Starting phenix.real_space_refine on Mon Jun 16 18:55:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ays_43998/06_2025/9ays_43998.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ays_43998/06_2025/9ays_43998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ays_43998/06_2025/9ays_43998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ays_43998/06_2025/9ays_43998.map" model { file = "/net/cci-nas-00/data/ceres_data/9ays_43998/06_2025/9ays_43998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ays_43998/06_2025/9ays_43998.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 11576 2.51 5 N 3229 2.21 5 O 3800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18710 Number of models: 1 Model: "" Number of chains: 40 Chain: "H" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 605 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 121} Link IDs: {'TRANS': 120} Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 121 Planarities with less than four sites: {'UNK:plan-1': 121} Unresolved non-hydrogen planarities: 121 Chain: "L" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 505 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'TRANS': 100} Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 303 Unresolved non-hydrogen dihedrals: 101 Planarities with less than four sites: {'UNK:plan-1': 101} Unresolved non-hydrogen planarities: 101 Chain: "A" Number of atoms: 3591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3591 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 20, 'TRANS': 434} 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: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3564 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 20, 'TRANS': 430} Chain breaks: 2 Chain: "D" Number of atoms: 1147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1147 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Chain: "E" Number of atoms: 3586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3586 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 20, 'TRANS': 434} Chain breaks: 2 Chain: "F" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1145 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "G" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 510 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'TRANS': 101} Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 306 Unresolved non-hydrogen dihedrals: 102 Planarities with less than four sites: {'UNK:plan-1': 102} Unresolved non-hydrogen planarities: 102 Chain: "I" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 575 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'TRANS': 114} Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 345 Unresolved non-hydrogen dihedrals: 115 Planarities with less than four sites: {'UNK:plan-1': 115} Unresolved non-hydrogen planarities: 115 Chain: "J" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 520 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'TRANS': 103} Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 312 Unresolved non-hydrogen dihedrals: 104 Planarities with less than four sites: {'UNK:plan-1': 104} Unresolved non-hydrogen planarities: 104 Chain: "K" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 470 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'TRANS': 93} Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 282 Unresolved non-hydrogen dihedrals: 94 Planarities with less than four sites: {'UNK:plan-1': 94} Unresolved non-hydrogen planarities: 94 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 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: "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: 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: "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: 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 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: "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: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 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: 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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 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: "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 Time building chain proxies: 11.72, per 1000 atoms: 0.63 Number of scatterers: 18710 At special positions: 0 Unit cell: (150.48, 155.705, 142.12, 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 3800 8.00 N 3229 7.00 C 11576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, 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=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.02 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=2.04 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 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=2.04 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=2.02 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 Q 3 " - " MAN Q 4 " " BMA W 3 " - " MAN W 4 " " BMA c 3 " - " MAN c 4 " ALPHA1-4 " BMA Q 3 " - " MAN Q 5 " ALPHA1-6 " BMA Q 3 " - " MAN Q 6 " " BMA W 3 " - " MAN W 5 " " BMA c 3 " - " MAN c 5 " BETA1-3 " NAG f 2 " - " NAG f 3 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " 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 c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " BETA1-6 " NAG O 1 " - " NAG O 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 234 " " NAG A 604 " - " ASN A 276 " " NAG A 605 " - " ASN A 301 " " NAG A 606 " - " ASN A 338 " " NAG A 607 " - " ASN A 354 " " NAG A 608 " - " ASN A 362 " " NAG A 609 " - " ASN A 391 " " NAG A 610 " - " ASN A 447 " " NAG A 611 " - " ASN A 289 " " 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 152 " " NAG C 605 " - " ASN C 276 " " NAG C 606 " - " ASN C 295 " " NAG C 607 " - " ASN C 301 " " NAG C 608 " - " ASN C 338 " " NAG C 609 " - " ASN C 354 " " NAG C 610 " - " ASN C 385 " " NAG C 611 " - " ASN C 391 " " NAG C 612 " - " ASN C 289 " " NAG C 613 " - " ASN C 234 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 618 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 152 " " NAG E 603 " - " ASN E 197 " " NAG E 604 " - " ASN E 234 " " NAG E 605 " - " ASN E 289 " " NAG E 606 " - " ASN E 295 " " NAG E 607 " - " ASN E 301 " " NAG E 608 " - " ASN E 354 " " NAG E 609 " - " ASN E 385 " " NAG E 610 " - " ASN E 447 " " NAG E 611 " - " ASN E 461 " " NAG E 612 " - " ASN E 241 " " NAG E 613 " - " ASN E 338 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG M 1 " - " ASN A 148 " " NAG N 1 " - " ASN A 152 " " NAG O 1 " - " ASN A 197 " " NAG P 1 " - " ASN A 241 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 295 " " NAG S 1 " - " ASN A 385 " " NAG T 1 " - " ASN A 331 " " NAG U 1 " - " ASN C 148 " " NAG V 1 " - " ASN C 197 " " NAG W 1 " - " ASN C 262 " " NAG X 1 " - " ASN C 331 " " NAG Y 1 " - " ASN C 362 " " NAG Z 1 " - " ASN C 447 " " NAG a 1 " - " ASN C 241 " " NAG b 1 " - " ASN D 611 " " NAG c 1 " - " ASN E 262 " " NAG d 1 " - " ASN E 276 " " NAG