Starting phenix.real_space_refine on Sun Jun 15 00:21:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9axd_43935/06_2025/9axd_43935.cif Found real_map, /net/cci-nas-00/data/ceres_data/9axd_43935/06_2025/9axd_43935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9axd_43935/06_2025/9axd_43935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9axd_43935/06_2025/9axd_43935.map" model { file = "/net/cci-nas-00/data/ceres_data/9axd_43935/06_2025/9axd_43935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9axd_43935/06_2025/9axd_43935.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 10296 2.51 5 N 2798 2.21 5 O 3381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16580 Number of models: 1 Model: "" Number of chains: 41 Chain: "H" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 580 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'TRANS': 115} Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 116 Planarities with less than four sites: {'UNK:plan-1': 116} Unresolved non-hydrogen planarities: 116 Chain: "L" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 525 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'TRANS': 104} Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 105 Planarities with less than four sites: {'UNK:plan-1': 105} Unresolved non-hydrogen planarities: 105 Chain: "A" Number of atoms: 3586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3586 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 20, 'TRANS': 433} Chain breaks: 2 Chain: "B" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1139 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "C" Number of atoms: 3571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3571 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 20, 'TRANS': 431} Chain breaks: 2 Chain: "D" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1076 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 1, 'TRANS': 133} Chain breaks: 1 Chain: "E" Number of atoms: 3540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3540 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 20, 'TRANS': 427} Chain breaks: 2 Chain: "F" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1134 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 2, 'TRANS': 139} 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: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: "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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" 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: "V" 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: "W" 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: "X" 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: "Y" 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: "Z" 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: 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: "b" 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: "c" 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: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" 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: "C" 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: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 10.40, per 1000 atoms: 0.63 Number of scatterers: 16580 At special positions: 0 Unit cell: (130.625, 133.76, 121.22, 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 105 16.00 O 3381 8.00 N 2798 7.00 C 10296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 330 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 444 " distance=1.58 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 500 " - pdb=" SG CYS B 605 " distance=2.12 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 330 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 444 " distance=2.03 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 500 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 330 " distance=2.03 Simple disulfide: pdb=" SG CYS E 377 " - pdb=" SG CYS E 444 " distance=2.03 Simple disulfide: pdb=" SG CYS E 384 " - pdb=" SG CYS E 417 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " 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 Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA T 3 " - " MAN T 4 " " BMA d 3 " - " MAN d 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA T 3 " - " MAN T 5 " " BMA d 3 " - " MAN d 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " 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 " BETA1-6 " NAG N 2 " - " NAG N 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 152 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 234 " " NAG A 606 " - " ASN A 241 " " NAG A 607 " - " ASN A 289 " " NAG A 608 " - " ASN A 301 " " NAG A 609 " - " ASN A 338 " " NAG A 610 " - " ASN A 354 " " NAG A 611 " - " ASN A 385 " " NAG A 612 " - " ASN A 391 " " NAG A 613 " - " ASN A 447 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 137 " " NAG C 604 " - " ASN C 276 " " NAG C 605 " - " ASN C 301 " " NAG C 606 " - " ASN C 338 " " NAG C 607 " - " ASN C 391 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 637 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 197 " " NAG E 603 " - " ASN E 152 " " NAG E 604 " - " ASN E 289 " " NAG E 605 " - " ASN E 295 " " NAG E 606 " - " ASN E 301 " " NAG E 607 " - " ASN E 338 " " NAG E 608 " - " ASN E 354 " " NAG E 609 " - " ASN E 391 " " NAG E 610 " - " ASN E 447 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 625 " " NAG F 704 " - " ASN F 637 " " NAG G 1 " - " ASN A 148 " " NAG I 1 " - " ASN A 262 " " NAG J 1 " - " ASN A 276 " " NAG K 1 " - " ASN A 295 " " NAG M 1 " - " ASN A 331 " " NAG N 1 " - " ASN A 362 " " NAG O 1 " - " ASN C 148 " " NAG P 1 " - " ASN C 152 " " NAG Q 1 " - " ASN C 197 " " NAG R 1 " - " ASN C 234 " " NAG S 1 " - " ASN C 241 " " NAG T 1 " - " ASN C 262 " " NAG U 1 " - " ASN C 289 " " NAG V 1 " - " ASN C 295 " " NAG W 1 " - " ASN C 331 " " NAG X 1 " - " ASN C 362 " " NAG Y 1 " - " ASN C 385 " " NAG Z 1 " - " ASN C 447 " " NAG a 1 " - " ASN E 148 " " NAG b 1 " - " ASN E 234 " " NAG c 1 " - " ASN E 241 " " NAG d 1 " - " ASN E 262 " " NAG e 1 " - " ASN E 276 " " NAG f 1 " - " ASN E 331 " " NAG g 1 " - " ASN E 362 " " NAG h 1 " - " ASN E 385 " " NAG i 1 " - " ASN E 88 " Time building additional restraints: 4.94 Conformation dependent library (CDL) restraints added in 1.7 seconds 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3768 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 28 sheets defined 30.8% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'L' and resid 46 through 50 removed outlier: 3.554A pdb=" N UNK L 50 " --> pdb=" O UNK L 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 