 Angle : 0.901 20.419 35776 Z= 0.442 Chirality : 0.051 0.310 4182 Planarity : 0.005 0.069 4550 Dihedral : 12.878 97.560 4542 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.20 % Favored : 91.65 % Rotamer: Outliers : 5.52 % Allowed : 18.98 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.13), residues: 3172 helix: 0.45 (0.19), residues: 665 sheet: -1.79 (0.20), residues: 575 loop : -3.00 (0.12), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 64 HIS 0.005 0.001 HIS C 516 PHE 0.041 0.002 PHE C 339 TYR 0.021 0.002 TYR A 450 ARG 0.006 0.001 ARG A 980 Details of bonding type rmsd link_NAG-ASN : bond 0.01045 ( 20) link_NAG-ASN : angle 5.27550 ( 60) link_BETA1-4 : bond 0.00594 ( 12) link_BETA1-4 : angle 1.20424 ( 36) hydrogen bonds : bond 0.07871 ( 873) hydrogen bonds : angle 7.02680 ( 2343) SS BOND : bond 0.00965 ( 37) SS BOND : angle 2.64287 ( 74) covalent geometry : bond 0.00411 (26155) covalent geometry : angle 0.86762 (35606) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 154 time to evaluate : 2.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.6813 (m-10) cc_final: 0.5473 (m-10) REVERT: A 197 TYR cc_start: 0.8535 (OUTLIER) cc_final: 0.8249 (p90) REVERT: A 209 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8551 (tt) REVERT: A 284 ASP cc_start: 0.8900 (t0) cc_final: 0.8696 (t0) REVERT: A 286 VAL cc_start: 0.9281 (OUTLIER) cc_final: 0.8951 (m) REVERT: A 655 ASN cc_start: 0.8622 (OUTLIER) cc_final: 0.8346 (p0) REVERT: A 660 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7718 (p0) REVERT: A 737 MET cc_start: 0.8665 (mmm) cc_final: 0.8408 (mmm) REVERT: A 847 ILE cc_start: 0.6030 (OUTLIER) cc_final: 0.5818 (pt) REVERT: A 899 MET cc_start: 0.9007 (tpp) cc_final: 0.8659 (tpp) REVERT: A 976 ASP cc_start: 0.8400 (t70) cc_final: 0.8158 (t0) REVERT: A 977 ILE cc_start: 0.8646 (mm) cc_final: 0.8042 (mm) REVERT: B 61 ASN cc_start: 0.4874 (OUTLIER) cc_final: 0.4613 (t0) REVERT: B 385 ASN cc_start: 0.7677 (t0) cc_final: 0.7116 (m-40) REVERT: B 690 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8484 (pp) REVERT: B 807 SER cc_start: 0.8953 (OUTLIER) cc_final: 0.8713 (p) REVERT: B 846 LEU cc_start: 0.7883 (tt) cc_final: 0.6907 (mm) REVERT: B 959 LEU cc_start: 0.9611 (tp) cc_final: 0.9314 (tp) REVERT: B 981 LEU cc_start: 0.7896 (tp) cc_final: 0.7611 (tp) REVERT: C 199 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8371 (mptt) REVERT: C 502 TYR cc_start: 0.8262 (m-80) cc_final: 0.7867 (t80) REVERT: C 525 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8408 (mmtp) outliers start: 153 outliers final: 68 residues processed: 287 average time/residue: 0.3463 time to fit residues: 163.3072 Evaluate side-chains 187 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 108 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 657 TYR Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 827 ASP Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 883 TRP Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 949 VAL Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1095 ASN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 525 LYS Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 657 TYR Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 783 LYS Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 910 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 964 SER Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 1018 SER Chi-restraints excluded: chain C residue 1029 CYS Chi-restraints excluded: chain C residue 1047 MET Chi-restraints excluded: chain C residue 1113 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 42 optimal weight: 10.0000 chunk 214 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 200 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 221 optimal weight: 4.9990 chunk 296 optimal weight: 0.2980 chunk 142 optimal weight: 6.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1033 GLN B 30 ASN B 85 ASN B 236 GLN B 801 GLN B 898 GLN B 954 GLN ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.072034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.050357 restraints weight = 149695.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.051617 restraints weight = 84666.