e 1 " - " ASN E 331 " " NAG f 1 " - " ASN E 362 " " NAG g 1 " - " ASN E 148 " " NAG h 1 " - " ASN E 391 " Time building additional restraints: 5.32 Conformation dependent library (CDL) restraints added in 1.8 seconds 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4632 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 35 sheets defined 30.7% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.773A pdb=" N UNK H 90 " --> pdb=" O UNK H 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.767A 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: 3.785A pdb=" N HIS A 351 " --> pdb=" O GLN A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 424 through 428 Processing helix chain 'A' and resid 473 through 482 removed outlier: 3.651A pdb=" N ASN A 477 " --> pdb=" O ASP A 473 " (cutoff:3.500A) removed outlier: 4.457A 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 542 Processing helix chain 'B' and resid 543 through 545 No H-bonds generated for 'chain 'B' and resid 543 through 545' Processing helix chain 'B' and resid 546 through 554 removed outlier: 4.413A pdb=" N GLN B 552 " --> pdb=" O ILE B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 568 removed outlier: 3.640A pdb=" N GLN B 562 " --> pdb=" O ALA B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 596 removed outlier: 3.518A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.024A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 334 through 350 removed outlier: 3.731A pdb=" N LYS C 350 " --> pdb=" O LYS C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'C' and resid 474 through 483 removed outlier: 3.887A pdb=" N TRP C 478 " --> pdb=" O MET C 474 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLU C 481 " --> pdb=" O ASN C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 552 removed outlier: 3.720A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE D 548 " --> pdb=" O LEU D 544 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL D 549 " --> pdb=" O LEU D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 595 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 57 through 64 Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 98 through 116 removed outlier: 4.034A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.525A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 143 removed outlier: 3.700A pdb=" N ARG E 143 " --> pdb=" O ASP E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 349 Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 367 through 372 Processing helix chain 'E' and resid 376 through 380 removed outlier: 3.824A pdb=" N GLY E 379 " --> pdb=" O ASN E 376 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU E 380 " --> pdb=" O CYS E 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 376 through 380' Processing helix chain 'E' and resid 386 through 389 Processing helix chain 'E' and resid 424 through 428 Processing helix chain 'E' and resid 473 through 482 removed outlier: 4.337A pdb=" N GLU E 481 " --> pdb=" O ASN E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 537 through 557 removed outlier: 4.032A pdb=" N LEU F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE F 548 " --> pdb=" O LEU F 544 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG F 557 " --> pdb=" O SER F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 561 through 566 Processing helix chain 'F' and resid 568 through 595 removed outlier: 3.539A pdb=" N GLY F 572 " --> pdb=" O LEU F 568 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 661 removed outlier: 3.631A pdb=" N GLN F 652 " --> pdb=" O GLU F 648 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN F 653 " --> pdb=" O SER F 649 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 81 removed outlier: 4.239A pdb=" N UNK G 81 " --> pdb=" O UNK G 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 96 No H-bonds generated for 'chain 'I' and resid 93 through 96' Processing helix chain 'K' and resid 41 through 46 removed outlier: 3.785A pdb=" N UNK K 45 " --> pdb=" O UNK K 41 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.837A pdb=" N UNK H 46 " --> pdb=" O UNK H 37 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N UNK H 37 " --> pdb=" O UNK H 46 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N UNK H 48 " --> pdb=" O UNK H 35 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N UNK H 33 " --> pdb=" O UNK H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AA4, first strand: chain 'L' and resid 12 through 13 Processing sheet with id=AA5, first strand: chain 'L' and resid 43 through 44 Processing sheet with id=AA6, first strand: chain 'A' and resid 493 through 498 removed outlier: 5.040A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.419A 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 Processing sheet with id=AA8, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.689A 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 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.841A pdb=" N THR A 202 " --> pdb=" O TYR A 434 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 310 removed outlier: 3.831A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASP A 320 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LYS A 305 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N THR A 318 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE A 307 " --> pdb=" O TYR A 316 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N TYR A 316 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE A 309 " --> pdb=" O TRP A 314 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N TRP A 314 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 313 through 322 current: chain 'A' and resid 380 through 384 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 380 through 384 current: chain 'A' and resid 464 through 469 Processing sheet with id=AB4, first strand: chain 'C' and resid 494 through 498 removed outlier: 5.526A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.878A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB7, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB8, first strand: chain 'C' and resid 161 through 169 removed outlier: 4.043A pdb=" N GLU C 190 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.613A pdb=" N THR C 202 " --> pdb=" O TYR C 434 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 302 removed outlier: 6.089A pdb=" N GLN C 293 " --> pdb=" O SER C 333 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 328 through 333 current: chain 'C' and resid 380 through 384 removed outlier: 3.876A pdb=" N PHE C 381 " --> pdb=" O LYS C 420 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 412 through 420 current: chain 'C' and resid 465 through 469 Processing sheet with id=AC2, first strand: chain 'C' and resid 304 through 310 removed outlier: 6.612A pdb=" N GLN C 313 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 493 through 498 removed outlier: 5.596A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (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 