66 removed outlier: 3.686A pdb=" N LYS A 65 " --> pdb=" O GLU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.919A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 353 removed outlier: 3.670A pdb=" N HIS A 351 " --> pdb=" O GLN A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.640A pdb=" N THR A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 4.373A pdb=" N GLY A 388 " --> pdb=" O ASN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 428 Processing helix chain 'A' and resid 474 through 483 removed outlier: 3.963A pdb=" N SER A 480 " --> pdb=" O ASP A 476 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLU A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 544 removed outlier: 3.556A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 554 removed outlier: 4.554A pdb=" N GLN B 552 " --> pdb=" O ILE B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 568 Processing helix chain 'B' and resid 568 through 596 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 663 Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.594A pdb=" N HIS C 72 " --> pdb=" O VAL C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.142A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 143 removed outlier: 3.603A pdb=" N ARG C 143 " --> pdb=" O ASP C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 353 removed outlier: 3.830A pdb=" N LYS C 350 " --> pdb=" O LYS C 346 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS C 351 " --> pdb=" O GLN C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'C' and resid 424 through 428 removed outlier: 3.823A pdb=" N GLN C 427 " --> pdb=" O ASN C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 480 removed outlier: 3.701A pdb=" N SER C 480 " --> pdb=" O ASP C 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 547 removed outlier: 3.970A pdb=" N LEU D 544 " --> pdb=" O GLN D 540 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER D 546 " --> pdb=" O ARG D 542 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY D 547 " --> pdb=" O ASN D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 596 Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 663 Processing helix chain 'E' and resid 58 through 61 Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 98 through 117 removed outlier: 3.962A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 334 through 350 removed outlier: 3.821A pdb=" N LYS E 350 " --> pdb=" O LYS E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 372 removed outlier: 3.761A pdb=" N THR E 372 " --> pdb=" O LEU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 380 removed outlier: 3.708A pdb=" N GLU E 380 " --> pdb=" O CYS E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 389 Processing helix chain 'E' and resid 424 through 428 removed outlier: 3.578A pdb=" N ARG E 428 " --> pdb=" O MET E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 480 removed outlier: 3.699A pdb=" N ASN E 477 " --> pdb=" O ASP E 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 537 through 556 removed outlier: 3.580A pdb=" N ALA F 541 " --> pdb=" O LEU F 537 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE F 548 " --> pdb=" O LEU F 544 " (cutoff:3.500A) Processing helix chain 'F' and resid 561 through 566 Processing helix chain 'F' and resid 568 through 596 removed outlier: 3.963A pdb=" N GLY F 572 " --> pdb=" O LEU F 568 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 624 removed outlier: 3.694A pdb=" N ASP F 624 " --> pdb=" O SER F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 661 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.715A pdb=" N UNK H 19 " --> pdb=" O UNK H 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.305A pdb=" N UNK H 46 " --> pdb=" O UNK H 37 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N UNK H 37 " --> pdb=" O UNK H 46 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N UNK H 33 " --> pdb=" O UNK H 50 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N UNK H 38 " --> pdb=" O UNK H 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 12 through 13 Processing sheet with id=AA4, first strand: chain 'L' and resid 18 through 21 removed outlier: 3.923A pdb=" N UNK L 20 " --> pdb=" O UNK L 72 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N UNK L 72 " --> pdb=" O UNK L 20 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 43 through 45 removed outlier: 4.201A pdb=" N UNK L 86 " --> pdb=" O UNK L 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 493 through 498 removed outlier: 5.571A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.746A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.653A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AB1, first strand: chain 'A' and resid 162 through 169 removed outlier: 3.867A pdb=" N LYS A 189 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 201 through 203 Processing sheet with id=AB3, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.621A pdb=" N GLN A 293 " --> pdb=" O SER A 333 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER A 333 " --> pdb=" O GLN A 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 329 through 333 current: chain 'A' and resid 392 through 394 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 392 through 394 current: chain 'A' and resid 464 through 469 Processing sheet with id=AB4, first strand: chain 'A' and resid 301 through 310 removed outlier: 6.565A pdb=" N ASN A 301 " --> pdb=" O ILE A 321 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ILE A 321 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N THR A 303 " --> pdb=" O GLY A 319 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLN A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 373 through 377 removed outlier: 3.542A pdb=" N PHE A 375 " --> pdb=" O PHE A 382 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 494 through 498 removed outlier: 5.710A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.513A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 91 through 92 Processing sheet with id=AB9, first strand: chain 'C' and resid 161 through 169 Processing sheet with id=AC1, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.430A pdb=" N ALA C 200 " --> pdb=" O ALA C 432 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N TYR C 434 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR C 202 " --> pdb=" O TYR C 434 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 260 through 261 current: chain 'C' and resid 284 through 287 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 284 through 287 current: chain 'C' and resid 313 through 321 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 313 