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.051887 restraints weight = 52880.596| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 26224 Z= 0.231 Angle : 0.787 11.641 35776 Z= 0.392 Chirality : 0.047 0.248 4182 Planarity : 0.005 0.063 4550 Dihedral : 10.274 93.945 4433 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.71 % Favored : 90.20 % Rotamer: Outliers : 4.98 % Allowed : 20.21 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.14), residues: 3172 helix: 1.18 (0.20), residues: 672 sheet: -1.63 (0.20), residues: 582 loop : -2.77 (0.12), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 149 HIS 0.010 0.001 HIS A 49 PHE 0.035 0.002 PHE B 339 TYR 0.017 0.002 TYR B1064 ARG 0.010 0.001 ARG B 980 Details of bonding type rmsd link_NAG-ASN : bond 0.00632 ( 20) link_NAG-ASN : angle 4.01433 ( 60) link_BETA1-4 : bond 0.00525 ( 12) link_BETA1-4 : angle 1.74892 ( 36) hydrogen bonds : bond 0.07181 ( 873) hydrogen bonds : angle 6.59763 ( 2343) SS BOND : bond 0.00409 ( 37) SS BOND : angle 1.90849 ( 74) covalent geometry : bond 0.00509 (26155) covalent geometry : angle 0.76410 (35606) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 110 time to evaluate : 2.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9103 (mt) cc_final: 0.8524 (pp) REVERT: A 88 VAL cc_start: 0.8832 (m) cc_final: 0.8578 (t) REVERT: A 197 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.8362 (p90) REVERT: A 284 ASP cc_start: 0.9119 (t0) cc_final: 0.8843 (t0) REVERT: A 655 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.8183 (p0) REVERT: A 737 MET cc_start: 0.8455 (mmm) cc_final: 0.8171 (mmm) REVERT: A 847 ILE cc_start: 0.5956 (OUTLIER) cc_final: 0.5733 (pt) REVERT: A 899 MET cc_start: 0.9203 (tpp) cc_final: 0.8950 (tpp) REVERT: A 932 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.8887 (tm-30) REVERT: A 976 ASP cc_start: 0.8451 (t70) cc_final: 0.8188 (t0) REVERT: B 174 MET cc_start: 0.7456 (mtt) cc_final: 0.6783 (mtt) REVERT: B 385 ASN cc_start: 0.7840 (t0) cc_final: 0.7181 (m-40) REVERT: B 807 SER cc_start: 0.8988 (OUTLIER) cc_final: 0.8739 (p) REVERT: C 199 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8308 (mppt) REVERT: C 268 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8871 (pt0) REVERT: C 339 PHE cc_start: 0.7613 (OUTLIER) cc_final: 0.6754 (p90) REVERT: C 502 TYR cc_start: 0.8382 (m-80) cc_final: 0.8035 (t80) REVERT: C 525 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8536 (mmtp) REVERT: C 770 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7847 (tm-30) outliers start: 138 outliers final: 79 residues processed: 237 average time/residue: 0.3230 time to fit residues: 128.8317 Evaluate side-chains 181 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 92 time to evaluate : 2.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 657 TYR Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 668 CYS Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 932 GLN Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 827 ASP Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 870 TYR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 883 TRP Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 525 LYS Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 657 TYR Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 770 GLU Chi-restraints excluded: chain C residue 783 LYS Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 964 SER Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1018 SER Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1113 THR Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain C residue 1125 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 241 optimal weight: 0.0670 chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 265 optimal weight: 0.7980 chunk 230 optimal weight: 10.0000 chunk 318 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1007 GLN B 204 HIS B 236 GLN ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 HIS ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.072443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.050808 restraints weight = 150260.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.052338 restraints weight = 85505.