75 through 76 removed outlier: 4.242A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.649A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) 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: 6.446A pdb=" N ALA E 200 " --> pdb=" O ALA E 432 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N TYR E 434 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.560A 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 310 removed outlier: 6.876A pdb=" N ASN E 301 " --> pdb=" O ILE E 321 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ILE E 321 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR E 303 " --> pdb=" O GLY E 319 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLN E 313 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 313 through 322 current: chain 'E' and resid 381 through 384 removed outlier: 3.892A pdb=" N PHE E 381 " --> pdb=" O LYS E 420 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 412 through 420 current: chain 'E' and resid 467 through 469 Processing sheet with id=AD1, first strand: chain 'E' and resid 358 through 360 Processing sheet with id=AD2, first strand: chain 'G' and resid 21 through 22 removed outlier: 3.812A pdb=" N UNK G 62 " --> pdb=" O UNK G 72 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 44 through 46 Processing sheet with id=AD4, first strand: chain 'G' and resid 48 through 49 Processing sheet with id=AD5, first strand: chain 'I' and resid 3 through 4 removed outlier: 4.054A pdb=" N UNK I 20 " --> pdb=" O UNK I 4 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 30 through 34 Processing sheet with id=AD7, first strand: chain 'K' and resid 17 through 21 Processing sheet with id=AD8, first strand: chain 'K' and resid 79 through 81 562 hydrogen bonds defined for protein. 1524 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: 5.71 Time building geometry restraints manager: 6.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6052 1.34 - 1.46: 4219 1.46 - 1.58: 8575 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 18984 Sorted by residual: bond pdb=" C1 NAG f 2 " pdb=" O5 NAG f 2 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" N VAL C 242 " pdb=" CA VAL C 242 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.14e-02 7.69e+03 1.11e+01 bond pdb=" N ILE C 138 " pdb=" CA ILE C 138 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.15e-02 7.56e+03 1.08e+01 bond pdb=" C1 BMA M 3 " pdb=" C2 BMA M 3 " ideal model delta sigma weight residual 1.519 1.581 -0.062 2.00e-02 2.50e+03 9.72e+00 bond pdb=" C1 NAG W 2 " pdb=" O5 NAG W 2 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 9.05e+00 ... (remaining 18979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 24223 1.88 - 3.75: 1457 3.75 - 5.63: 159 5.63 - 7.50: 46 7.50 - 9.38: 9 Bond angle restraints: 25894 Sorted by residual: angle pdb=" C ALA C 48 " pdb=" N GLU C 49 " pdb=" CA GLU C 49 " ideal model delta sigma weight residual 121.94 129.69 -7.75 1.76e+00 3.23e-01 1.94e+01 angle pdb=" N GLY A 41 " pdb=" CA GLY A 41 " pdb=" C GLY A 41 " ideal model delta sigma weight residual 115.67 108.73 6.94 1.59e+00 3.96e-01 1.91e+01 angle pdb=" N SER D 553 " pdb=" CA SER D 553 " pdb=" CB SER D 553 " ideal model delta sigma weight residual 114.17 110.23 3.94 1.14e+00 7.69e-01 1.20e+01 angle pdb=" C LEU B 556 " pdb=" N ARG B 557 " pdb=" CA ARG B 557 " ideal model delta sigma weight residual 121.54 128.14 -6.60 1.91e+00 2.74e-01 1.19e+01 angle pdb=" C PHE C 233 " pdb=" N ASN C 234 " pdb=" CA ASN C 234 " ideal model delta sigma weight residual 126.45 132.48 -6.03 1.77e+00 3.19e-01 1.16e+01 ... (remaining 25889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.85: 12062 21.85 - 43.71: 516 43.71 - 65.56: 86 65.56 - 87.42: 38 87.42 - 109.27: 21 Dihedral angle restraints: 12723 sinusoidal: 5636 harmonic: 7087 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 93.00 152.65 -59.65 1 1.00e+01 1.00e-02 4.75e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -134.91 48.91 1 1.00e+01 1.00e-02 3.29e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -132.13 46.13 1 1.00e+01 1.00e-02 2.95e+01 ... (remaining 12720 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.199: 3335 0.199 - 0.398: 17 0.398 - 0.597: 1 0.597 - 0.795: 0 0.795 - 0.994: 1 Chirality restraints: 3354 Sorted by residual: chirality pdb=" C1 NAG h 2 " pdb=" O4 NAG h 1 " pdb=" C2 NAG h 2 " pdb=" O5 NAG h 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.48e+01 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN C 241 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-01 2.50e+01 2.47e+01 chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.23e+01 ... (remaining 3351 not shown) Planarity restraints: 3299 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 613 " -0.345 2.00e-02 2.50e+03 2.99e-01 1.11e+03 pdb=" C7 NAG E 613 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG E 613 " -0.106 2.00e-02 2.50e+03 pdb=" N2 NAG E 613 " 0.532 2.00e-02 2.50e+03 pdb=" O7 NAG E 613 " -0.161 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 612 " 0.291 2.00e-02 2.50e+03 2.49e-01 7.74e+02 pdb=" C7 NAG E 612 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG E 612 " -0.016 2.00e-02 2.50e+03 pdb=" N2 NAG E 612 " -0.420 2.00e-02 2.50e+03 pdb=" O7 NAG E 612 " 0.209 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG h 2 " 0.235 2.00e-02 2.50e+03 1.96e-01 4.78e+02 pdb=" C7 NAG h 2 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG h 2 " 0.166 2.00e-02 2.50e+03 pdb=" N2 NAG h 2 " -0.322 2.00e-02 2.50e+03 pdb=" O7 NAG h 2 " -0.014 2.00e-02 2.50e+03 ... (remaining 3296 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1686 2.74 - 3.28: 20082 3.28 - 3.82: 30470 3.82 - 4.36: 35959 4.36 - 4.90: 58748 Nonbonded interactions: 146945 Sorted by model distance: nonbonded pdb=" OE2 GLU A 269 " pdb=" NE2 GLN A 347 " model vdw 2.199 3.120 nonbonded pdb=" OG1 THR E 297 " pdb=" O ILE E 442 " model vdw 2.224 3.040 nonbonded pdb=" NE2 GLN A 203 " pdb=" O ALA A 204 " model vdw 2.242 3.120 nonbonded pdb=" O VAL A 68 " pdb=" OG1 THR A 71 " model vdw 2.242 3.040 nonbonded pdb=" O3 NAG M 2 " pdb=" O5 BMA M 3 " model vdw 2.279 3.040 ... (remaining 146940 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 178 or resid 189 through 398 or resid 410 throu \ gh 503 or resid 601 through 611)) selection = (chain 'C' and (resid 33 through 178 or resid 189 through 503 or resid 601 throu \ gh 611)) selection = (chain 'E' and (resid 33 through 398 or resid 410 through 503 or resid 601 throu \ gh 611)) } ncs_group { reference = (chain 'B' and (resid 521 through 661 or resid 701 through 702)) selection = (chain 'D' and (resid 521 through 661 or resid 701 through 702)) selection = (chain 'F' and (resid 521 through 661 or resid 701 through 702)) } ncs_group { reference = (chain 'G' and resid 9 through 102) selection = (chain 'I' and resid 21 through 114) selection = (chain 'J' and resid 11 through 104) selection = chain 'K' selection = (chain 'L' and resid 8 