through 321 current: chain 'C' and resid 380 through 384 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 380 through 384 current: chain 'C' and resid 464 through 469 No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 494 through 498 removed outlier: 5.490A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC5, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AC6, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC7, first strand: chain 'E' and resid 161 through 169 Processing sheet with id=AC8, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.016A pdb=" N ALA E 200 " --> pdb=" O ALA E 432 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N TYR E 434 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR E 202 " --> pdb=" O TYR E 434 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 298 removed outlier: 7.148A pdb=" N GLN E 293 " --> pdb=" O SER E 333 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N SER E 333 " --> pdb=" O GLN E 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 328 through 333 current: chain 'E' and resid 382 through 384 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 382 through 384 current: chain 'E' and resid 464 through 469 Processing sheet with id=AD1, first strand: chain 'E' and resid 304 through 310 removed outlier: 6.755A pdb=" N GLN E 313 " --> pdb=" O ILE E 309 " (cutoff:3.500A) 524 hydrogen bonds defined for protein. 1413 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: 4.93 Time building geometry restraints manager: 5.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2871 1.33 - 1.45: 4460 1.45 - 1.57: 9386 1.57 - 1.69: 0 1.69 - 1.82: 138 Bond restraints: 16855 Sorted by residual: bond pdb=" N ILE C 395 " pdb=" CA ILE C 395 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.09e-02 8.42e+03 1.16e+01 bond pdb=" N VAL D 570 " pdb=" CA VAL D 570 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.14e-02 7.69e+03 1.07e+01 bond pdb=" N ILE C 358 " pdb=" CA ILE C 358 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.08e-02 8.57e+03 8.81e+00 bond pdb=" N ARG E 468 " pdb=" CA ARG E 468 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.18e-02 7.18e+03 8.42e+00 bond pdb=" N THR E 460 " pdb=" CA THR E 460 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.14e-02 7.69e+03 7.87e+00 ... (remaining 16850 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 21923 1.85 - 3.70: 863 3.70 - 5.55: 107 5.55 - 7.40: 26 7.40 - 9.25: 1 Bond angle restraints: 22920 Sorted by residual: angle pdb=" N LEU D 565 " pdb=" CA LEU D 565 " pdb=" C LEU D 565 " ideal model delta sigma weight residual 113.88 108.44 5.44 1.23e+00 6.61e-01 1.96e+01 angle pdb=" CA TRP E 394 " pdb=" C TRP E 394 " pdb=" O TRP E 394 " ideal model delta sigma weight residual 122.64 118.09 4.55 1.25e+00 6.40e-01 1.32e+01 angle pdb=" CA THR E 464 " pdb=" C THR E 464 " pdb=" O THR E 464 " ideal model delta sigma weight residual 122.64 118.33 4.31 1.25e+00 6.40e-01 1.19e+01 angle pdb=" N TRP D 571 " pdb=" CA TRP D 571 " pdb=" C TRP D 571 " ideal model delta sigma weight residual 113.38 109.53 3.85 1.17e+00 7.31e-01 1.08e+01 angle pdb=" CA ILE D 573 " pdb=" C ILE D 573 " pdb=" O ILE D 573 " ideal model delta sigma weight residual 121.27 118.03 3.24 1.04e+00 9.25e-01 9.70e+00 ... (remaining 22915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.32: 11113 23.32 - 46.65: 318 46.65 - 69.97: 45 69.97 - 93.30: 26 93.30 - 116.62: 12 Dihedral angle restraints: 11514 sinusoidal: 5721 harmonic: 5793 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 140.14 -47.14 1 1.00e+01 1.00e-02 3.07e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 131.37 -38.37 1 1.00e+01 1.00e-02 2.07e+01 dihedral pdb=" CB CYS A 377 " pdb=" SG CYS A 377 " pdb=" SG CYS A 444 " pdb=" CB CYS A 444 " ideal model delta sinusoidal sigma weight residual 93.00 130.45 -37.45 1 1.00e+01 1.00e-02 1.98e+01 ... (remaining 11511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 2784 0.112 - 0.224: 141 0.224 - 0.336: 13 0.336 - 0.448: 1 0.448 - 0.560: 2 Chirality restraints: 2941 Sorted by residual: chirality pdb=" C1 NAG f 2 " pdb=" O4 NAG f 1 " pdb=" C2 NAG f 2 " pdb=" O5 NAG f 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 8.68e+01 chirality pdb=" C1 NAG e 2 " pdb=" O4 NAG e 1 " pdb=" C2 NAG e 2 " pdb=" O5 NAG e 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.41e+01 chirality pdb=" C1 NAG E 607 " pdb=" ND2 ASN E 338 " pdb=" C2 NAG E 607 " pdb=" O5 NAG E 607 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.85e+00 ... (remaining 2938 not shown) Planarity restraints: 2871 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 601 " -0.354 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG A 601 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG A 601 " -0.102 2.00e-02 2.50e+03 pdb=" N2 NAG A 601 " 0.542 2.00e-02 2.50e+03 pdb=" O7 NAG A 601 " -0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG f 2 " -0.345 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG f 2 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG f 2 " -0.078 2.00e-02 2.50e+03 pdb=" N2 NAG f 2 " 0.530 2.00e-02 2.50e+03 pdb=" O7 NAG f 2 " -0.185 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 604 " -0.316 2.00e-02 2.50e+03 2.66e-01 8.84e+02 pdb=" C7 NAG E 604 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG E 604 " -0.189 2.00e-02 2.50e+03 pdb=" N2 NAG E 604 " 0.458 2.00e-02 2.50e+03 pdb=" O7 NAG E 604 " -0.038 2.00e-02 2.50e+03 ... (remaining 2868 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 24 2.41 - 3.04: 10391 3.04 - 3.66: 22565 3.66 - 4.28: 35762 4.28 - 4.90: 58111 Nonbonded interactions: 126853 Sorted by model distance: nonbonded pdb=" OD1 ASN D 607 " pdb=" NE2 GLN D 653 " model vdw 1.793 3.120 nonbonded pdb=" OD1 ASP C 456 " pdb=" N GLY C 457 " model vdw 2.146 3.120 nonbonded pdb=" O ILE C 395 " pdb=" OG SER C 396 " model vdw 2.163 3.040 nonbonded pdb=" OE1 GLU B 647 " pdb=" NH1 ARG D 542 " model vdw 2.257 3.120 nonbonded pdb=" ND2 ASN E 295 " pdb=" O7 NAG E 605 " model vdw 2.277 3.120 ... (remaining 126848 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 33 through 177 or resid 189 through 397 or resid 410 throu \ gh 503 or resid 606 through 613)) selection = (chain 'C' and (resid 33 through 177 or resid 189 through 397 or resid 410 throu \ gh 503 or resid 601 through 608)) selection = (chain 'E' and (resid 33 through 503 or resid 603 through 610)) } ncs_group { reference = (chain 'B' and (resid 521 through 550 or resid 560 through 661 or resid 701 thro \ ugh 702)) selection = (chain 'D' and (resid 521 through 661 or resid 701 through 702)) selection = (chain 'F' and (resid 521 through 550 or resid 560 through 661 or resid 