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.052697 restraints weight = 50629.993| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26224 Z= 0.135 Angle : 0.684 13.304 35776 Z= 0.336 Chirality : 0.045 0.244 4182 Planarity : 0.004 0.045 4550 Dihedral : 9.048 89.111 4418 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.22 % Favored : 92.69 % Rotamer: Outliers : 4.40 % Allowed : 20.93 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.14), residues: 3172 helix: 1.69 (0.20), residues: 680 sheet: -1.36 (0.21), residues: 544 loop : -2.63 (0.12), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 433 HIS 0.004 0.001 HIS C 204 PHE 0.029 0.001 PHE C 339 TYR 0.016 0.001 TYR A 450 ARG 0.005 0.001 ARG A 400 Details of bonding type rmsd link_NAG-ASN : bond 0.00671 ( 20) link_NAG-ASN : angle 3.64292 ( 60) link_BETA1-4 : bond 0.00401 ( 12) link_BETA1-4 : angle 0.93379 ( 36) hydrogen bonds : bond 0.05970 ( 873) hydrogen bonds : angle 5.99932 ( 2343) SS BOND : bond 0.00537 ( 37) SS BOND : angle 1.64614 ( 74) covalent geometry : bond 0.00295 (26155) covalent geometry : angle 0.66392 (35606) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 110 time to evaluate : 2.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.8878 (m) cc_final: 0.8604 (t) REVERT: A 197 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.8370 (p90) REVERT: A 655 ASN cc_start: 0.8842 (OUTLIER) cc_final: 0.8247 (p0) REVERT: A 737 MET cc_start: 0.8606 (mmm) cc_final: 0.8227 (mmt) REVERT: A 847 ILE cc_start: 0.6047 (OUTLIER) cc_final: 0.5820 (pt) REVERT: A 976 ASP cc_start: 0.8485 (t70) cc_final: 0.8216 (t0) REVERT: B 174 MET cc_start: 0.7375 (mtt) cc_final: 0.6627 (mtt) REVERT: B 225 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8060 (t0) REVERT: B 385 ASN cc_start: 0.7840 (t0) cc_final: 0.7005 (m-40) REVERT: B 807 SER cc_start: 0.8989 (OUTLIER) cc_final: 0.8725 (p) REVERT: B 959 LEU cc_start: 0.9384 (tp) cc_final: 0.9174 (tt) REVERT: B 1047 MET cc_start: 0.8213 (ptp) cc_final: 0.7164 (mtm) REVERT: C 150 MET cc_start: 0.8170 (pmm) cc_final: 0.7504 (pmm) REVERT: C 175 ASP cc_start: 0.4199 (OUTLIER) cc_final: 0.3714 (t70) REVERT: C 199 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8267 (mppt) REVERT: C 268 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8895 (pt0) REVERT: C 339 PHE cc_start: 0.7607 (OUTLIER) cc_final: 0.6680 (p90) REVERT: C 384 LEU cc_start: 0.8257 (mp) cc_final: 0.7459 (tt) REVERT: C 481 LYS cc_start: 0.4327 (OUTLIER) cc_final: 0.3971 (tppt) REVERT: C 525 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8433 (mmtp) outliers start: 122 outliers final: 67 residues processed: 220 average time/residue: 0.3436 time to fit residues: 125.5260 Evaluate side-chains 176 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 98 time to evaluate : 3.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 657 TYR Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 668 CYS Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1028 GLU Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 827 ASP Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 870 TYR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 883 TRP Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 1111 ILE Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 481 LYS Chi-restraints excluded: chain C residue 525 LYS Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 657 TYR Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 783 LYS Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1113 THR Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1123 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 214 optimal weight: 7.9990 chunk 190 optimal weight: 2.9990 chunk 71 optimal weight: 0.0670 chunk 284 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 188 optimal weight: 0.7980 chunk 233 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 147 optimal weight: 10.0000 chunk 126 optimal weight: 20.0000 overall best weight: 1.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 GLN C 784 GLN ** C1080 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 = 0.3770 r_free = 0.3770 target = 0.071719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.050325 restraints weight = 150773.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.051400 restraints weight = 84979.