Starting phenix.real_space_refine on Thu Sep 18 12:22:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9axd_43935/09_2025/9axd_43935.cif Found real_map, /net/cci-nas-00/data/ceres_data/9axd_43935/09_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_43935/09_2025/9axd_43935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9axd_43935/09_2025/9axd_43935.map" model { file = "/net/cci-nas-00/data/ceres_data/9axd_43935/09_2025/9axd_43935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9axd_43935/09_2025/9axd_43935.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.57, per 1000 atoms: 0.22 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: 1.50 Conformation dependent library (CDL) restraints added in 576.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.60 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: 2.70 Time building geometry restraints manager: 1.95 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 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: 3.820 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.550 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.640 ------------------------------------------------------------------------------- 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 : 4.45 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG C 308 TYR 0.016 0.001 TYR A 191 PHE 0.011 0.002 PHE E 53 TRP 0.009 0.001 TRP B 623 HIS 0.005 0.001 HIS B 564 Details of bonding type rmsd covalent geometry : bond 0.00592 (16855) covalent geometry : angle 0.82082 (22920) SS BOND : bond 0.08043 ( 32) SS BOND : angle 3.89244 ( 64) hydrogen bonds : bond 0.19074 ( 524) hydrogen bonds : angle 7.39518 ( 1413) link_ALPHA1-3 : bond 0.00430 ( 3) link_ALPHA1-3 : angle 2.33547 ( 9) 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_BETA1-6 : bond 0.01255 ( 1) link_BETA1-6 : angle 1.47332 ( 3) link_NAG-ASN : bond 0.00774 ( 66) link_NAG-ASN : angle 2.38506 ( 198) *********************** 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 : 0.609 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: 0.8634 (ttt) REVERT: A 177 ASN cc_start: 0.7172 (t0) cc_final: 0.6712 (p0) REVERT: A 376 ASN cc_start: 0.8559 (t0) cc_final: 0.7212 (p0) REVERT: A 473 ASP cc_start: 0.7999 (t0) cc_final: 0.7745 (t0) REVERT: B 571 TRP cc_start: 0.8106 (m100) cc_final: 0.7699 (m100) REVERT: B 617 ARG cc_start: 0.7174 (mtp180) cc_final: 0.6754 (mtt-85) REVERT: B 624 ASP cc_start: 0.8010 (t0) cc_final: 0.7585 (t0) REVERT: B 626 MET cc_start: 0.7705 (ttp) cc_final: 0.7113 (ttm) REVERT: B 630 GLN cc_start: 0.8617 (mt0) cc_final: 0.8119 (tt0) REVERT: C 97 LYS cc_start: 0.8272 (mmtt) cc_final: 0.8061 (tptt) REVERT: C 142 MET cc_start: 0.7794 (mmm) cc_final: 0.7414 (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: 0.8885 (m-10) REVERT: D 584 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7517 (mt-10) REVERT: E 35 TRP cc_start: 0.7842 (m100) cc_final: 0.7527 (m-10) REVERT: E 102 GLU cc_start: 0.8209 (tp30) cc_final: 0.7870 (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: 0.8371 (tmtt) REVERT: E 209 SER cc_start: 0.9121 (t) cc_final: 0.8776 (m) REVERT: E 474 MET cc_start: 0.7765 (mmm) cc_final: 0.7509 (mmt) REVERT: F 627 THR cc_start: 0.9062 (p) cc_final: 0.8128 (p) outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.1273 time to fit residues: 77.2810 Evaluate side-chains 209 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 424 ASN C 477 ASN D 543 ASN D 564 HIS E 287 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.129797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.114009 restraints weight = 26374.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.115801 restraints weight = 19625.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.117002 restraints weight = 15940.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.118007 restraints weight = 13719.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.118653 restraints weight = 12243.884| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16990 Z= 0.155 Angle : 0.701 12.539 23293 Z= 0.326 Chirality : 0.046 0.321 2941 Planarity : 0.004 0.040 2805 Dihedral : 9.445 75.195 4271 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.96 % Allowed : 9.17 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.20), residues: 1748 helix: 1.70 (0.26), residues: 435 sheet: -0.33 (0.23), residues: 480 loop : -0.06 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 585 TYR 0.027 0.002 TYR E 485 PHE 0.010 0.002 PHE C 168 TRP 0.014 0.001 TRP D 596 HIS 0.005 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00345 (16855) covalent geometry : angle 0.64385 (22920) SS BOND : bond 0.00306 ( 32) SS BOND : angle 1.17988 ( 64) hydrogen bonds : bond 0.04602 ( 524) hydrogen bonds : angle 5.59434 ( 1413) link_ALPHA1-3 : bond 0.00819 ( 3) link_ALPHA1-3 : angle 1.85658 ( 9) link_ALPHA1-6 : bond 0.00580 ( 3) link_ALPHA1-6 : angle 1.59443 ( 9) link_BETA1-4 : bond 0.00817 ( 30) link_BETA1-4 : angle 3.04940 ( 90) link_BETA1-6 : bond 0.00799 ( 1) link_BETA1-6 : angle 0.77622 ( 3) link_NAG-ASN : bond 0.00383 ( 66) link_NAG-ASN : angle 2.19622 ( 198) *********************** 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 286 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 255 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ASN cc_start: 0.7056 (t0) cc_final: 0.6662 (p0) REVERT: A 376 ASN cc_start: 0.8474 (t0) cc_final: 0.7065 (p0) REVERT: B 566 LEU cc_start: 0.8677 (mt) cc_final: 0.7793 (tp) REVERT: B 596 TRP cc_start: 0.9155 (m-10) cc_final: 0.8907 (m-10) REVERT: B 624 ASP cc_start: 0.8128 (t0) cc_final: 0.7367 (m-30) REVERT: B 638 TYR cc_start: 0.6729 (m-80) cc_final: 0.6109 (m-10) REVERT: B 647 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6839 (mt-10) REVERT: C 159 ASP cc_start: 0.8231 (m-30) cc_final: 0.7864 (t0) REVERT: C 376 ASN cc_start: 0.8453 (t0) cc_final: 0.8141 (t0) REVERT: C 485 TYR cc_start: 0.9152 (m-80) cc_final: 0.8865 (m-80) REVERT: E 35 TRP cc_start: 0.7737 (m100) cc_final: 0.7327 (m100) REVERT: E 209 SER cc_start: 0.9170 (t) cc_final: 0.8826 (m) REVERT: E 217 TYR cc_start: 0.8707 (m-80) cc_final: 0.7702 (m-80) REVERT: E 367 ASP cc_start: 0.7274 (p0) cc_final: 0.7034 (p0) REVERT: E 474 MET cc_start: 0.7779 (mmm) cc_final: 0.7578 (mmt) REVERT: F 534 SER cc_start: 0.8962 (m) cc_final: 0.8608 (p) outliers start: 31 outliers final: 16 residues processed: 273 average time/residue: 0.1177 time to fit residues: 48.8772 Evaluate side-chains 211 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 195 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 324 ASP 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 296 CYS Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain D residue 542 ARG 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 358 ILE 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 112 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN C 477 ASN D 543 ASN D 564 HIS ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 ASN E 373 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.126699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.110970 restraints weight = 26871.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.112600 restraints weight = 20500.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.113800 restraints weight = 16942.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114655 restraints weight = 14730.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.114961 restraints weight = 13275.972| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16990 Z= 0.188 Angle : 0.689 9.924 23293 Z= 0.322 Chirality : 0.047 0.374 2941 Planarity : 0.004 0.037 2805 Dihedral : 8.093 57.128 4271 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.78 % Allowed : 9.99 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.20), residues: 1748 helix: 1.61 (0.26), residues: 436 sheet: -0.39 (0.23), residues: 473 loop : -0.18 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 326 TYR 0.027 0.002 TYR E 485 PHE 0.037 0.002 PHE E 53 TRP 0.011 0.001 TRP A 96 HIS 0.004 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00436 (16855) covalent geometry : angle 0.63531 (22920) SS BOND : bond 0.00398 ( 32) SS BOND : angle 1.11520 ( 64) hydrogen bonds : bond 0.04395 ( 524) hydrogen bonds : angle 5.23753 ( 1413) link_ALPHA1-3 : bond 0.00757 ( 3) link_ALPHA1-3 : angle 1.61228 ( 9) link_ALPHA1-6 : bond 0.00239 ( 3) link_ALPHA1-6 : angle 2.49741 ( 9) link_BETA1-4 : bond 0.00818 ( 30) link_BETA1-4 : angle 2.97818 ( 90) link_BETA1-6 : bond 0.00869 ( 1) link_BETA1-6 : angle 0.81461 ( 3) link_NAG-ASN : bond 0.00428 ( 66) link_NAG-ASN : angle 2.08318 ( 198) *********************** 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 256 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 212 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 177 ASN cc_start: 0.7119 (t0) cc_final: 0.6662 (p0) REVERT: A 376 ASN cc_start: 0.8366 (t0) cc_final: 0.7027 (p0) REVERT: A 434 TYR cc_start: 0.8827 (t80) cc_final: 0.8536 (t80) REVERT: A 441 VAL cc_start: 0.9551 (t) cc_final: 0.9323 (p) REVERT: B 562 GLN cc_start: 0.8584 (mm110) cc_final: 0.8323 (mm110) REVERT: B 566 LEU cc_start: 0.8663 (mt) cc_final: 0.7784 (tp) REVERT: B 624 ASP cc_start: 0.8174 (t0) cc_final: 0.7397 (m-30) REVERT: B 638 TYR cc_start: 0.6317 (m-80) cc_final: 0.6030 (m-10) REVERT: B 647 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6956 (mt-10) REVERT: C 61 TYR cc_start: 0.6897 (OUTLIER) cc_final: 0.5857 (m-80) REVERT: C 142 MET cc_start: 0.8008 (mmm) cc_final: 0.7653 (mmt) REVERT: C 145 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7381 (tp30) REVERT: C 159 ASP cc_start: 0.8215 (m-30) cc_final: 0.7849 (t0) REVERT: C 485 TYR cc_start: 0.9075 (m-80) cc_final: 0.8822 (m-80) REVERT: D 584 GLU cc_start: 0.7499 (mt-10) cc_final: 0.6970 (mt-10) REVERT: E 209 SER cc_start: 0.9169 (t) cc_final: 0.8819 (m) REVERT: E 474 MET cc_start: 0.7736 (mmm) cc_final: 0.7532 (mmt) REVERT: F 579 ARG cc_start: 0.8877 (mtp85) cc_final: 0.8596 (mtp85) outliers start: 44 outliers final: 29 residues processed: 241 average time/residue: 0.1086 time to fit residues: 39.8106 Evaluate side-chains 228 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 172 ASP Chi-restraints excluded: chain A residue 201 ILE 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 A residue 466 THR Chi-restraints excluded: chain B residue 606 THR 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 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 D residue 661 LEU 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 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 Chi-restraints excluded: chain F residue 648 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 188 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 195 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 C 477 ASN E 477 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.123423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.108149 restraints weight = 27029.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.109681 restraints weight = 20549.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.110811 restraints weight = 17023.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.111428 restraints weight = 14821.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.112098 restraints weight = 13497.547| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 16990 Z= 0.241 Angle : 0.744 15.706 23293 Z= 0.343 Chirality : 0.047 0.248 2941 Planarity : 0.004 0.045 2805 Dihedral : 7.693 54.304 4271 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.23 % Allowed : 11.39 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.20), residues: 1748 helix: 1.42 (0.25), residues: 441 sheet: -0.56 (0.23), residues: 472 loop : -0.40 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 326 TYR 0.031 0.002 TYR E 485 PHE 0.031 0.002 PHE E 53 TRP 0.012 0.002 TRP E 337 HIS 0.006 0.002 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00564 (16855) covalent geometry : angle 0.68162 (22920) SS BOND : bond 0.00561 ( 32) SS BOND : angle 1.22653 ( 64) hydrogen bonds : bond 0.04420 ( 524) hydrogen bonds : angle 5.21661 ( 1413) link_ALPHA1-3 : bond 0.00758 ( 3) link_ALPHA1-3 : angle 1.86467 ( 9) link_ALPHA1-6 : bond 0.00225 ( 3) link_ALPHA1-6 : angle 1.89726 ( 9) link_BETA1-4 : bond 0.00772 ( 30) link_BETA1-4 : angle 2.99790 ( 90) link_BETA1-6 : bond 0.00885 ( 1) link_BETA1-6 : angle 0.94971 ( 3) link_NAG-ASN : bond 0.00502 ( 66) link_NAG-ASN : angle 2.53127 ( 198) *********************** 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 275 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 224 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 177 ASN cc_start: 0.7071 (t0) cc_final: 0.6654 (p0) REVERT: A 376 ASN cc_start: 0.8371 (t0) cc_final: 0.7263 (p0) REVERT: A 441 VAL cc_start: 0.9573 (t) cc_final: 0.9367 (p) REVERT: B 562 GLN cc_start: 0.8452 (mm110) cc_final: 0.8109 (mm110) REVERT: B 624 ASP cc_start: 0.8184 (t0) cc_final: 0.7411 (m-30) REVERT: B 638 TYR cc_start: 0.6419 (m-80) cc_final: 0.6154 (m-10) REVERT: B 647 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6974 (mt-10) REVERT: C 61 TYR cc_start: 0.6850 (OUTLIER) cc_final: 0.5878 (m-80) REVERT: C 145 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7558 (tp30) REVERT: C 159 ASP cc_start: 0.8294 (m-30) cc_final: 0.7859 (t0) REVERT: C 485 TYR cc_start: 0.9065 (m-80) cc_final: 0.8766 (m-80) REVERT: C 493 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8828 (tt) REVERT: D 584 GLU cc_start: 0.7384 (mt-10) cc_final: 0.6903 (mt-10) REVERT: E 122 LEU cc_start: 0.9243 (mm) cc_final: 0.8799 (tt) REVERT: F 585 ARG cc_start: 0.8336 (tmm160) cc_final: 0.7928 (mtm110) outliers start: 51 outliers final: 38 residues processed: 253 average time/residue: 0.1081 time to fit residues: 41.7638 Evaluate side-chains 248 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 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 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 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 576 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 358 ILE 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 620 SER Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 648 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 151 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 105 optimal weight: 0.3980 chunk 89 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 477 ASN D 543 ASN D 564 HIS E 66 HIS E 114 GLN E 410 ASN E 424 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.126170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.110527 restraints weight = 26951.