703 thro \ ugh 704)) } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' } ncs_group { reference = (chain 'H' and resid 13 through 117) selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'T' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 38.290 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 : 0.007 0.446 16990 Z= 0.361 Angle : 0.911 22.194 23293 Z= 0.445 Chirality : 0.055 0.560 2941 Planarity : 0.012 0.305 2805 Dihedral : 11.945 116.619 7650 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % 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: 0.23 (0.20), residues: 1748 helix: 1.58 (0.26), residues: 426 sheet: -0.32 (0.24), residues: 454 loop : -0.20 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 623 HIS 0.005 0.001 HIS B 564 PHE 0.011 0.002 PHE E 53 TYR 0.016 0.001 TYR A 191 ARG 0.003 0.000 ARG C 308 Details of bonding type rmsd link_NAG-ASN : bond 0.00774 ( 66) link_NAG-ASN : angle 2.38506 ( 198) link_ALPHA1-6 : bond 0.00695 ( 3) link_ALPHA1-6 : angle 1.83657 ( 9) link_BETA1-4 : bond 0.01351 ( 30) link_BETA1-4 : angle 4.33846 ( 90) link_ALPHA1-3 : bond 0.00430 ( 3) link_ALPHA1-3 : angle 2.33547 ( 9) hydrogen bonds : bond 0.19074 ( 524) hydrogen bonds : angle 7.39518 ( 1413) link_BETA1-6 : bond 0.01255 ( 1) link_BETA1-6 : angle 1.47332 ( 3) SS BOND : bond 0.08043 ( 32) SS BOND : angle 3.89244 ( 64) covalent geometry : bond 0.00592 (16855) covalent geometry : angle 0.82082 (22920) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8858 (ttt) cc_final: 0.8635 (ttt) REVERT: A 177 ASN cc_start: 0.7172 (t0) cc_final: 0.6711 (p0) REVERT: A 376 ASN cc_start: 0.8559 (t0) cc_final: 0.7207 (p0) REVERT: A 473 ASP cc_start: 0.7999 (t0) cc_final: 0.7760 (t0) REVERT: B 571 TRP cc_start: 0.8106 (m100) cc_final: 0.7697 (m100) REVERT: B 617 ARG cc_start: 0.7174 (mtp180) cc_final: 0.6756 (mtt-85) REVERT: B 624 ASP cc_start: 0.8010 (t0) cc_final: 0.7597 (t0) REVERT: B 626 MET cc_start: 0.7705 (ttp) cc_final: 0.7121 (ttm) REVERT: B 630 GLN cc_start: 0.8617 (mt0) cc_final: 0.8120 (tt0) REVERT: C 97 LYS cc_start: 0.8272 (mmtt) cc_final: 0.8060 (tptt) REVERT: C 142 MET cc_start: 0.7794 (mmm) cc_final: 0.7412 (mmt) REVERT: C 159 ASP cc_start: 0.8529 (m-30) cc_final: 0.7998 (t0) REVERT: C 474 MET cc_start: 0.7929 (mmp) cc_final: 0.7690 (mmt) REVERT: C 485 TYR cc_start: 0.9267 (m-80) cc_final: 0.8847 (m-80) REVERT: D 584 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7518 (mt-10) REVERT: E 35 TRP cc_start: 0.7842 (m100) cc_final: 0.7528 (m-10) REVERT: E 102 GLU cc_start: 0.8209 (tp30) cc_final: 0.7867 (tp30) REVERT: E 104 MET cc_start: 0.8912 (ttt) cc_final: 0.8590 (ttm) REVERT: E 207 LYS cc_start: 0.8681 (mttt) cc_final: 0.8373 (tmtt) REVERT: E 209 SER cc_start: 0.9121 (t) cc_final: 0.8776 (m) REVERT: E 357 ILE cc_start: 0.8209 (mt) cc_final: 0.7843 (mt) REVERT: E 474 MET cc_start: 0.7765 (mmm) cc_final: 0.7515 (mmt) REVERT: F 627 THR cc_start: 0.9062 (p) cc_final: 0.8132 (p) outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.3069 time to fit residues: 185.7965 Evaluate side-chains 214 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 153 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 543 ASN B 653 GLN C 258 GLN C 424 ASN C 477 ASN D 543 ASN D 564 HIS E 287 GLN E 373 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.129217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.113860 restraints weight = 26266.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.115023 restraints weight = 21266.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.115466 restraints weight = 17144.889| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16990 Z= 0.166 Angle : 0.710 12.634 23293 Z= 0.330 Chirality : 0.047 0.363 2941 Planarity : 0.004 0.045 2805 Dihedral : 9.457 75.658 4271 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.21 % Allowed : 9.30 % Favored : 88.49 % 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: 0.38 (0.20), residues: 1748 helix: 1.74 (0.26), residues: 435 sheet: -0.32 (0.23), residues: 468 loop : -0.09 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 596 HIS 0.004 0.001 HIS A 85 PHE 0.011 0.002 PHE C 168 TYR 0.026 0.002 TYR E 485 ARG 0.006 0.001 ARG F 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00407 ( 66) link_NAG-ASN : angle 2.16003 ( 198) link_ALPHA1-6 : bond 0.00573 ( 3) link_ALPHA1-6 : angle 1.72641 ( 9) link_BETA1-4 : bond 0.00800 ( 30) link_BETA1-4 : angle 3.07341 ( 90) link_ALPHA1-3 : bond 0.00833 ( 3) link_ALPHA1-3 : angle 1.88741 ( 9) hydrogen bonds : bond 0.04592 ( 524) hydrogen bonds : angle 5.58790 ( 1413) link_BETA1-6 : bond 0.00850 ( 1) link_BETA1-6 : angle 0.72342 ( 3) SS BOND : bond 0.00332 ( 32) SS BOND : angle 1.13404 ( 64) covalent geometry : bond 0.00380 (16855) covalent geometry : angle 0.65466 (22920) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 254 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 ASN cc_start: 0.7169 (t0) cc_final: 0.6698 (p0) REVERT: A 376 ASN cc_start: 0.8448 (t0) cc_final: 0.7045 (p0) REVERT: B 566 LEU cc_start: 0.8683 (mt) cc_final: 0.7826 (tp) REVERT: B 596 TRP cc_start: 0.9143 (m-10) cc_final: 0.8880 (m-10) REVERT: B 624 ASP cc_start: 0.8161 (t0) cc_final: 0.7389 (m-30) REVERT: B 638 TYR cc_start: 0.6742 (m-80) cc_final: 0.6075 (m-10) REVERT: B 647 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6814 (mt-10) REVERT: C 142 MET cc_start: 0.7965 (mmm) cc_final: 0.7593 (mmt) REVERT: C 159 ASP cc_start: 0.8230 (m-30) cc_final: 0.7858 (t0) REVERT: C 485 TYR cc_start: 0.9144 (m-80) cc_final: 0.8865 (m-80) REVERT: E 103 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8238 (tm-30) REVERT: E 209 SER cc_start: 0.9172 (t) cc_final: 0.8808 (m) REVERT: E 217 TYR cc_start: 0.8730 (m-80) cc_final: 0.7714 (m-80) REVERT: E 367 ASP cc_start: 0.7300 (p0) cc_final: 0.7066 (p0) REVERT: F 534 SER cc_start: 0.8936 (m) cc_final: 0.8568 (p) outliers start: 35 outliers final: 18 residues processed: 273 average time/residue: 0.2786 time to fit residues: 116.1238 Evaluate side-chains 213 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 195 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain F residue 545 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 73 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 185 optimal weight: 0.0970 chunk 77 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 111 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 146 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN D 543 ASN D 564 HIS ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 373 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.128867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.113290 restraints weight = 26278.