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.051689 restraints weight = 54835.142| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26224 Z= 0.150 Angle : 0.660 11.855 35776 Z= 0.324 Chirality : 0.044 0.294 4182 Planarity : 0.004 0.045 4550 Dihedral : 8.382 83.320 4414 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.29 % Favored : 91.61 % Rotamer: Outliers : 5.02 % Allowed : 19.96 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.14), residues: 3172 helix: 1.74 (0.20), residues: 681 sheet: -1.32 (0.20), residues: 587 loop : -2.52 (0.13), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 149 HIS 0.004 0.001 HIS C 204 PHE 0.028 0.001 PHE C 339 TYR 0.014 0.001 TYR B1064 ARG 0.004 0.000 ARG A 187 Details of bonding type rmsd link_NAG-ASN : bond 0.00499 ( 20) link_NAG-ASN : angle 3.46503 ( 60) link_BETA1-4 : bond 0.00283 ( 12) link_BETA1-4 : angle 1.24573 ( 36) hydrogen bonds : bond 0.05811 ( 873) hydrogen bonds : angle 5.85180 ( 2343) SS BOND : bond 0.00366 ( 37) SS BOND : angle 1.68450 ( 74) covalent geometry : bond 0.00338 (26155) covalent geometry : angle 0.63984 (35606) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 103 time to evaluate : 2.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.8944 (m) cc_final: 0.8684 (t) REVERT: A 197 TYR cc_start: 0.8627 (OUTLIER) cc_final: 0.8372 (p90) REVERT: A 655 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8110 (p0) REVERT: A 847 ILE cc_start: 0.6184 (OUTLIER) cc_final: 0.5951 (pt) REVERT: A 976 ASP cc_start: 0.8427 (t70) cc_final: 0.8191 (t0) REVERT: B 174 MET cc_start: 0.7299 (mtt) cc_final: 0.6592 (mtt) REVERT: B 385 ASN cc_start: 0.7972 (t0) cc_final: 0.7143 (m-40) REVERT: C 175 ASP cc_start: 0.4284 (OUTLIER) cc_final: 0.3815 (t70) REVERT: C 199 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8255 (mppt) REVERT: C 220 LEU cc_start: 0.8557 (mt) cc_final: 0.8294 (mp) REVERT: C 268 GLN cc_start: 0.9228 (OUTLIER) cc_final: 0.9008 (pt0) REVERT: C 339 PHE cc_start: 0.7493 (OUTLIER) cc_final: 0.6621 (p90) REVERT: C 481 LYS cc_start: 0.3947 (OUTLIER) cc_final: 0.3590 (tppt) REVERT: C 525 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8333 (mmtp) outliers start: 139 outliers final: 91 residues processed: 232 average time/residue: 0.3602 time to fit residues: 141.8956 Evaluate side-chains 187 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 87 time to evaluate : 3.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 657 TYR Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 668 CYS Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1028 GLU Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 827 ASP Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 870 TYR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 883 TRP Chi-restraints excluded: chain B residue 944 LYS Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1005 VAL Chi-restraints excluded: chain B residue 1111 ILE Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 481 LYS Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 525 LYS Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 657 TYR Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 783 LYS Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 964 SER Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1113 THR Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1123 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 97 optimal weight: 2.9990 chunk 173 optimal weight: 0.2980 chunk 221 optimal weight: 10.0000 chunk 285 optimal weight: 0.0770 chunk 34 optimal weight: 0.4980 chunk 242 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 214 optimal weight: 7.9990 chunk 143 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN B 916 ASN ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 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 = 0.3754 r_free = 0.3754 target = 0.071093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.049798 restraints weight = 151232.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.050598 restraints weight = 85135.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.050946 restraints weight = 56858.821| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26224 Z= 0.149 Angle : 0.643 11.871 35776 Z= 0.317 Chirality : 0.044 0.248 4182 Planarity : 0.004 0.053 4550 Dihedral : 8.033 78.547 4413 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.63 % Favored : 92.28 % Rotamer: Outliers : 4.98 % Allowed : 20.57 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.14), residues: 3172 helix: 1.83 (0.20), residues: 680 sheet: -1.19 (0.21), residues: 585 loop : -2.50 (0.13), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 433 HIS 0.003 0.001 HIS C 204 PHE 0.027 0.001 PHE C 339 TYR 0.015 0.001 TYR B 446 ARG 0.004 0.000 ARG A 187 Details of bonding type rmsd link_NAG-ASN : bond 0.00763 ( 20) link_NAG-ASN : angle 3.37455 ( 60) link_BETA1-4 : bond 0.00335 ( 12) link_BETA1-4 : angle 1.09477 ( 36) hydrogen bonds : bond 0.05593 ( 873) hydrogen bonds : angle 5.74699 ( 2343) SS BOND : bond 0.00346 ( 37) SS BOND : angle 1.51000 ( 74) covalent geometry : bond 0.00330 (26155) covalent geometry : angle 0.62458 (35606) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 91 time to evaluate : 2.