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.112011 restraints weight = 20708.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.113237 restraints weight = 17261.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.114059 restraints weight = 15064.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.114444 restraints weight = 13625.881| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16990 Z= 0.135 Angle : 0.650 10.666 23293 Z= 0.300 Chirality : 0.044 0.245 2941 Planarity : 0.003 0.056 2805 Dihedral : 6.970 54.396 4271 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.09 % Allowed : 14.17 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.20), residues: 1748 helix: 1.66 (0.26), residues: 430 sheet: -0.35 (0.24), residues: 456 loop : -0.39 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 326 TYR 0.034 0.002 TYR E 485 PHE 0.030 0.001 PHE E 53 TRP 0.022 0.001 TRP E 35 HIS 0.007 0.001 HIS B 564 Details of bonding type rmsd covalent geometry : bond 0.00305 (16855) covalent geometry : angle 0.59029 (22920) SS BOND : bond 0.00414 ( 32) SS BOND : angle 1.30954 ( 64) hydrogen bonds : bond 0.03835 ( 524) hydrogen bonds : angle 4.95489 ( 1413) link_ALPHA1-3 : bond 0.00925 ( 3) link_ALPHA1-3 : angle 1.64945 ( 9) link_ALPHA1-6 : bond 0.00201 ( 3) link_ALPHA1-6 : angle 1.76205 ( 9) link_BETA1-4 : bond 0.00785 ( 30) link_BETA1-4 : angle 2.84028 ( 90) link_BETA1-6 : bond 0.00906 ( 1) link_BETA1-6 : angle 0.74189 ( 3) link_NAG-ASN : bond 0.00385 ( 66) link_NAG-ASN : angle 2.19625 ( 198) *********************** 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 257 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 224 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: A 177 ASN cc_start: 0.7065 (t0) cc_final: 0.6626 (p0) REVERT: A 376 ASN cc_start: 0.8304 (t0) cc_final: 0.7322 (p0) REVERT: A 441 VAL cc_start: 0.9559 (t) cc_final: 0.9358 (p) REVERT: B 562 GLN cc_start: 0.8363 (mm110) cc_final: 0.8124 (mm110) REVERT: B 624 ASP cc_start: 0.8059 (t0) cc_final: 0.7404 (m-30) REVERT: B 638 TYR cc_start: 0.6403 (m-80) cc_final: 0.6079 (m-10) REVERT: C 61 TYR cc_start: 0.6816 (OUTLIER) cc_final: 0.5806 (m-80) REVERT: C 142 MET cc_start: 0.7952 (mmm) cc_final: 0.7494 (tpt) REVERT: C 145 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7459 (tp30) REVERT: C 159 ASP cc_start: 0.8208 (m-30) cc_final: 0.7835 (t0) REVERT: C 485 TYR cc_start: 0.8936 (m-80) cc_final: 0.8649 (m-80) REVERT: D 522 PHE cc_start: 0.8504 (t80) cc_final: 0.8140 (t80) REVERT: D 633 LYS cc_start: 0.7566 (mmtm) cc_final: 0.7355 (mmtm) REVERT: E 217 TYR cc_start: 0.8487 (m-80) cc_final: 0.7676 (m-80) outliers start: 33 outliers final: 23 residues processed: 238 average time/residue: 0.1126 time to fit residues: 40.6169 Evaluate side-chains 231 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 372 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 296 CYS Chi-restraints excluded: chain C residue 297 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 E residue 236 THR Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 648 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 56 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 477 ASN D 564 HIS E 114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.119691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.103414 restraints weight = 27979.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.105178 restraints weight = 20748.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.106434 restraints weight = 16801.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.107275 restraints weight = 14493.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.107914 restraints weight = 13018.178| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 16990 Z= 0.356 Angle : 0.881 11.436 23293 Z= 0.408 Chirality : 0.051 0.252 2941 Planarity : 0.005 0.078 2805 Dihedral : 7.744 55.943 4271 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.54 % Allowed : 14.55 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.20), residues: 1748 helix: 1.02 (0.25), residues: 442 sheet: -0.72 (0.24), residues: 454 loop : -0.75 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 326 TYR 0.029 0.003 TYR E 217 PHE 0.032 0.003 PHE E 53 TRP 0.021 0.002 TRP E 35 HIS 0.007 0.002 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00839 (16855) covalent geometry : angle 0.82765 (22920) SS BOND : bond 0.00666 ( 32) SS BOND : angle 1.45777 ( 64) hydrogen bonds : bond 0.04976 ( 524) hydrogen bonds : angle 5.48933 ( 1413) link_ALPHA1-3 : bond 0.00640 ( 3) link_ALPHA1-3 : angle 1.85766 ( 9) link_ALPHA1-6 : bond 0.00294 ( 3) link_ALPHA1-6 : angle 1.94338 ( 9) link_BETA1-4 : bond 0.00741 ( 30) link_BETA1-4 : angle 3.19369 ( 90) link_BETA1-6 : bond 0.00885 ( 1) link_BETA1-6 : angle 1.33467 ( 3) link_NAG-ASN : bond 0.00590 ( 66) link_NAG-ASN : angle 2.51131 ( 198) *********************** 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 271 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 215 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 ASN cc_start: 0.7504 (t0) cc_final: 0.6940 (p0) REVERT: A 376 ASN cc_start: 0.8452 (t0) cc_final: 0.7395 (p0) REVERT: A 474 MET cc_start: 0.7886 (mmm) cc_final: 0.7220 (mmt) REVERT: B 562 GLN cc_start: 0.8490 (mm110) cc_final: 0.8204 (mm110) REVERT: B 624 ASP cc_start: 0.8245 (t0) cc_final: 0.7558 (m-30) REVERT: B 638 TYR cc_start: 0.6791 (m-80) cc_final: 0.6280 (m-10) REVERT: C 34 LEU cc_start: 0.8511 (mm) cc_final: 0.8224 (mp) REVERT: C 142 MET cc_start: 0.7952 (mmm) cc_final: 0.7560 (tpt) REVERT: C 145 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7773 (tp30) REVERT: C 159 ASP cc_start: 0.8481 (m-30) cc_final: 0.7958 (t0) REVERT: C 269 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7529 (tt0) REVERT: C 485 TYR cc_start: 0.9107 (m-80) cc_final: 0.8747 (m-80) REVERT: C 493 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8961 (tt) REVERT: D 633 LYS cc_start: 0.7826 (mmtm) cc_final: 0.7591 (mmtm) outliers start: 56 outliers final: 39 residues processed: 252 average time/residue: 0.1150 time to fit residues: 43.8564 Evaluate side-chains 237 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 196 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 172 ASP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 393 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 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 165 TYR 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 372 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 D residue 661 LEU Chi-restraints excluded: chain E residue 66 HIS 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 528 SER Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 620 SER Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 648 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 162 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 477 ASN D 543 ASN D 564 HIS E 287 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.123187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.107777 restraints weight = 27076.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.109326 restraints weight = 20798.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.110442 restraints weight = 17317.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.111063 restraints weight = 15176.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.111684 restraints weight = 13855.911| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16990 Z= 0.145 Angle : 0.683 10.994 23293 Z= 0.316 Chirality : 0.045 0.249 2941 Planarity : 0.003 0.041 2805 Dihedral : 7.031 58.631 4271 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.40 % Allowed : 15.94 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.20), residues: 1748 helix: 1.30 (0.25), residues: 441 sheet: -0.59 (0.24), residues: 452 loop : -0.56 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 326 TYR 0.030 0.002 TYR E 485 PHE 0.029 0.001 PHE E 53 TRP 0.019 0.001 TRP D 596 HIS 0.006 0.001 HIS B 564 Details of bonding type rmsd covalent geometry : bond 0.00331 (16855) covalent geometry : angle 0.62480 (22920) SS BOND : bond 0.00324 ( 32) SS BOND : angle 1.77789 ( 64) hydrogen bonds : bond 0.04015 ( 524) hydrogen bonds : angle 5.08516 ( 1413) link_ALPHA1-3 : bond 0.00841 ( 3) link_ALPHA1-3 : angle 1.57403 ( 9) link_ALPHA1-6 : bond 0.00312 ( 3) link_ALPHA1-6 : angle 1.73679 ( 9) link_BETA1-4 : bond 0.00769 ( 30) link_BETA1-4 : angle 2.88570 ( 90) link_BETA1-6 : bond 0.00982 ( 1) link_BETA1-6 : angle 0.85640 ( 3) link_NAG-ASN : bond 0.00341 ( 66) link_NAG-ASN : angle 2.15894 ( 198) *********************** 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 247 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 209 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 177 ASN cc_start: 0.7299 (t0) cc_final: 0.6804 (p0) REVERT: A 376 ASN cc_start: 0.8355 (t0) cc_final: 0.7554 (p0) REVERT: B 624 ASP cc_start: 0.8117 (t0) cc_final: 0.7547 (m-30) REVERT: B 638 TYR cc_start: 0.6510 (m-80) cc_final: 0.6129 (m-10) REVERT: B 647 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6992 (mt-10) REVERT: C 34 LEU cc_start: 0.8392 (mm) cc_final: 0.8141 (mp) REVERT: C 42 VAL cc_start: 0.9126 (OUTLIER) cc_final: 0.8912 (p) REVERT: C 142 MET cc_start: 0.7919 (mmm) cc_final: 0.7572 (tpt) REVERT: C 145 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7454 (tp30) REVERT: C 159 ASP cc_start: 0.8209 (m-30) cc_final: 0.7835 (t0) REVERT: C 269 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7436 (tt0) REVERT: C 485 TYR cc_start: 0.8931 (m-80) cc_final: 0.8645 (m-80) REVERT: D 584 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7153 (mp0) REVERT: E 501 LYS cc_start: 0.6908 (ptmm) cc_final: 0.6571 (pttm) outliers start: 38 outliers final: 27 residues processed: 233 average time/residue: 0.1177 time to fit residues: 41.5770 Evaluate side-chains 229 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 172 ASP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 254 VAL 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 636 SER Chi-restraints excluded: chain B residue 641 ILE 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 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 E residue 100 MET Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 348 LEU 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 648 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 89 optimal weight: 0.6980 chunk 128 optimal weight: 0.0970 chunk 67 optimal weight: 10.0000 chunk 150 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 178 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.124369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.108929 restraints weight = 27296.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.110161 restraints weight = 21969.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.111215 restraints weight = 18198.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.111568 restraints weight = 16078.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.111726 restraints weight = 14607.595| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16990 Z= 0.145 Angle : 0.662 11.209 23293 Z= 0.306 Chirality : 0.045 0.251 2941 Planarity : 0.003 0.048 2805 Dihedral : 6.594 54.978 4271 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.53 % Allowed : 16.26 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.20), residues: 1748 helix: 1.40 (0.26), residues: 442 sheet: -0.41 (0.24), residues: 442 loop : -0.55 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 326 TYR 0.020 0.001 TYR E 485 PHE 0.031 0.002 PHE E 53 TRP 0.022 0.001 TRP D 596 HIS 0.004 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00335 (16855) covalent geometry : angle 0.60726 (22920) SS BOND : bond 0.00386 ( 32) SS BOND : angle 1.40899 ( 64) hydrogen bonds : bond 0.03815 ( 524) hydrogen bonds : angle 4.88261 ( 1413) link_ALPHA1-3 : bond 0.00803 ( 3) link_ALPHA1-3 : angle 1.50215 ( 9) link_ALPHA1-6 : bond 0.00321 ( 3) link_ALPHA1-6 : angle 1.75029 ( 9) link_BETA1-4 : bond 0.00760 ( 30) link_BETA1-4 : angle 2.84998 ( 90) link_BETA1-6 : bond 0.00915 ( 1) link_BETA1-6 : angle 0.87594 ( 3) link_NAG-ASN : bond 0.00319 ( 66) link_NAG-ASN : angle 2.06425 ( 198) *********************** 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 253 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 213 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: A 177 ASN cc_start: 0.7451 (t0) cc_final: 0.6903 (p0) REVERT: A 376 ASN cc_start: 0.8398 (t0) cc_final: 0.7591 (p0) REVERT: B 624 ASP cc_start: 0.8109 (t0) cc_final: 0.7599 (m-30) REVERT: B 638 TYR cc_start: 0.6641 (m-80) cc_final: 0.6240 (m-10) REVERT: B 647 GLU cc_start: 0.7287 (mt-10) cc_final: 0.7026 (mt-10) REVERT: C 34 LEU cc_start: 0.8389 (mm) cc_final: 0.8147 (mp) REVERT: C 142 MET cc_start: 0.7858 (mmm) cc_final: 0.7517 (tpt) REVERT: C 145 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7517 (tp30) REVERT: C 159 ASP cc_start: 0.8236 (m-30) cc_final: 0.7841 (t0) REVERT: C 269 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7371 (tt0) REVERT: C 485 TYR cc_start: 0.8942 (m-80) cc_final: 0.8594 (m-80) REVERT: D 584 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7289 (mt-10) REVERT: E 35 TRP cc_start: 0.7799 (m100) cc_final: 0.7545 (m100) REVERT: E 50 THR cc_start: 0.9088 (t) cc_final: 0.8816 (m) REVERT: F 529 THR cc_start: 0.9045 (p) cc_final: 0.8813 (t) REVERT: F 565 LEU cc_start: 0.7694 (mp) cc_final: 0.7365 (mt) outliers start: 40 outliers final: 33 residues processed: 238 average time/residue: 0.1133 time to fit residues: 41.0259 Evaluate side-chains 236 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 202 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 115 SER 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 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 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 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 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 100 MET Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 348 LEU 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 648 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 106 optimal weight: 0.9980 chunk 190 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 562 GLN ** 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.120886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.105219 restraints weight = 27928.