through 101) } ncs_group { reference = (chain 'M' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' } ncs_group { reference = chain 'W' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.910 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: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.140 Process input model: 42.040 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 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 0.068 19113 Z= 0.341 Angle : 1.088 20.476 26251 Z= 0.538 Chirality : 0.057 0.994 3354 Planarity : 0.010 0.299 3234 Dihedral : 13.517 109.274 8001 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.19), residues: 1767 helix: 0.09 (0.24), residues: 435 sheet: -0.79 (0.27), residues: 372 loop : -0.59 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP D 571 HIS 0.012 0.002 HIS A 72 PHE 0.044 0.003 PHE A 467 TYR 0.047 0.003 TYR A 61 ARG 0.019 0.001 ARG F 557 Details of bonding type rmsd link_NAG-ASN : bond 0.00751 ( 65) link_NAG-ASN : angle 3.20680 ( 195) link_ALPHA1-4 : bond 0.00556 ( 1) link_ALPHA1-4 : angle 2.05965 ( 3) link_ALPHA1-6 : bond 0.00900 ( 3) link_ALPHA1-6 : angle 1.58024 ( 9) link_BETA1-4 : bond 0.01731 ( 24) link_BETA1-4 : angle 6.15966 ( 72) link_ALPHA1-3 : bond 0.00483 ( 3) link_ALPHA1-3 : angle 2.87534 ( 9) hydrogen bonds : bond 0.15482 ( 562) hydrogen bonds : angle 7.46235 ( 1524) link_BETA1-6 : bond 0.01761 ( 2) link_BETA1-6 : angle 4.12368 ( 6) SS BOND : bond 0.00447 ( 30) SS BOND : angle 1.29759 ( 60) link_BETA1-3 : bond 0.03534 ( 1) link_BETA1-3 : angle 12.61569 ( 3) covalent geometry : bond 0.00671 (18984) covalent geometry : angle 0.99312 (25894) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.7550 (m-80) cc_final: 0.7289 (m-80) REVERT: A 151 PHE cc_start: 0.6825 (t80) cc_final: 0.6185 (t80) REVERT: A 167 LEU cc_start: 0.9150 (mm) cc_final: 0.8898 (mm) REVERT: A 322 ILE cc_start: 0.7922 (mm) cc_final: 0.7636 (mm) REVERT: A 360 PHE cc_start: 0.8410 (m-80) cc_final: 0.7917 (m-80) REVERT: A 367 ASP cc_start: 0.8994 (p0) cc_final: 0.8762 (p0) REVERT: A 369 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8102 (mm-30) REVERT: A 383 TYR cc_start: 0.8258 (m-80) cc_final: 0.7769 (m-80) REVERT: A 426 TRP cc_start: 0.8166 (m100) cc_final: 0.7946 (m100) REVERT: B 537 LEU cc_start: 0.8725 (mt) cc_final: 0.8401 (mt) REVERT: B 543 ASN cc_start: 0.9286 (m110) cc_final: 0.8788 (m110) REVERT: B 571 TRP cc_start: 0.8201 (m-90) cc_final: 0.7925 (m-10) REVERT: B 584 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8213 (mt-10) REVERT: B 596 TRP cc_start: 0.9010 (m-10) cc_final: 0.8669 (m-90) REVERT: C 45 TRP cc_start: 0.8880 (p90) cc_final: 0.8330 (p90) REVERT: C 100 MET cc_start: 0.8584 (ptp) cc_final: 0.8251 (ppp) REVERT: C 104 MET cc_start: 0.8935 (ttt) cc_final: 0.8628 (ttm) REVERT: C 125 LEU cc_start: 0.9074 (tt) cc_final: 0.8814 (tt) REVERT: C 321 ILE cc_start: 0.7956 (mm) cc_final: 0.7418 (tp) REVERT: C 389 LEU cc_start: 0.9627 (mt) cc_final: 0.9405 (mt) REVERT: C 419 ILE cc_start: 0.9612 (mm) cc_final: 0.9406 (mm) REVERT: C 473 ASP cc_start: 0.9278 (t0) cc_final: 0.9002 (t0) REVERT: D 522 PHE cc_start: 0.9036 (t80) cc_final: 0.8826 (t80) REVERT: D 543 ASN cc_start: 0.9059 (m-40) cc_final: 0.8835 (m-40) REVERT: D 545 LEU cc_start: 0.9280 (tp) cc_final: 0.8773 (mt) REVERT: D 549 VAL cc_start: 0.7586 (t) cc_final: 0.7192 (t) REVERT: D 560 GLU cc_start: 0.8737 (pm20) cc_final: 0.8491 (pm20) REVERT: E 49 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8050 (mt-10) REVERT: E 107 ASP cc_start: 0.9354 (m-30) cc_final: 0.9083 (m-30) REVERT: E 108 ILE cc_start: 0.9358 (tt) cc_final: 0.9117 (mm) REVERT: E 375 PHE cc_start: 0.7935 (p90) cc_final: 0.7305 (p90) REVERT: F 549 VAL cc_start: 0.8521 (t) cc_final: 0.8032 (t) REVERT: F 588 ARG cc_start: 0.8944 (ttp80) cc_final: 0.8628 (ttp-110) REVERT: F 628 TRP cc_start: 0.9039 (m100) cc_final: 0.8714 (m100) REVERT: F 635 ILE cc_start: 0.8588 (pt) cc_final: 0.7842 (tt) REVERT: F 647 GLU cc_start: 0.9402 (pt0) cc_final: 0.8968 (pp20) REVERT: F 650 GLN cc_start: 0.9319 (tp40) cc_final: 0.8796 (tp40) REVERT: F 651 ASN cc_start: 0.9293 (m-40) cc_final: 0.8811 (m-40) outliers start: 0 outliers final: 0 residues processed: 402 average time/residue: 0.2938 time to fit residues: 178.1920 Evaluate side-chains 279 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 201 optimal weight: 20.0000 chunk 181 optimal weight: 0.1980 chunk 100 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 122 optimal weight: 0.0970 chunk 96 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 217 optimal weight: 20.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 HIS ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 431 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS E 424 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.089931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.077118 restraints weight = 79943.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.079195 restraints weight = 47999.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.080672 restraints weight = 32678.841| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19113 Z= 0.147 Angle : 0.768 19.155 26251 Z= 0.352 Chirality : 0.046 0.476 3354 Planarity : 0.004 0.056 3234 Dihedral : 8.928 78.853 4593 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.31 % Allowed : 3.32 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.20), residues: 1767 helix: 0.64 (0.25), residues: 437 sheet: -0.44 (0.25), residues: 407 loop : -0.49 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 610 HIS 0.009 0.001 HIS A 66 PHE 0.020 0.002 PHE C 53 TYR 0.020 0.002 TYR A 61 ARG 0.009 0.001 ARG D 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00594 ( 65) link_NAG-ASN : angle 2.79305 ( 195) link_ALPHA1-4 : bond 0.01295 ( 1) link_ALPHA1-4 : angle 1.34106 ( 3) link_ALPHA1-6 : bond 0.00851 ( 3) link_ALPHA1-6 : angle 2.26418 ( 9) link_BETA1-4 : bond 0.01505 ( 24) link_BETA1-4 : angle 4.43033 ( 72) link_ALPHA1-3 : bond 0.01014 ( 3) link_ALPHA1-3 : angle 2.87237 ( 9) hydrogen bonds : bond 0.04946 ( 562) hydrogen bonds : angle 5.79467 ( 1524) link_BETA1-6 : bond 0.01196 ( 2) link_BETA1-6 : angle 2.11438 ( 6) SS BOND : bond 0.00240 ( 30) SS BOND : angle 1.07629 ( 60) link_BETA1-3 : bond 0.03258 ( 1) link_BETA1-3 : angle 9.69416 ( 3) covalent geometry : bond 0.00303 (18984) covalent geometry : angle 0.68238 (25894) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 367 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.7570 (m-80) cc_final: 0.7097 (m-80) REVERT: A 83 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7860 (tm-30) REVERT: A 116 LEU cc_start: 0.9317 (mt) cc_final: 0.8607 (mt) REVERT: A 141 ASP cc_start: 0.8744 (m-30) cc_final: 0.8510 (p0) REVERT: A 142 MET cc_start: 0.8471 (mmt) cc_final: 0.8004 (tpp) REVERT: A 151 PHE cc_start: 0.6779 (t80) cc_final: 0.6213 (t80) REVERT: A 172 ASP cc_start: 0.8503 (m-30) cc_final: 0.8060 (m-30) REVERT: A 367 ASP cc_start: 0.8914 (p0) cc_final: 0.8612 (p0) REVERT: A 