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.114920 restraints weight = 19965.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.116050 restraints weight = 16484.987| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16990 Z= 0.135 Angle : 0.652 9.981 23293 Z= 0.304 Chirality : 0.046 0.391 2941 Planarity : 0.003 0.043 2805 Dihedral : 8.052 56.690 4271 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.53 % Allowed : 10.12 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.20), residues: 1748 helix: 1.74 (0.26), residues: 435 sheet: -0.25 (0.23), residues: 472 loop : -0.11 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 35 HIS 0.003 0.001 HIS A 85 PHE 0.023 0.001 PHE C 53 TYR 0.029 0.002 TYR E 485 ARG 0.005 0.000 ARG A 326 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 66) link_NAG-ASN : angle 2.03719 ( 198) link_ALPHA1-6 : bond 0.00320 ( 3) link_ALPHA1-6 : angle 2.09564 ( 9) link_BETA1-4 : bond 0.00829 ( 30) link_BETA1-4 : angle 2.89961 ( 90) link_ALPHA1-3 : bond 0.00856 ( 3) link_ALPHA1-3 : angle 1.61339 ( 9) hydrogen bonds : bond 0.04119 ( 524) hydrogen bonds : angle 5.20774 ( 1413) link_BETA1-6 : bond 0.00867 ( 1) link_BETA1-6 : angle 0.61956 ( 3) SS BOND : bond 0.00328 ( 32) SS BOND : angle 1.04601 ( 64) covalent geometry : bond 0.00302 (16855) covalent geometry : angle 0.59810 (22920) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 219 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 ASN cc_start: 0.7160 (t0) cc_final: 0.6703 (p0) REVERT: A 434 TYR cc_start: 0.8767 (t80) cc_final: 0.8363 (t80) REVERT: A 441 VAL cc_start: 0.9549 (t) cc_final: 0.9286 (p) REVERT: B 562 GLN cc_start: 0.8569 (mm110) cc_final: 0.8349 (mm110) REVERT: B 616 ASN cc_start: 0.7610 (p0) cc_final: 0.7345 (p0) REVERT: B 624 ASP cc_start: 0.8143 (t0) cc_final: 0.7403 (m-30) REVERT: B 638 TYR cc_start: 0.6361 (m-80) cc_final: 0.6037 (m-10) REVERT: B 647 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6957 (mt-10) REVERT: C 61 TYR cc_start: 0.6944 (OUTLIER) cc_final: 0.5886 (m-80) REVERT: C 159 ASP cc_start: 0.8204 (m-30) cc_final: 0.7852 (t0) REVERT: C 485 TYR cc_start: 0.9051 (m-80) cc_final: 0.8801 (m-80) REVERT: D 584 GLU cc_start: 0.7461 (mt-10) cc_final: 0.6693 (mt-10) REVERT: E 103 GLN cc_start: 0.8585 (tm-30) cc_final: 0.8276 (tm-30) REVERT: E 209 SER cc_start: 0.9147 (t) cc_final: 0.8791 (m) REVERT: E 217 TYR cc_start: 0.8612 (m-80) cc_final: 0.7665 (m-80) REVERT: F 579 ARG cc_start: 0.8822 (mtp85) cc_final: 0.8384 (mtp85) outliers start: 40 outliers final: 27 residues processed: 242 average time/residue: 0.2925 time to fit residues: 107.1330 Evaluate side-chains 227 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 61 TYR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain D residue 542 ARG Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 627 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 121 optimal weight: 0.4980 chunk 50 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 179 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 564 HIS C 246 GLN C 258 GLN C 477 ASN D 564 HIS E 300 ASN E 373 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.126218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.110931 restraints weight = 26700.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.112485 restraints weight = 20455.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.113586 restraints weight = 16938.067| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16990 Z= 0.187 Angle : 0.682 13.800 23293 Z= 0.315 Chirality : 0.045 0.242 2941 Planarity : 0.003 0.040 2805 Dihedral : 7.474 56.345 4271 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.91 % Allowed : 10.88 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.20), residues: 1748 helix: 1.68 (0.26), residues: 436 sheet: -0.33 (0.23), residues: 466 loop : -0.21 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 35 HIS 0.004 0.001 HIS C 216 PHE 0.041 0.002 PHE E 53 TYR 0.031 0.002 TYR E 485 ARG 0.006 0.000 ARG A 326 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 66) link_NAG-ASN : angle 2.44116 ( 198) link_ALPHA1-6 : bond 0.00217 ( 3) link_ALPHA1-6 : angle 1.82594 ( 9) link_BETA1-4 : bond 0.00780 ( 30) link_BETA1-4 : angle 2.89755 ( 90) link_ALPHA1-3 : bond 0.00815 ( 3) link_ALPHA1-3 : angle 1.76728 ( 9) hydrogen bonds : bond 0.04101 ( 524) hydrogen bonds : angle 5.07258 ( 1413) link_BETA1-6 : bond 0.00827 ( 1) link_BETA1-6 : angle 0.83057 ( 3) SS BOND : bond 0.00417 ( 32) SS BOND : angle 1.10086 ( 64) covalent geometry : bond 0.00435 (16855) covalent geometry : angle 0.61801 (22920) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 218 time to evaluate : 1.908 Fit side-chains REVERT: A 177 ASN cc_start: 0.7141 (t0) cc_final: 0.6721 (p0) REVERT: A 376 ASN cc_start: 0.8370 (t0) cc_final: 0.7114 (p0) REVERT: A 434 TYR cc_start: 0.8844 (t80) cc_final: 0.8624 (t80) REVERT: A 441 VAL cc_start: 0.9525 (t) cc_final: 0.9309 (p) REVERT: B 562 GLN cc_start: 0.8456 (mm110) cc_final: 0.8074 (mm110) REVERT: B 624 ASP cc_start: 0.8080 (t0) cc_final: 0.7422 (m-30) REVERT: B 638 TYR cc_start: 0.6328 (m-80) cc_final: 0.6090 (m-10) REVERT: B 647 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6980 (mt-10) REVERT: C 61 TYR cc_start: 0.6900 (OUTLIER) cc_final: 0.5875 (m-80) REVERT: C 142 MET cc_start: 0.8005 (mmm) cc_final: 0.7584 (tpt) REVERT: C 145 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7435 (tp30) REVERT: C 159 ASP cc_start: 0.8234 (m-30) cc_final: 0.7845 (t0) REVERT: C 195 ASN cc_start: 0.7384 (m-40) cc_final: 0.7155 (t0) REVERT: C 485 TYR cc_start: 0.9022 (m-80) cc_final: 0.8777 (m-80) REVERT: D 584 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6959 (mt-10) REVERT: E 35 TRP cc_start: 0.7841 (m100) cc_final: 0.7627 (m100) REVERT: E 103 GLN cc_start: 0.8659 (tm-30) cc_final: 0.8393 (tm-30) REVERT: E 122 LEU cc_start: 0.9184 (mm) cc_final: 0.8805 (tt) REVERT: E 209 SER cc_start: 0.9115 (t) cc_final: 0.8789 (m) outliers start: 46 outliers final: 32 residues processed: 244 average time/residue: 0.3352 time to fit residues: 125.7601 Evaluate side-chains 239 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 206 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 61 TYR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain D residue 542 ARG Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 627 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 180 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 87 optimal weight: 0.0970 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN D 564 HIS E 477 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.121353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.105782 restraints weight = 27837.