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.106698 restraints weight = 21703.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.107793 restraints weight = 18145.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.108581 restraints weight = 15939.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.109042 restraints weight = 14506.986| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 16990 Z= 0.261 Angle : 0.777 11.491 23293 Z= 0.360 Chirality : 0.048 0.252 2941 Planarity : 0.004 0.057 2805 Dihedral : 7.060 55.710 4271 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.78 % Allowed : 16.51 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.20), residues: 1748 helix: 1.10 (0.25), residues: 449 sheet: -0.53 (0.24), residues: 451 loop : -0.68 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 326 TYR 0.027 0.002 TYR A 434 PHE 0.026 0.002 PHE E 53 TRP 0.026 0.002 TRP D 596 HIS 0.005 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00613 (16855) covalent geometry : angle 0.72417 (22920) SS BOND : bond 0.00516 ( 32) SS BOND : angle 1.53682 ( 64) hydrogen bonds : bond 0.04460 ( 524) hydrogen bonds : angle 5.15205 ( 1413) link_ALPHA1-3 : bond 0.00662 ( 3) link_ALPHA1-3 : angle 1.63362 ( 9) link_ALPHA1-6 : bond 0.00377 ( 3) link_ALPHA1-6 : angle 1.91643 ( 9) link_BETA1-4 : bond 0.00720 ( 30) link_BETA1-4 : angle 3.01235 ( 90) link_BETA1-6 : bond 0.00903 ( 1) link_BETA1-6 : angle 1.12619 ( 3) link_NAG-ASN : bond 0.00463 ( 66) link_NAG-ASN : angle 2.28149 ( 198) *********************** 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 244 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 200 time to evaluate : 0.579 Fit side-chains revert: symmetry clash REVERT: A 177 ASN cc_start: 0.7515 (t0) cc_final: 0.6953 (p0) REVERT: A 376 ASN cc_start: 0.8334 (t0) cc_final: 0.7683 (p0) REVERT: B 624 ASP cc_start: 0.8137 (t0) cc_final: 0.7561 (m-30) REVERT: B 638 TYR cc_start: 0.6688 (m-80) cc_final: 0.6277 (m-10) REVERT: C 34 LEU cc_start: 0.8495 (mm) cc_final: 0.8234 (mp) REVERT: C 142 MET cc_start: 0.7905 (mmm) cc_final: 0.7556 (tpt) REVERT: C 145 GLU cc_start: 0.8383 (tm-30) cc_final: 0.7681 (tp30) REVERT: C 159 ASP cc_start: 0.8326 (m-30) cc_final: 0.7884 (t0) REVERT: C 269 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7465 (tt0) REVERT: C 485 TYR cc_start: 0.9013 (m-80) cc_final: 0.8668 (m-80) REVERT: C 493 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8938 (tt) REVERT: D 584 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7217 (mt-10) REVERT: E 50 THR cc_start: 0.9160 (t) cc_final: 0.8872 (m) REVERT: F 534 SER cc_start: 0.9005 (m) cc_final: 0.8616 (p) REVERT: F 565 LEU cc_start: 0.7619 (mp) cc_final: 0.7289 (mt) outliers start: 44 outliers final: 34 residues processed: 234 average time/residue: 0.1191 time to fit residues: 42.0141 Evaluate side-chains 230 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 194 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 115 SER 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 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 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 173 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 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 208 VAL 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 648 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 124 optimal weight: 0.7980 chunk 174 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 186 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 F 591 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.123015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.106733 restraints weight = 27215.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.108530 restraints weight = 20096.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.109813 restraints weight = 16300.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.110586 restraints weight = 14033.