383 TYR cc_start: 0.8340 (m-80) cc_final: 0.7940 (m-80) REVERT: A 433 MET cc_start: 0.8665 (ttp) cc_final: 0.8410 (ttp) REVERT: A 478 TRP cc_start: 0.8182 (m100) cc_final: 0.7570 (m100) REVERT: B 537 LEU cc_start: 0.8711 (mt) cc_final: 0.8416 (mt) REVERT: B 543 ASN cc_start: 0.9348 (m110) cc_final: 0.8890 (m110) REVERT: B 584 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8162 (mt-10) REVERT: B 596 TRP cc_start: 0.9034 (m-10) cc_final: 0.8743 (m-90) REVERT: C 107 ASP cc_start: 0.8816 (m-30) cc_final: 0.8590 (m-30) REVERT: C 125 LEU cc_start: 0.8991 (tt) cc_final: 0.8601 (tt) REVERT: C 419 ILE cc_start: 0.9581 (mm) cc_final: 0.9367 (mm) REVERT: D 545 LEU cc_start: 0.9362 (tp) cc_final: 0.9024 (mt) REVERT: D 587 LEU cc_start: 0.9729 (mm) cc_final: 0.9389 (mm) REVERT: D 656 ASN cc_start: 0.9264 (m-40) cc_final: 0.8638 (t0) REVERT: E 95 MET cc_start: 0.9038 (ppp) cc_final: 0.8600 (ppp) REVERT: E 108 ILE cc_start: 0.9360 (tt) cc_final: 0.9005 (mm) REVERT: E 355 ASN cc_start: 0.9016 (p0) cc_final: 0.8748 (p0) REVERT: E 375 PHE cc_start: 0.7917 (p90) cc_final: 0.7709 (p90) REVERT: F 530 MET cc_start: 0.7418 (ttt) cc_final: 0.7069 (tpp) REVERT: F 647 GLU cc_start: 0.9260 (pt0) cc_final: 0.8920 (pp20) REVERT: F 650 GLN cc_start: 0.9173 (tp40) cc_final: 0.8540 (tp40) REVERT: F 656 ASN cc_start: 0.9243 (t0) cc_final: 0.8928 (m-40) outliers start: 5 outliers final: 0 residues processed: 371 average time/residue: 0.3062 time to fit residues: 172.7653 Evaluate side-chains 263 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 1 optimal weight: 20.0000 chunk 189 optimal weight: 0.5980 chunk 51 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 249 HIS C 99 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 HIS ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS E 85 HIS E 293 GLN F 564 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.086936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.074466 restraints weight = 82556.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.076436 restraints weight = 50115.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.077815 restraints weight = 34502.453| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19113 Z= 0.172 Angle : 0.763 19.849 26251 Z= 0.353 Chirality : 0.045 0.467 3354 Planarity : 0.004 0.071 3234 Dihedral : 8.106 67.352 4593 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.19 % Allowed : 3.26 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.20), residues: 1767 helix: 0.74 (0.24), residues: 442 sheet: -0.41 (0.24), residues: 425 loop : -0.50 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 571 HIS 0.010 0.001 HIS A 66 PHE 0.019 0.002 PHE F 522 TYR 0.013 0.001 TYR F 643 ARG 0.010 0.001 ARG E 418 Details of bonding type rmsd link_NAG-ASN : bond 0.00493 ( 65) link_NAG-ASN : angle 2.76448 ( 195) link_ALPHA1-4 : bond 0.01430 ( 1) link_ALPHA1-4 : angle 1.44259 ( 3) link_ALPHA1-6 : bond 0.00806 ( 3) link_ALPHA1-6 : angle 1.80379 ( 9) link_BETA1-4 : bond 0.01463 ( 24) link_BETA1-4 : angle 4.31684 ( 72) link_ALPHA1-3 : bond 0.00786 ( 3) link_ALPHA1-3 : angle 2.88573 ( 9) hydrogen bonds : bond 0.04536 ( 562) hydrogen bonds : angle 5.57850 ( 1524) link_BETA1-6 : bond 0.00855 ( 2) link_BETA1-6 : angle 1.68636 ( 6) SS BOND : bond 0.00289 ( 30) SS BOND : angle 1.24989 ( 60) link_BETA1-3 : bond 0.02920 ( 1) link_BETA1-3 : angle 9.33576 ( 3) covalent geometry : bond 0.00364 (18984) covalent geometry : angle 0.67970 (25894) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 350 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.7571 (m-80) cc_final: 0.7290 (m-80) REVERT: A 116 LEU cc_start: 0.9266 (mt) cc_final: 0.9050 (mt) REVERT: A 151 PHE cc_start: 0.7045 (t80) cc_final: 0.6433 (t80) REVERT: A 172 ASP cc_start: 0.8546 (m-30) cc_final: 0.8173 (m-30) REVERT: A 367 ASP cc_start: 0.9063 (p0) cc_final: 0.8816 (p0) REVERT: A 383 TYR cc_start: 0.8506 (m-80) cc_final: 0.8246 (m-80) REVERT: A 434 TYR cc_start: 0.8665 (t80) cc_final: 0.8427 (t80) REVERT: A 481 GLU cc_start: 0.8271 (pm20) cc_final: 0.8029 (pm20) REVERT: B 537 LEU cc_start: 0.8706 (mt) cc_final: 0.8362 (mt) REVERT: B 543 ASN cc_start: 0.9324 (m110) cc_final: 0.8858 (m110) REVERT: B 579 ARG cc_start: 0.8037 (mtp180) cc_final: 0.7668 (mtp180) REVERT: B 584 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8175 (mt-10) REVERT: C 285 LEU cc_start: 0.9298 (mp) cc_final: 0.9056 (tp) REVERT: C 419 ILE cc_start: 0.9585 (mm) cc_final: 0.9350 (mm) REVERT: D 545 LEU cc_start: 0.9289 (tp) cc_final: 0.8939 (mt) REVERT: D 560 GLU cc_start: 0.8723 (pm20) cc_final: 0.8304 (pm20) REVERT: D 570 VAL cc_start: 0.7975 (m) cc_final: 0.7734 (p) REVERT: D 588 ARG cc_start: 0.9235 (mmm-85) cc_final: 0.8860 (mmm-85) REVERT: D 643 TYR cc_start: 0.9031 (m-10) cc_final: 0.8613 (m-80) REVERT: E 107 ASP cc_start: 0.9486 (m-30) cc_final: 0.9248 (m-30) REVERT: E 108 ILE cc_start: 0.9241 (tt) cc_final: 0.8943 (mm) REVERT: E 153 MET cc_start: 0.8383 (tpt) cc_final: 0.7555 (tmm) REVERT: E 257 THR cc_start: 0.8687 (p) cc_final: 0.8414 (p) REVERT: E 355 ASN cc_start: 0.8994 (p0) cc_final: 0.8740 (p0) REVERT: E 394 TRP cc_start: 0.8830 (m100) cc_final: 0.8205 (m-10) REVERT: F 522 PHE cc_start: 0.8583 (t80) cc_final: 0.8311 (t80) REVERT: F 628 TRP cc_start: 0.8994 (m100) cc_final: 0.8635 (m100) REVERT: F 647 GLU cc_start: 0.9327 (pt0) cc_final: 0.8991 (pp20) REVERT: F 651 ASN cc_start: 0.9047 (m110) cc_final: 0.8626 (m110) outliers start: 3 outliers final: 1 residues processed: 352 average time/residue: 0.3247 time to fit residues: 172.3004 Evaluate side-chains 262 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 261 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 115 optimal weight: 7.9990 chunk 92 optimal weight: 0.5980 chunk 180 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 126 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 212 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 136 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 overall best weight: 6.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 GLN B 554 ASN ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 HIS ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 249 HIS ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 GLN E 477 ASN F 564 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.079440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.067680 restraints weight = 88161.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.069457 restraints weight = 53357.