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.8918 (m) cc_final: 0.8639 (t) REVERT: A 197 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.8486 (p90) REVERT: A 430 VAL cc_start: 0.5952 (OUTLIER) cc_final: 0.5602 (p) REVERT: A 655 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8076 (p0) REVERT: A 976 ASP cc_start: 0.8478 (t70) cc_final: 0.8261 (t0) REVERT: B 174 MET cc_start: 0.7357 (mtt) cc_final: 0.6665 (mtt) REVERT: B 189 PHE cc_start: 0.8433 (m-80) cc_final: 0.8233 (m-10) REVERT: B 1047 MET cc_start: 0.8237 (ptp) cc_final: 0.7901 (mtm) REVERT: C 150 MET cc_start: 0.8153 (pmm) cc_final: 0.7402 (pmm) REVERT: C 175 ASP cc_start: 0.4487 (OUTLIER) cc_final: 0.3969 (t70) REVERT: C 199 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8243 (mppt) REVERT: C 268 GLN cc_start: 0.9237 (OUTLIER) cc_final: 0.8942 (pt0) REVERT: C 339 PHE cc_start: 0.7493 (OUTLIER) cc_final: 0.7181 (t80) REVERT: C 481 LYS cc_start: 0.4279 (OUTLIER) cc_final: 0.3906 (tppt) REVERT: C 525 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8453 (mmtp) outliers start: 138 outliers final: 94 residues processed: 218 average time/residue: 0.3768 time to fit residues: 137.1774 Evaluate side-chains 191 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 88 time to evaluate : 2.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 657 TYR Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 668 CYS Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1131 ASN Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 457 ASN Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 827 ASP Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 867 ILE Chi-restraints excluded: chain B residue 870 TYR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 883 TRP Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1068 GLN Chi-restraints excluded: chain B residue 1111 ILE Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 481 LYS Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 525 LYS Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 657 TYR Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 783 LYS Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1047 MET Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1123 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 114 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 274 optimal weight: 0.9980 chunk 207 optimal weight: 8.9990 chunk 46 optimal weight: 0.0020 chunk 299 optimal weight: 8.9990 chunk 209 optimal weight: 1.9990 chunk 184 optimal weight: 0.0870 chunk 155 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 overall best weight: 0.7768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN B1007 GLN ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.071536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.050159 restraints weight = 150890.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.051122 restraints weight = 90469.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.051645 restraints weight = 58527.179| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26224 Z= 0.119 Angle : 0.624 12.054 35776 Z= 0.306 Chirality : 0.043 0.251 4182 Planarity : 0.004 0.051 4550 Dihedral : 7.717 74.506 4411 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.50 % Favored : 92.40 % Rotamer: Outliers : 4.08 % Allowed : 21.51 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.15), residues: 3172 helix: 1.95 (0.20), residues: 680 sheet: -1.02 (0.21), residues: 591 loop : -2.43 (0.13), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 433 HIS 0.004 0.000 HIS C 204 PHE 0.033 0.001 PHE B 483 TYR 0.012 0.001 TYR B1064 ARG 0.004 0.000 ARG C 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00464 ( 20) link_NAG-ASN : angle 3.14770 ( 60) link_BETA1-4 : bond 0.00374 ( 12) link_BETA1-4 : angle 1.00813 ( 36) hydrogen bonds : bond 0.05306 ( 873) hydrogen bonds : angle 5.58171 ( 2343) SS BOND : bond 0.00327 ( 37) SS BOND : angle 1.62198 ( 74) covalent geometry : bond 0.00263 (26155) covalent geometry : angle 0.60624 (35606) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 93 time to evaluate : 3.