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.107020 restraints weight = 22409.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.107996 restraints weight = 18334.529| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 16990 Z= 0.289 Angle : 0.789 10.038 23293 Z= 0.366 Chirality : 0.049 0.292 2941 Planarity : 0.004 0.046 2805 Dihedral : 7.527 53.930 4271 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.04 % Allowed : 12.84 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.20), residues: 1748 helix: 1.26 (0.25), residues: 447 sheet: -0.55 (0.24), residues: 462 loop : -0.45 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 596 HIS 0.007 0.002 HIS C 216 PHE 0.033 0.002 PHE E 53 TYR 0.029 0.002 TYR E 485 ARG 0.007 0.001 ARG A 326 Details of bonding type rmsd link_NAG-ASN : bond 0.00585 ( 66) link_NAG-ASN : angle 2.43012 ( 198) link_ALPHA1-6 : bond 0.00247 ( 3) link_ALPHA1-6 : angle 1.89666 ( 9) link_BETA1-4 : bond 0.00747 ( 30) link_BETA1-4 : angle 3.06601 ( 90) link_ALPHA1-3 : bond 0.00743 ( 3) link_ALPHA1-3 : angle 1.85214 ( 9) hydrogen bonds : bond 0.04547 ( 524) hydrogen bonds : angle 5.27748 ( 1413) link_BETA1-6 : bond 0.00895 ( 1) link_BETA1-6 : angle 1.10527 ( 3) SS BOND : bond 0.00547 ( 32) SS BOND : angle 1.38108 ( 64) covalent geometry : bond 0.00677 (16855) covalent geometry : angle 0.73224 (22920) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 216 time to evaluate : 2.119 Fit side-chains revert: symmetry clash REVERT: A 177 ASN cc_start: 0.7316 (t0) cc_final: 0.6818 (p0) REVERT: A 376 ASN cc_start: 0.8334 (t0) cc_final: 0.7334 (p0) REVERT: B 562 GLN cc_start: 0.8414 (mm110) cc_final: 0.7961 (mm110) REVERT: B 616 ASN cc_start: 0.7701 (p0) cc_final: 0.7486 (p0) REVERT: B 624 ASP cc_start: 0.8203 (t0) cc_final: 0.7417 (m-30) REVERT: B 638 TYR cc_start: 0.6622 (m-80) cc_final: 0.6263 (m-10) REVERT: B 647 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6990 (mt-10) REVERT: C 142 MET cc_start: 0.8071 (mmm) cc_final: 0.7734 (mmt) REVERT: C 145 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7605 (tp30) REVERT: C 159 ASP cc_start: 0.8310 (m-30) cc_final: 0.7869 (t0) REVERT: C 269 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7462 (tt0) REVERT: C 485 TYR cc_start: 0.9019 (m-80) cc_final: 0.8697 (m-80) REVERT: C 493 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8843 (tt) REVERT: E 103 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8461 (tm-30) REVERT: E 122 LEU cc_start: 0.9183 (mm) cc_final: 0.8950 (tt) outliers start: 48 outliers final: 36 residues processed: 247 average time/residue: 0.3391 time to fit residues: 127.9605 Evaluate side-chains 235 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 627 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 74 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 193 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 chunk 60 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 115 optimal weight: 0.5980 chunk 176 optimal weight: 7.9990 chunk 172 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN C 246 GLN C 477 ASN D 564 HIS E 66 HIS E 410 ASN E 424 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.125670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.110062 restraints weight = 27084.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.111619 restraints weight = 20775.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.112761 restraints weight = 17300.929| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16990 Z= 0.126 Angle : 0.645 11.707 23293 Z= 0.298 Chirality : 0.044 0.243 2941 Planarity : 0.003 0.057 2805 Dihedral : 6.758 55.175 4271 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.47 % Allowed : 14.42 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.20), residues: 1748 helix: 1.56 (0.26), residues: 435 sheet: -0.40 (0.24), residues: 456 loop : -0.38 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 35 HIS 0.008 0.001 HIS B 564 PHE 0.033 0.001 PHE E 53 TYR 0.032 0.002 TYR E 485 ARG 0.012 0.000 ARG A 326 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 66) link_NAG-ASN : angle 2.11856 ( 198) link_ALPHA1-6 : bond 0.00256 ( 3) link_ALPHA1-6 : angle 1.71667 ( 9) link_BETA1-4 : bond 0.00794 ( 30) link_BETA1-4 : angle 2.82306 ( 90) link_ALPHA1-3 : bond 0.00927 ( 3) link_ALPHA1-3 : angle 1.59135 ( 9) hydrogen bonds : bond 0.03809 ( 524) hydrogen bonds : angle 4.95973 ( 1413) link_BETA1-6 : bond 0.00909 ( 1) link_BETA1-6 : angle 0.71424 ( 3) SS BOND : bond 0.00361 ( 32) SS BOND : angle 0.95771 ( 64) covalent geometry : bond 0.00283 (16855) covalent geometry : angle 0.58963 (22920) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 1.593 Fit side-chains revert: symmetry clash REVERT: A 177 ASN cc_start: 0.7083 (t0) cc_final: 0.6656 (p0) REVERT: A 376 ASN cc_start: 0.8322 (t0) cc_final: 0.7377 (p0) REVERT: A 474 MET cc_start: 0.7524 (mmm) cc_final: 0.7017 (mmt) REVERT: B 562 GLN cc_start: 0.8424 (mm110) cc_final: 0.8126 (mm110) REVERT: B 616 ASN cc_start: 0.7664 (p0) cc_final: 0.7421 (p0) REVERT: B 624 ASP cc_start: 0.7978 (t0) cc_final: 0.7461 (m-30) REVERT: B 638 TYR cc_start: 0.6378 (m-80) cc_final: 0.6052 (m-10) REVERT: C 42 VAL cc_start: 0.9062 (OUTLIER) cc_final: 0.8851 (p) REVERT: C 61 TYR cc_start: 0.6877 (OUTLIER) cc_final: 0.5915 (m-80) REVERT: C 142 MET cc_start: 0.7966 (mmm) cc_final: 0.7594 (tpt) REVERT: C 145 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7492 (tp30) REVERT: C 159 ASP cc_start: 0.8178 (m-30) cc_final: 0.7807 (t0) REVERT: C 485 TYR cc_start: 0.8880 (m-80) cc_final: 0.8609 (m-80) REVERT: D 584 GLU cc_start: 0.7472 (mt-10) cc_final: 0.6828 (mt-10) REVERT: E 103 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8378 (tm-30) REVERT: E 217 TYR cc_start: 0.8410 (m-80) cc_final: 0.7585 (m-80) REVERT: F 579 ARG cc_start: 0.8808 (mtp85) cc_final: 0.8448 (ttm-80) outliers start: 39 outliers final: 24 residues processed: 240 average time/residue: 0.2776 time to fit residues: 101.8393 Evaluate side-chains 229 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 61 TYR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 627 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 50 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 131 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN C 246 GLN C 477 ASN D 564 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.122376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.107004 restraints weight = 27469.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.107754 restraints weight = 22472.