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.070700 restraints weight = 36996.668| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.106 19113 Z= 0.390 Angle : 1.149 19.191 26251 Z= 0.533 Chirality : 0.055 0.442 3354 Planarity : 0.006 0.058 3234 Dihedral : 9.414 67.591 4593 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.89 % Favored : 94.06 % Rotamer: Outliers : 0.25 % Allowed : 5.01 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.19), residues: 1767 helix: -0.20 (0.23), residues: 429 sheet: -0.94 (0.25), residues: 408 loop : -1.04 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.004 TRP A 426 HIS 0.009 0.003 HIS A 373 PHE 0.037 0.004 PHE A 151 TYR 0.018 0.003 TYR D 638 ARG 0.012 0.001 ARG C 308 Details of bonding type rmsd link_NAG-ASN : bond 0.00901 ( 65) link_NAG-ASN : angle 3.39360 ( 195) link_ALPHA1-4 : bond 0.02421 ( 1) link_ALPHA1-4 : angle 1.32529 ( 3) link_ALPHA1-6 : bond 0.00721 ( 3) link_ALPHA1-6 : angle 1.98521 ( 9) link_BETA1-4 : bond 0.01329 ( 24) link_BETA1-4 : angle 4.67996 ( 72) link_ALPHA1-3 : bond 0.00693 ( 3) link_ALPHA1-3 : angle 3.89747 ( 9) hydrogen bonds : bond 0.05783 ( 562) hydrogen bonds : angle 6.64307 ( 1524) link_BETA1-6 : bond 0.00616 ( 2) link_BETA1-6 : angle 2.47188 ( 6) SS BOND : bond 0.00702 ( 30) SS BOND : angle 1.49811 ( 60) link_BETA1-3 : bond 0.02024 ( 1) link_BETA1-3 : angle 8.88176 ( 3) covalent geometry : bond 0.00828 (18984) covalent geometry : angle 1.08079 (25894) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 295 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.7716 (m-80) cc_final: 0.7031 (m-80) REVERT: A 100 MET cc_start: 0.9273 (ptp) cc_final: 0.8591 (ptp) REVERT: A 151 PHE cc_start: 0.8058 (t80) cc_final: 0.7045 (t80) REVERT: A 163 LYS cc_start: 0.9066 (tttt) cc_final: 0.8824 (mmtt) REVERT: A 167 LEU cc_start: 0.9193 (mm) cc_final: 0.8973 (mm) REVERT: A 172 ASP cc_start: 0.8430 (m-30) cc_final: 0.8093 (m-30) REVERT: A 426 TRP cc_start: 0.8370 (m-90) cc_final: 0.8039 (m-90) REVERT: A 431 GLN cc_start: 0.8904 (mm-40) cc_final: 0.8378 (mp10) REVERT: A 433 MET cc_start: 0.8426 (ttm) cc_final: 0.8122 (ttm) REVERT: B 543 ASN cc_start: 0.9299 (m110) cc_final: 0.8778 (t0) REVERT: B 584 GLU cc_start: 0.8545 (mt-10) cc_final: 0.7959 (mt-10) REVERT: C 285 LEU cc_start: 0.9435 (mp) cc_final: 0.9082 (tp) REVERT: C 425 MET cc_start: 0.8251 (ptm) cc_final: 0.7928 (ptm) REVERT: D 542 ARG cc_start: 0.8875 (tmm-80) cc_final: 0.8648 (tmm-80) REVERT: D 548 ILE cc_start: 0.8299 (pt) cc_final: 0.8040 (pt) REVERT: D 601 LYS cc_start: 0.9328 (mtpp) cc_final: 0.9071 (mtmm) REVERT: E 95 MET cc_start: 0.9449 (ppp) cc_final: 0.8955 (ppp) REVERT: E 143 ARG cc_start: 0.8007 (mmt90) cc_final: 0.7303 (mtp-110) REVERT: E 316 TYR cc_start: 0.7531 (m-80) cc_final: 0.7015 (m-80) REVERT: E 355 ASN cc_start: 0.9175 (p0) cc_final: 0.8952 (p0) REVERT: E 373 HIS cc_start: 0.8970 (t70) cc_final: 0.8628 (t-90) REVERT: F 530 MET cc_start: 0.8200 (ttt) cc_final: 0.7805 (ttt) REVERT: F 549 VAL cc_start: 0.8431 (t) cc_final: 0.7977 (t) REVERT: F 588 ARG cc_start: 0.8974 (ptm-80) cc_final: 0.8416 (ptm160) REVERT: F 624 ASP cc_start: 0.8244 (m-30) cc_final: 0.7944 (m-30) REVERT: F 626 MET cc_start: 0.7130 (ttm) cc_final: 0.6837 (mtt) REVERT: F 643 TYR cc_start: 0.9271 (m-10) cc_final: 0.8919 (m-10) REVERT: F 647 GLU cc_start: 0.9299 (pt0) cc_final: 0.8974 (pp20) REVERT: F 651 ASN cc_start: 0.9266 (m110) cc_final: 0.8528 (m110) outliers start: 4 outliers final: 1 residues processed: 298 average time/residue: 0.3208 time to fit residues: 144.2810 Evaluate side-chains 223 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 134 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 196 optimal weight: 0.9980 chunk 185 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 HIS ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN C 249 HIS C 302 ASN C 427 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.082920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.071015 restraints weight = 84865.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.072861 restraints weight = 51639.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.074168 restraints weight = 35766.215| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19113 Z= 0.161 Angle : 0.814 16.029 26251 Z= 0.373 Chirality : 0.047 0.430 3354 Planarity : 0.004 0.047 3234 Dihedral : 8.151 59.321 4593 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.19), residues: 1767 helix: 0.45 (0.24), residues: 434 sheet: -0.75 (0.26), residues: 388 loop : -0.95 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP A 112 HIS 0.008 0.002 HIS A 373 PHE 0.017 0.002 PHE E 390 TYR 0.022 0.002 TYR A 61 ARG 0.007 0.001 ARG D 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00577 ( 65) link_NAG-ASN : angle 3.05671 ( 195) link_ALPHA1-4 : bond 0.01614 ( 1) link_ALPHA1-4 : angle 1.09965 ( 3) link_ALPHA1-6 : bond 0.00781 ( 3) link_ALPHA1-6 : angle 1.33163 ( 9) link_BETA1-4 : bond 0.01165 ( 24) link_BETA1-4 : angle 4.11153 ( 72) link_ALPHA1-3 : bond 0.00934 ( 3) link_ALPHA1-3 : angle 2.97376 ( 9) hydrogen bonds : bond 0.04364 ( 562) hydrogen bonds : angle 5.72526 ( 1524) link_BETA1-6 : bond 0.01109 ( 2) link_BETA1-6 : angle 2.08314 ( 6) SS BOND : bond 0.00358 ( 30) SS BOND : angle 1.26193 ( 60) link_BETA1-3 : bond 0.02389 ( 1) link_BETA1-3 : angle 9.72118 ( 3) covalent geometry : bond 0.00347 (18984) covalent geometry : angle 0.73132 (25894) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 2.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6867 (m-70) cc_final: 0.6635 (m-70) REVERT: A 151 PHE cc_start: 0.7708 (t80) cc_final: 0.6489 (t80) REVERT: A 163 LYS cc_start: 0.9164 (tttt) cc_final: 0.8904 (mmtt) REVERT: A 172 ASP cc_start: 0.8483 (m-30) cc_final: 0.8277 (m-30) REVERT: A 431 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8407 (mp10) REVERT: B 543 ASN cc_start: 0.9244 (m110) cc_final: 0.8759 (t0) REVERT: B 584 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8035 (mt-10) REVERT: B 603 ILE cc_start: 0.8427 (mm) cc_final: 0.8188 (mm) REVERT: C 39 TYR cc_start: 0.8862 (m-10) cc_final: 0.8362 (m-10) REVERT: C 111 LEU cc_start: 0.9129 (mm) cc_final: 0.8896 (mm) REVERT: C 142 MET cc_start: 0.9186 (mmm) cc_final: 0.8874 (mtp) REVERT: C 153 MET cc_start: 0.8691 (tpt) cc_final: 0.7859 (tpp) REVERT: C 249 HIS cc_start: 0.9123 (p-80) cc_final: 0.8898 (p90) REVERT: C 434 TYR cc_start: 0.7923 (t80) cc_final: 0.7411 (t80) REVERT: D 536 THR cc_start: 0.8806 (p) cc_final: 0.8269 (t) REVERT: D 543 ASN cc_start: 0.8477 (t0) cc_final: 0.8198 (t0) REVERT: D 587 LEU cc_start: 0.9701 (mm) cc_final: 0.9281 (mm) REVERT: D 643 TYR cc_start: 0.9074 (m-10) cc_final: 0.8347 (m-80) REVERT: E 95 MET cc_start: 0.9286 (ppp) cc_final: 0.8618 (ppp) REVERT: E 100 MET cc_start: 0.9002 (tpp) cc_final: 0.8683 (tpp) REVERT: E 104 MET cc_start: 0.9220 (tmm) cc_final: 0.8709 (ppp) REVERT: E 153 MET cc_start: 0.8140 (tpt) cc_final: 0.7783 (tmm) REVERT: E 217 TYR cc_start: 0.8888 (m-80) cc_final: 0.8545 (m-80) REVERT: E 316 TYR cc_start: 0.7562 (m-80) cc_final: 0.6779 (m-80) REVERT: E 355 ASN cc_start: 0.9060 (p0) cc_final: 0.8790 (p0) REVERT: E 373 HIS cc_start: 0.8842 (t70) cc_final: 0.8476 (t-90) REVERT: E 478 TRP cc_start: 0.8546 (m100) cc_final: 0.8068 (m100) REVERT: F 530 MET cc_start: 0.7741 (ttt) cc_final: 0.7477 (ttt) REVERT: F 648 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8249 (tp30) REVERT: F 651 ASN cc_start: 0.9174 (m110) cc_final: 0.8621 (m110) REVERT: F 656 ASN cc_start: 0.9159 (t0) cc_final: 0.8908 (m-40) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.3234 time to fit residues: 163.6776 Evaluate side-chains 247 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 168 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 177 optimal weight: 0.0970 chunk 116 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 102 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 HIS ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.083461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.071371 restraints weight = 84172.