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.8930 (m) cc_final: 0.8659 (t) REVERT: A 197 TYR cc_start: 0.8687 (OUTLIER) cc_final: 0.8469 (p90) REVERT: A 213 LEU cc_start: 0.6679 (tp) cc_final: 0.6403 (tp) REVERT: A 430 VAL cc_start: 0.5914 (OUTLIER) cc_final: 0.5574 (p) REVERT: A 655 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8121 (p0) REVERT: A 847 ILE cc_start: 0.6259 (OUTLIER) cc_final: 0.6029 (pt) REVERT: A 976 ASP cc_start: 0.8491 (t70) cc_final: 0.8241 (t0) REVERT: B 174 MET cc_start: 0.7353 (mtt) cc_final: 0.6614 (mtt) REVERT: B 225 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8114 (t70) REVERT: B 807 SER cc_start: 0.9062 (OUTLIER) cc_final: 0.8799 (p) REVERT: B 1047 MET cc_start: 0.8192 (ptp) cc_final: 0.6921 (mtm) REVERT: C 150 MET cc_start: 0.8206 (pmm) cc_final: 0.7444 (pmm) REVERT: C 175 ASP cc_start: 0.4530 (OUTLIER) cc_final: 0.4046 (t70) REVERT: C 199 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8260 (mppt) REVERT: C 220 LEU cc_start: 0.8567 (mt) cc_final: 0.8225 (mp) REVERT: C 268 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.8950 (pt0) REVERT: C 339 PHE cc_start: 0.7462 (OUTLIER) cc_final: 0.7147 (t80) REVERT: C 481 LYS cc_start: 0.4224 (OUTLIER) cc_final: 0.3818 (tppt) REVERT: C 525 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8364 (mmtp) outliers start: 113 outliers final: 86 residues processed: 201 average time/residue: 0.4458 time to fit residues: 149.3485 Evaluate side-chains 181 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 83 time to evaluate : 3.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 657 TYR Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 668 CYS Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 457 ASN Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 827 ASP Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 870 TYR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain B residue 883 TRP Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 944 LYS Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1068 GLN Chi-restraints excluded: chain B residue 1111 ILE Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 481 LYS Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 525 LYS Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 657 TYR Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 783 LYS Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1123 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.4835 > 50: distance: 14 - 18: 34.906 distance: 18 - 19: 21.691 distance: 19 - 20: 34.147 distance: 20 - 21: 14.562 distance: 20 - 22: 20.144 distance: 22 - 23: 12.036 distance: 23 - 24: 7.789 distance: 23 - 26: 16.063 distance: 24 - 25: 12.007 distance: 24 - 29: 9.836 distance: 26 - 27: 15.459 distance: 26 - 28: 6.136 distance: 29 - 30: 7.726 distance: 30 - 31: 13.210 distance: 30 - 33: 3.578 distance: 31 - 32: 8.191 distance: 31 - 37: 14.364 distance: 33 - 34: 3.381 distance: 34 - 35: 5.874 distance: 34 - 36: 3.551 distance: 36 - 115: 5.326 distance: 37 - 38: 8.017 distance: 38 - 39: 15.055 distance: 38 - 41: 7.703 distance: 39 - 40: 16.984 distance: 39 - 43: 30.273 distance: 41 - 42: 7.368 distance: 42 - 111: 16.412 distance: 43 - 44: 5.785 distance: 44 - 45: 6.399 distance: 44 - 47: 9.583 distance: 45 - 46: 18.805 distance: 45 - 50: 12.371 distance: 47 - 48: 14.499 distance: 47 - 49: 20.694 distance: 50 - 51: 6.101 distance: 51 - 52: 5.824 distance: 51 - 54: 6.686 distance: 52 - 53: 11.033 distance: 52 - 59: 13.581 distance: 55 - 56: 11.033 distance: 56 - 57: 8.609 distance: 56 - 58: 5.279 distance: 59 - 60: 5.294 distance: 60 - 61: 21.138 distance: 60 - 63: 5.620 distance: 61 - 62: 25.417 distance: 61 - 66: 24.888 distance: 63 - 64: 18.487 distance: 63 - 65: 8.053 distance: 66 - 67: 7.772 distance: 66 - 72: 13.175 distance: 67 - 68: 13.153 distance: 67 - 70: 16.273 distance: 68 - 69: 16.862 distance: 68 - 73: 8.340 distance: 70 - 71: 12.851 distance: 71 - 72: 8.025 distance: 74 - 75: 6.365 distance: 74 - 77: 8.332 distance: 75 - 76: 14.943 distance: 75 - 80: 9.238 distance: 77 - 78: 3.250 distance: 77 - 79: 4.535 distance: 81 - 82: 4.558 distance: 81 - 84: 6.145 distance: 82 - 83: 5.060 distance: 82 - 85: 3.341