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.108793 restraints weight = 18987.769| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 16990 Z= 0.244 Angle : 0.753 10.898 23293 Z= 0.349 Chirality : 0.047 0.247 2941 Planarity : 0.004 0.056 2805 Dihedral : 7.030 53.906 4271 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.72 % Allowed : 15.05 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.20), residues: 1748 helix: 1.36 (0.25), residues: 436 sheet: -0.58 (0.24), residues: 454 loop : -0.53 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 35 HIS 0.005 0.001 HIS C 216 PHE 0.024 0.002 PHE D 522 TYR 0.020 0.002 TYR A 434 ARG 0.008 0.001 ARG A 326 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 66) link_NAG-ASN : angle 2.23509 ( 198) link_ALPHA1-6 : bond 0.00264 ( 3) link_ALPHA1-6 : angle 1.84204 ( 9) link_BETA1-4 : bond 0.00735 ( 30) link_BETA1-4 : angle 2.98618 ( 90) link_ALPHA1-3 : bond 0.00753 ( 3) link_ALPHA1-3 : angle 1.70576 ( 9) hydrogen bonds : bond 0.04289 ( 524) hydrogen bonds : angle 5.16418 ( 1413) link_BETA1-6 : bond 0.00907 ( 1) link_BETA1-6 : angle 1.10117 ( 3) SS BOND : bond 0.00453 ( 32) SS BOND : angle 1.95145 ( 64) covalent geometry : bond 0.00575 (16855) covalent geometry : angle 0.69650 (22920) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 210 time to evaluate : 1.722 Fit side-chains REVERT: A 177 ASN cc_start: 0.7390 (t0) cc_final: 0.6851 (p0) REVERT: A 376 ASN cc_start: 0.8381 (t0) cc_final: 0.7612 (p0) REVERT: B 562 GLN cc_start: 0.8477 (mm110) cc_final: 0.8147 (mm110) REVERT: B 624 ASP cc_start: 0.8118 (t0) cc_final: 0.7546 (m-30) REVERT: B 638 TYR cc_start: 0.6660 (m-80) cc_final: 0.6319 (m-10) REVERT: C 142 MET cc_start: 0.8060 (mmm) cc_final: 0.7788 (mmt) REVERT: C 145 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7606 (tp30) REVERT: C 159 ASP cc_start: 0.8277 (m-30) cc_final: 0.7868 (t0) REVERT: C 485 TYR cc_start: 0.8969 (m-80) cc_final: 0.8680 (m-80) REVERT: C 493 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8837 (tt) outliers start: 43 outliers final: 36 residues processed: 238 average time/residue: 0.2828 time to fit residues: 102.3007 Evaluate side-chains 234 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 197 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 627 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 113 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 180 optimal weight: 0.0770 chunk 122 optimal weight: 0.8980 chunk 123 optimal weight: 0.5980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS C 195 ASN D 564 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.126138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.111074 restraints weight = 26898.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.111853 restraints weight = 21693.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.111968 restraints weight = 19513.487| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16990 Z= 0.123 Angle : 0.646 11.516 23293 Z= 0.301 Chirality : 0.044 0.248 2941 Planarity : 0.003 0.043 2805 Dihedral : 6.472 56.013 4271 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.15 % Allowed : 15.62 % Favored : 82.23 % 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: 0.03 (0.20), residues: 1748 helix: 1.51 (0.26), residues: 436 sheet: -0.39 (0.24), residues: 462 loop : -0.44 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 596 HIS 0.005 0.001 HIS B 564 PHE 0.026 0.001 PHE D 522 TYR 0.018 0.001 TYR E 217 ARG 0.011 0.000 ARG A 326 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 66) link_NAG-ASN : angle 2.01461 ( 198) link_ALPHA1-6 : bond 0.00342 ( 3) link_ALPHA1-6 : angle 1.74357 ( 9) link_BETA1-4 : bond 0.00783 ( 30) link_BETA1-4 : angle 2.78601 ( 90) link_ALPHA1-3 : bond 0.00890 ( 3) link_ALPHA1-3 : angle 1.50220 ( 9) hydrogen bonds : bond 0.03691 ( 524) hydrogen bonds : angle 4.93044 ( 1413) link_BETA1-6 : bond 0.00923 ( 1) link_BETA1-6 : angle 0.70036 ( 3) SS BOND : bond 0.00363 ( 32) SS BOND : angle 1.46135 ( 64) covalent geometry : bond 0.00275 (16855) covalent geometry : angle 0.59250 (22920) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 220 time to evaluate : 1.697 Fit side-chains revert: symmetry clash REVERT: A 177 ASN cc_start: 0.7341 (t0) cc_final: 0.6787 (p0) REVERT: A 376 ASN cc_start: 0.8347 (t0) cc_final: 0.7458 (p0) REVERT: B 562 GLN cc_start: 0.8324 (mm110) cc_final: 0.8067 (mm110) REVERT: B 596 TRP cc_start: 0.8953 (m-10) cc_final: 0.8674 (m-10) REVERT: B 624 ASP cc_start: 0.8029 (t0) cc_final: 0.7624 (m-30) REVERT: B 638 TYR cc_start: 0.6551 (m-80) cc_final: 0.6118 (m-10) REVERT: C 42 VAL cc_start: 0.9043 (OUTLIER) cc_final: 0.8798 (p) REVERT: C 61 TYR cc_start: 0.7028 (OUTLIER) cc_final: 0.6019 (m-80) REVERT: C 142 MET cc_start: 0.7997 (mmm) cc_final: 0.7646 (tpt) REVERT: C 145 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7560 (tp30) REVERT: C 159 ASP cc_start: 0.8219 (m-30) cc_final: 0.7825 (t0) REVERT: C 485 TYR cc_start: 0.8859 (m-80) cc_final: 0.8585 (m-80) REVERT: D 584 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7214 (mp0) REVERT: F 565 LEU cc_start: 0.7144 (mt) cc_final: 0.6912 (mt) outliers start: 34 outliers final: 29 residues processed: 238 average time/residue: 0.2850 time to fit residues: 103.5025 Evaluate side-chains 238 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 207 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 61 TYR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 615 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 119 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS C 195 ASN D 564 HIS D 575 GLN E 355 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.123743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.108674 restraints weight = 27148.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.109470 restraints weight = 22123.