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.073250 restraints weight = 51335.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.074570 restraints weight = 35638.467| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19113 Z= 0.144 Angle : 0.760 16.269 26251 Z= 0.348 Chirality : 0.046 0.436 3354 Planarity : 0.004 0.046 3234 Dihedral : 7.607 55.973 4593 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.19), residues: 1767 helix: 0.75 (0.25), residues: 437 sheet: -0.58 (0.25), residues: 424 loop : -0.94 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 112 HIS 0.006 0.001 HIS A 66 PHE 0.040 0.002 PHE E 210 TYR 0.015 0.002 TYR E 383 ARG 0.007 0.001 ARG E 308 Details of bonding type rmsd link_NAG-ASN : bond 0.00534 ( 65) link_NAG-ASN : angle 2.84296 ( 195) link_ALPHA1-4 : bond 0.01494 ( 1) link_ALPHA1-4 : angle 1.13214 ( 3) link_ALPHA1-6 : bond 0.00699 ( 3) link_ALPHA1-6 : angle 1.29174 ( 9) link_BETA1-4 : bond 0.01155 ( 24) link_BETA1-4 : angle 3.84345 ( 72) link_ALPHA1-3 : bond 0.00888 ( 3) link_ALPHA1-3 : angle 2.98178 ( 9) hydrogen bonds : bond 0.04024 ( 562) hydrogen bonds : angle 5.46976 ( 1524) link_BETA1-6 : bond 0.00990 ( 2) link_BETA1-6 : angle 1.87627 ( 6) SS BOND : bond 0.00291 ( 30) SS BOND : angle 1.21934 ( 60) link_BETA1-3 : bond 0.02085 ( 1) link_BETA1-3 : angle 9.40267 ( 3) covalent geometry : bond 0.00314 (18984) covalent geometry : angle 0.68204 (25894) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 2.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.7030 (m-80) cc_final: 0.6733 (m-80) REVERT: A 66 HIS cc_start: 0.6846 (m-70) cc_final: 0.6613 (m-70) REVERT: A 112 TRP cc_start: 0.9025 (t-100) cc_final: 0.8638 (t-100) REVERT: A 151 PHE cc_start: 0.7620 (t80) cc_final: 0.6361 (t80) REVERT: A 163 LYS cc_start: 0.9160 (tttt) cc_final: 0.8858 (mmtt) REVERT: A 172 ASP cc_start: 0.8408 (m-30) cc_final: 0.8156 (m-30) REVERT: A 431 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8380 (mp10) REVERT: A 481 GLU cc_start: 0.8214 (pm20) cc_final: 0.7995 (pm20) REVERT: B 543 ASN cc_start: 0.9199 (m110) cc_final: 0.8718 (t0) REVERT: B 584 GLU cc_start: 0.8554 (mt-10) cc_final: 0.7952 (mt-10) REVERT: B 603 ILE cc_start: 0.8426 (mm) cc_final: 0.8179 (mm) REVERT: C 39 TYR cc_start: 0.8815 (m-10) cc_final: 0.8384 (m-10) REVERT: C 91 GLU cc_start: 0.6639 (tm-30) cc_final: 0.5873 (tm-30) REVERT: C 153 MET cc_start: 0.8715 (tpt) cc_final: 0.7963 (tpp) REVERT: C 159 ASP cc_start: 0.8135 (m-30) cc_final: 0.7752 (m-30) REVERT: C 337 TRP cc_start: 0.8362 (t-100) cc_final: 0.8061 (t-100) REVERT: C 434 TYR cc_start: 0.7919 (t80) cc_final: 0.7441 (t80) REVERT: C 478 TRP cc_start: 0.9014 (m-10) cc_final: 0.8789 (m-10) REVERT: D 536 THR cc_start: 0.8769 (p) cc_final: 0.8222 (t) REVERT: D 543 ASN cc_start: 0.8513 (t0) cc_final: 0.8193 (t0) REVERT: D 587 LEU cc_start: 0.9692 (mm) cc_final: 0.9346 (mm) REVERT: D 643 TYR cc_start: 0.9083 (m-10) cc_final: 0.8363 (m-80) REVERT: E 47 ASP cc_start: 0.8157 (m-30) cc_final: 0.7860 (m-30) REVERT: E 104 MET cc_start: 0.9213 (tmm) cc_final: 0.8577 (ppp) REVERT: E 108 ILE cc_start: 0.9447 (tt) cc_final: 0.9109 (mm) REVERT: E 153 MET cc_start: 0.7760 (tpt) cc_final: 0.7422 (tmm) REVERT: E 217 TYR cc_start: 0.8909 (m-80) cc_final: 0.8688 (m-10) REVERT: E 260 LEU cc_start: 0.9186 (mm) cc_final: 0.8968 (mp) REVERT: E 316 TYR cc_start: 0.7564 (m-80) cc_final: 0.6767 (m-80) REVERT: E 355 ASN cc_start: 0.9058 (p0) cc_final: 0.8830 (p0) REVERT: E 373 HIS cc_start: 0.8921 (t70) cc_final: 0.8558 (t-90) REVERT: E 478 TRP cc_start: 0.8564 (m100) cc_final: 0.8090 (m100) REVERT: F 522 PHE cc_start: 0.8720 (t80) cc_final: 0.8517 (t80) REVERT: F 530 MET cc_start: 0.7785 (ttt) cc_final: 0.7413 (ttt) REVERT: F 628 TRP cc_start: 0.8970 (m100) cc_final: 0.8507 (m100) REVERT: F 647 GLU cc_start: 0.9238 (pt0) cc_final: 0.8901 (pp20) REVERT: F 651 ASN cc_start: 0.9217 (m110) cc_final: 0.8370 (m110) outliers start: 0 outliers final: 0 residues processed: 324 average time/residue: 0.3651 time to fit residues: 183.4103 Evaluate side-chains 243 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 207 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 138 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 128 optimal weight: 10.0000 chunk 220 optimal weight: 20.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 HIS ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 HIS C 293 GLN C 347 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 ASN ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.077029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.065705 restraints weight = 89616.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.067384 restraints weight = 53805.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.068685 restraints weight = 36838.113| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.5218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.081 19113 Z= 0.443 Angle : 1.199 16.337 26251 Z= 0.557 Chirality : 0.058 0.546 3354 Planarity : 0.006 0.054 3234 Dihedral : 9.492 61.976 4593 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.47 % Favored : 92.47 % Rotamer: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.19), residues: 1767 helix: -0.27 (0.23), residues: 436 sheet: -1.07 (0.27), residues: 359 loop : -1.47 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.004 TRP F 614 HIS 0.011 0.003 HIS A 216 PHE 0.032 0.004 PHE A 210 TYR 0.026 0.003 TYR C 485 ARG 0.011 0.001 ARG C 428 Details of bonding type rmsd link_NAG-ASN : bond 0.01004 ( 65) link_NAG-ASN : angle 3.49016 ( 195) link_ALPHA1-4 : bond 0.02633 ( 1) link_ALPHA1-4 : angle 2.72111 ( 3) link_ALPHA1-6 : bond 0.00668 ( 3) link_ALPHA1-6 : angle 2.24240 ( 9) link_BETA1-4 : bond 0.01109 ( 24) link_BETA1-4 : angle 4.30064 ( 72) link_ALPHA1-3 : bond 0.00507 ( 3) link_ALPHA1-3 : angle 4.57943 ( 9) hydrogen bonds : bond 0.05728 ( 562) hydrogen bonds : angle 6.87773 ( 1524) link_BETA1-6 : bond 0.00391 ( 2) link_BETA1-6 : angle 2.25519 ( 6) SS BOND : bond 0.00759 ( 30) SS BOND : angle 1.92848 ( 60) link_BETA1-3 : bond 0.00966 ( 1) link_BETA1-3 : angle 7.89210 ( 3) covalent geometry : bond 0.00940 (18984) covalent geometry : angle 1.13485 (25894) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 PHE cc_start: 0.8396 (t80) cc_final: 0.7521 (t80) REVERT: A 163 LYS cc_start: 0.9099 (tttt) cc_final: 0.8874 (mmtt) REVERT: A 172 ASP cc_start: 0.8451 (m-30) cc_final: 0.8221 (m-30) REVERT: A 431 GLN cc_start: 