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.111334 restraints weight = 12633.747| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3961 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 : 0.700 12.696 23293 Z= 0.326 Chirality : 0.046 0.254 2941 Planarity : 0.003 0.041 2805 Dihedral : 6.675 56.882 4271 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.53 % Allowed : 16.89 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.20), residues: 1748 helix: 1.25 (0.25), residues: 443 sheet: -0.51 (0.24), residues: 463 loop : -0.63 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 326 TYR 0.024 0.002 TYR E 217 PHE 0.029 0.002 PHE D 522 TRP 0.042 0.001 TRP D 596 HIS 0.005 0.001 HIS B 564 Details of bonding type rmsd covalent geometry : bond 0.00382 (16855) covalent geometry : angle 0.64872 (22920) SS BOND : bond 0.00370 ( 32) SS BOND : angle 1.25071 ( 64) hydrogen bonds : bond 0.04065 ( 524) hydrogen bonds : angle 5.00243 ( 1413) link_ALPHA1-3 : bond 0.00748 ( 3) link_ALPHA1-3 : angle 1.48248 ( 9) link_ALPHA1-6 : bond 0.00393 ( 3) link_ALPHA1-6 : angle 1.83509 ( 9) link_BETA1-4 : bond 0.00750 ( 30) link_BETA1-4 : angle 2.86853 ( 90) link_BETA1-6 : bond 0.00956 ( 1) link_BETA1-6 : angle 0.88866 ( 3) link_NAG-ASN : bond 0.00335 ( 66) link_NAG-ASN : angle 2.11283 ( 198) ********************** 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 239 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 199 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 ASN cc_start: 0.7506 (t0) cc_final: 0.6933 (p0) REVERT: A 376 ASN cc_start: 0.8335 (t0) cc_final: 0.7605 (p0) REVERT: B 624 ASP cc_start: 0.8080 (t0) cc_final: 0.7606 (m-30) REVERT: B 638 TYR cc_start: 0.6613 (m-80) cc_final: 0.6226 (m-10) REVERT: B 647 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6780 (mt-10) REVERT: C 34 LEU cc_start: 0.8462 (mm) cc_final: 0.8220 (mp) REVERT: C 142 MET cc_start: 0.7950 (mmm) cc_final: 0.7626 (tpt) REVERT: C 145 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7569 (tp30) REVERT: C 159 ASP cc_start: 0.8256 (m-30) cc_final: 0.7847 (t0) REVERT: C 269 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7425 (tt0) REVERT: C 485 TYR cc_start: 0.8952 (m-80) cc_final: 0.8653 (m-80) REVERT: C 493 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8917 (tt) REVERT: D 584 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7248 (mt-10) REVERT: E 50 THR cc_start: 0.9132 (t) cc_final: 0.8861 (m) REVERT: E 358 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8579 (tt) REVERT: F 565 LEU cc_start: 0.7571 (mp) cc_final: 0.7275 (mt) REVERT: F 579 ARG cc_start: 0.8510 (mtm110) cc_final: 0.8291 (ttm-80) outliers start: 40 outliers final: 32 residues processed: 228 average time/residue: 0.1137 time to fit residues: 39.6788 Evaluate side-chains 228 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 172 ASP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 254 VAL 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 A residue 466 THR Chi-restraints excluded: chain B residue 606 THR 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 173 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 493 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 627 THR 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 208 VAL Chi-restraints excluded: chain E residue 236 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 648 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 15 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 121 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3481 r_free = 0.3481 target = 0.124576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.108912 restraints weight = 27177.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.110456 restraints weight = 20915.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.111596 restraints weight = 17408.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.112280 restraints weight = 15252.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.112890 restraints weight = 13897.355| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16990 Z= 0.137 Angle : 0.659 12.646 23293 Z= 0.305 Chirality : 0.044 0.253 2941 Planarity : 0.003 0.040 2805 Dihedral : 6.190 56.028 4271 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.28 % Allowed : 17.46 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.20), residues: 1748 helix: 1.43 (0.26), residues: 438 sheet: -0.32 (0.24), residues: 450 loop : -0.57 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 326 TYR 0.018 0.001 TYR A 434 PHE 0.031 0.002 PHE D 522 TRP 0.041 0.001 TRP D 596 HIS 0.005 0.001 HIS B 564 Details of bonding type rmsd covalent geometry : bond 0.00315 (16855) covalent geometry : angle 0.60930 (22920) SS BOND : bond 0.00320 ( 32) SS BOND : angle 1.09146 ( 64) hydrogen bonds : bond 0.03712 ( 524) hydrogen bonds : angle 4.79864 ( 1413) link_ALPHA1-3 : bond 0.00774 ( 3) link_ALPHA1-3 : angle 1.40953 ( 9) link_ALPHA1-6 : bond 0.00425 ( 3) link_ALPHA1-6 : angle 1.83952 ( 9) link_BETA1-4 : bond 0.00756 ( 30) link_BETA1-4 : angle 2.77143 ( 90) link_BETA1-6 : bond 0.00893 ( 1) link_BETA1-6 : angle 0.79858 ( 3) link_NAG-ASN : bond 0.00301 ( 66) link_NAG-ASN : angle 1.98004 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2095.58 seconds wall clock time: 37 minutes 15.70 seconds (2235.70 seconds total)