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.110442 restraints weight = 18687.451| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 16990 Z= 0.199 Angle : 0.699 11.663 23293 Z= 0.325 Chirality : 0.046 0.248 2941 Planarity : 0.004 0.059 2805 Dihedral : 6.602 54.604 4271 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.53 % Allowed : 16.32 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.20), residues: 1748 helix: 1.36 (0.25), residues: 443 sheet: -0.43 (0.24), residues: 452 loop : -0.49 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 596 HIS 0.005 0.001 HIS B 564 PHE 0.029 0.002 PHE E 53 TYR 0.025 0.002 TYR E 217 ARG 0.010 0.000 ARG A 326 Details of bonding type rmsd link_NAG-ASN : bond 0.00362 ( 66) link_NAG-ASN : angle 2.09710 ( 198) link_ALPHA1-6 : bond 0.00289 ( 3) link_ALPHA1-6 : angle 1.84765 ( 9) link_BETA1-4 : bond 0.00735 ( 30) link_BETA1-4 : angle 2.88068 ( 90) link_ALPHA1-3 : bond 0.00766 ( 3) link_ALPHA1-3 : angle 1.57717 ( 9) hydrogen bonds : bond 0.04002 ( 524) hydrogen bonds : angle 4.98992 ( 1413) link_BETA1-6 : bond 0.00882 ( 1) link_BETA1-6 : angle 0.96368 ( 3) SS BOND : bond 0.00435 ( 32) SS BOND : angle 1.41752 ( 64) covalent geometry : bond 0.00468 (16855) covalent geometry : angle 0.64664 (22920) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 206 time to evaluate : 2.000 Fit side-chains revert: symmetry clash REVERT: A 177 ASN cc_start: 0.7349 (t0) cc_final: 0.6811 (p0) REVERT: A 376 ASN cc_start: 0.8314 (t0) cc_final: 0.7545 (p0) REVERT: B 562 GLN cc_start: 0.8337 (mm110) cc_final: 0.8116 (mm110) REVERT: B 624 ASP cc_start: 0.8017 (t0) cc_final: 0.7573 (m-30) REVERT: B 638 TYR cc_start: 0.6602 (m-80) cc_final: 0.6216 (m-10) REVERT: C 142 MET cc_start: 0.8052 (mmm) cc_final: 0.7585 (mmt) REVERT: C 159 ASP cc_start: 0.8241 (m-30) cc_final: 0.7837 (t0) REVERT: C 269 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7524 (tt0) REVERT: C 485 TYR cc_start: 0.8930 (m-80) cc_final: 0.8622 (m-80) REVERT: D 535 MET cc_start: 0.7796 (mmp) cc_final: 0.7530 (mmt) REVERT: D 584 GLU cc_start: 0.7508 (mt-10) cc_final: 0.6646 (mp0) REVERT: E 50 THR cc_start: 0.9092 (t) cc_final: 0.8838 (m) REVERT: F 565 LEU cc_start: 0.7304 (mt) cc_final: 0.7066 (mt) REVERT: F 579 ARG cc_start: 0.8797 (mtp85) cc_final: 0.8270 (mtp-110) outliers start: 40 outliers final: 35 residues processed: 232 average time/residue: 0.2722 time to fit residues: 96.7638 Evaluate side-chains 234 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 198 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 615 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 8 optimal weight: 9.9990 chunk 181 optimal weight: 0.8980 chunk 97 optimal weight: 0.0770 chunk 13 optimal weight: 9.9990 chunk 156 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 190 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS C 195 ASN D 564 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.124533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.109407 restraints weight = 27099.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.110833 restraints weight = 20703.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.111997 restraints weight = 17147.105| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16990 Z= 0.165 Angle : 0.675 12.467 23293 Z= 0.313 Chirality : 0.045 0.245 2941 Planarity : 0.003 0.043 2805 Dihedral : 6.477 57.232 4271 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.28 % Allowed : 16.26 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.20), residues: 1748 helix: 1.40 (0.25), residues: 443 sheet: -0.35 (0.25), residues: 455 loop : -0.54 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 596 HIS 0.005 0.001 HIS B 564 PHE 0.038 0.002 PHE D 522 TYR 0.018 0.002 TYR A 434 ARG 0.008 0.000 ARG A 326 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 66) link_NAG-ASN : angle 2.04560 ( 198) link_ALPHA1-6 : bond 0.00354 ( 3) link_ALPHA1-6 : angle 1.82272 ( 9) link_BETA1-4 : bond 0.00748 ( 30) link_BETA1-4 : angle 2.81681 ( 90) link_ALPHA1-3 : bond 0.00776 ( 3) link_ALPHA1-3 : angle 1.49970 ( 9) hydrogen bonds : bond 0.03866 ( 524) hydrogen bonds : angle 4.89947 ( 1413) link_BETA1-6 : bond 0.00893 ( 1) link_BETA1-6 : angle 0.85631 ( 3) SS BOND : bond 0.00368 ( 32) SS BOND : angle 1.30978 ( 64) covalent geometry : bond 0.00385 (16855) covalent geometry : angle 0.62290 (22920) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 210 time to evaluate : 2.716 Fit side-chains revert: symmetry clash REVERT: A 177 ASN cc_start: 0.7331 (t0) cc_final: 0.6842 (p0) REVERT: A 376 ASN cc_start: 0.8336 (t0) cc_final: 0.7568 (p0) REVERT: A 474 MET cc_start: 0.7624 (mmm) cc_final: 0.7119 (mmm) REVERT: B 596 TRP cc_start: 0.8938 (m-10) cc_final: 0.8648 (m-10) REVERT: B 624 ASP cc_start: 0.7993 (t0) cc_final: 0.7586 (m-30) REVERT: B 638 TYR cc_start: 0.6579 (m-80) cc_final: 0.6223 (m-10) REVERT: B 647 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6764 (mt-10) REVERT: C 142 MET cc_start: 0.7992 (mmm) cc_final: 0.7632 (mmt) REVERT: C 159 ASP cc_start: 0.8186 (m-30) cc_final: 0.7814 (t0) REVERT: C 485 TYR cc_start: 0.8904 (m-80) cc_final: 0.8588 (m-80) REVERT: D 535 MET cc_start: 0.7782 (mmp) cc_final: 0.7539 (mmt) REVERT: D 584 GLU cc_start: 0.7505 (mt-10) cc_final: 0.6593 (mp0) REVERT: E 50 THR cc_start: 0.9077 (t) cc_final: 0.8834 (m) REVERT: F 565 LEU cc_start: 0.7153 (mt) cc_final: 0.6923 (mt) REVERT: F 579 ARG cc_start: 0.8852 (mtp85) cc_final: 0.8273 (mtp-110) outliers start: 36 outliers final: 34 residues processed: 233 average time/residue: 0.3099 time to fit residues: 109.5603 Evaluate side-chains 239 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 205 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 615 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 109 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 chunk 100 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS C 195 ASN D 564 HIS D 630 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.124046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.108701 restraints weight = 27413.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.110198 restraints weight = 21062.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.111323 restraints weight = 17517.316| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16990 Z= 0.170 Angle : 0.679 12.261 23293 Z= 0.317 Chirality : 0.045 0.250 2941 Planarity : 0.003 0.048 2805 Dihedral : 6.429 56.726 4271 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.40 % Allowed : 16.51 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.20), residues: 1748 helix: 1.39 (0.25), residues: 444 sheet: -0.36 (0.25), residues: 452 loop : -0.55 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 596 HIS 0.005 0.001 HIS B 564 PHE 0.040 0.002 PHE D 522 TYR 0.019 0.002 TYR E 217 ARG 0.009 0.000 ARG A 326 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 66) link_NAG-ASN : angle 2.03758 ( 198) link_ALPHA1-6 : bond 0.00359 ( 3) link_ALPHA1-6 : angle 1.84465 ( 9) link_BETA1-4 : bond 0.00741 ( 30) link_BETA1-4 : angle 2.81321 ( 90) link_ALPHA1-3 : bond 0.00758 ( 3) link_ALPHA1-3 : angle 1.48955 ( 9) hydrogen bonds : bond 0.03909 ( 524) hydrogen bonds : angle 4.90692 ( 1413) link_BETA1-6 : bond 0.00890 ( 1) link_BETA1-6 : angle 0.88298 ( 3) SS BOND : bond 0.00368 ( 32) SS BOND : angle 1.23826 ( 64) covalent geometry : bond 0.00396 (16855) covalent geometry : angle 0.62895 (22920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5023.92 seconds wall clock time: 91 minutes 41.27 seconds (5501.27 seconds total)