0.9074 (mm-40) cc_final: 0.8546 (mp10) REVERT: A 474 MET cc_start: 0.8863 (mmp) cc_final: 0.8595 (mmm) REVERT: B 543 ASN cc_start: 0.9255 (m110) cc_final: 0.8887 (t0) REVERT: B 584 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8042 (mp0) REVERT: C 39 TYR cc_start: 0.8964 (m-10) cc_final: 0.8518 (m-10) REVERT: C 142 MET cc_start: 0.9236 (mmm) cc_final: 0.8978 (mtp) REVERT: C 153 MET cc_start: 0.8545 (tpt) cc_final: 0.8006 (tpp) REVERT: D 536 THR cc_start: 0.9085 (p) cc_final: 0.8740 (t) REVERT: D 543 ASN cc_start: 0.8688 (t0) cc_final: 0.8317 (t0) REVERT: D 548 ILE cc_start: 0.8355 (pt) cc_final: 0.7700 (pt) REVERT: D 551 GLN cc_start: 0.8141 (mt0) cc_final: 0.7895 (mt0) REVERT: D 588 ARG cc_start: 0.8795 (ttt-90) cc_final: 0.8496 (ttt-90) REVERT: D 643 TYR cc_start: 0.9162 (m-10) cc_final: 0.8453 (m-80) REVERT: E 104 MET cc_start: 0.9223 (tmm) cc_final: 0.7671 (tmm) REVERT: E 316 TYR cc_start: 0.7878 (m-80) cc_final: 0.7287 (m-80) REVERT: E 478 TRP cc_start: 0.8699 (m100) cc_final: 0.8304 (m100) REVERT: F 588 ARG cc_start: 0.9077 (ptm-80) cc_final: 0.8288 (ptm160) REVERT: F 593 LEU cc_start: 0.9576 (mt) cc_final: 0.9167 (tp) REVERT: F 643 TYR cc_start: 0.9295 (m-10) cc_final: 0.8953 (m-10) REVERT: F 647 GLU cc_start: 0.9297 (pt0) cc_final: 0.8906 (pp20) REVERT: F 651 ASN cc_start: 0.9345 (m110) cc_final: 0.8688 (m110) REVERT: F 656 ASN cc_start: 0.9175 (t0) cc_final: 0.8910 (m-40) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.3564 time to fit residues: 144.5703 Evaluate side-chains 198 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 211 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 178 optimal weight: 0.5980 chunk 182 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 HIS D 540 GLN D 562 GLN D 575 GLN D 653 GLN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.082175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.070327 restraints weight = 85252.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.072192 restraints weight = 52435.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.073460 restraints weight = 36111.510| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.5150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19113 Z= 0.151 Angle : 0.818 16.358 26251 Z= 0.379 Chirality : 0.048 0.426 3354 Planarity : 0.004 0.043 3234 Dihedral : 7.977 55.795 4593 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.19), residues: 1767 helix: 0.48 (0.24), residues: 438 sheet: -0.79 (0.26), residues: 383 loop : -1.24 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 614 HIS 0.008 0.001 HIS F 564 PHE 0.055 0.002 PHE E 210 TYR 0.025 0.002 TYR A 61 ARG 0.008 0.001 ARG B 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00649 ( 65) link_NAG-ASN : angle 3.01752 ( 195) link_ALPHA1-4 : bond 0.01490 ( 1) link_ALPHA1-4 : angle 0.92600 ( 3) link_ALPHA1-6 : bond 0.00812 ( 3) link_ALPHA1-6 : angle 1.28560 ( 9) link_BETA1-4 : bond 0.01078 ( 24) link_BETA1-4 : angle 3.66891 ( 72) link_ALPHA1-3 : bond 0.01127 ( 3) link_ALPHA1-3 : angle 2.95545 ( 9) hydrogen bonds : bond 0.04408 ( 562) hydrogen bonds : angle 5.73667 ( 1524) link_BETA1-6 : bond 0.00826 ( 2) link_BETA1-6 : angle 2.21598 ( 6) SS BOND : bond 0.00311 ( 30) SS BOND : angle 1.42697 ( 60) link_BETA1-3 : bond 0.01278 ( 1) link_BETA1-3 : angle 9.09171 ( 3) covalent geometry : bond 0.00323 (18984) covalent geometry : angle 0.74394 (25894) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 1.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6792 (m-70) cc_final: 0.6500 (m-70) REVERT: A 110 SER cc_start: 0.9111 (t) cc_final: 0.8707 (p) REVERT: A 112 TRP cc_start: 0.9083 (t-100) cc_final: 0.8801 (t-100) REVERT: A 116 LEU cc_start: 0.8901 (mt) cc_final: 0.8409 (mt) REVERT: A 431 GLN cc_start: 0.8932 (mm-40) cc_final: 0.8536 (mp10) REVERT: A 474 MET cc_start: 0.8931 (mmp) cc_final: 0.8629 (mmm) REVERT: B 543 ASN cc_start: 0.9218 (m110) cc_final: 0.8770 (t0) REVERT: B 584 GLU cc_start: 0.8571 (mt-10) cc_final: 0.7981 (mp0) REVERT: B 643 TYR cc_start: 0.8827 (m-10) cc_final: 0.8409 (m-80) REVERT: C 39 TYR cc_start: 0.8793 (m-10) cc_final: 0.8385 (m-10) REVERT: C 100 MET cc_start: 0.8962 (ptt) cc_final: 0.8661 (ptt) REVERT: C 142 MET cc_start: 0.9205 (mmm) cc_final: 0.8883 (mtp) REVERT: C 153 MET cc_start: 0.8682 (tpt) cc_final: 0.8041 (tpp) REVERT: C 249 HIS cc_start: 0.9251 (p-80) cc_final: 0.8891 (p90) REVERT: D 536 THR cc_start: 0.8980 (p) cc_final: 0.8577 (t) REVERT: D 543 ASN cc_start: 0.8387 (t0) cc_final: 0.8082 (t0) REVERT: D 548 ILE cc_start: 0.8349 (pt) cc_final: 0.7663 (pt) REVERT: D 587 LEU cc_start: 0.9711 (mm) cc_final: 0.9322 (mm) REVERT: D 601 LYS cc_start: 0.9203 (pttp) cc_final: 0.8984 (ptmm) REVERT: D 643 TYR cc_start: 0.9084 (m-10) cc_final: 0.8363 (m-80) REVERT: E 104 MET cc_start: 0.8806 (tmm) cc_final: 0.7811 (tmm) REVERT: E 105 HIS cc_start: 0.9084 (t-90) cc_final: 0.8844 (t-90) REVERT: E 316 TYR cc_start: 0.7696 (m-80) cc_final: 0.6693 (m-80) REVERT: E 476 ASP cc_start: 0.9275 (m-30) cc_final: 0.8863 (p0) REVERT: E 478 TRP cc_start: 0.8617 (m100) cc_final: 0.8313 (m100) REVERT: F 628 TRP cc_start: 0.8992 (m100) cc_final: 0.8501 (m100) REVERT: F 647 GLU cc_start: 0.9212 (pt0) cc_final: 0.8815 (pp20) REVERT: F 650 GLN cc_start: 0.9312 (tp40) cc_final: 0.8783 (tm-30) REVERT: F 651 ASN cc_start: 0.9245 (m110) cc_final: 0.8521 (m110) REVERT: F 656 ASN cc_start: 0.9057 (t0) cc_final: 0.8826 (m-40) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.3499 time to fit residues: 175.7724 Evaluate side-chains 232 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 3.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 102 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 167 optimal weight: 8.9990 chunk 144 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 183 optimal weight: 8.9990 chunk 158 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 HIS ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 424 ASN E 477 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.082073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.070461 restraints weight = 86069.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.072223 restraints weight = 53437.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.073462 restraints weight = 37382.563| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19113 Z= 0.148 Angle : 0.785 16.332 26251 Z= 0.366 Chirality : 0.047 0.485 3354 Planarity : 0.004 0.045 3234 Dihedral : 7.557 56.222 4593 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.06 % Allowed : 0.44 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.19), residues: 1767 helix: 0.55 (0.25), residues: 442 sheet: -0.51 (0.26), residues: 402 loop : -1.22 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 426 HIS 0.007 0.001 HIS A 249 PHE 0.019 0.002 PHE A 375 TYR 0.030 0.002 TYR C 217 ARG 0.010 0.001 ARG D 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00542 ( 65) link_NAG-ASN : angle 2.84627 ( 195) link_ALPHA1-4 : bond 0.01625 ( 1) link_ALPHA1-4 : angle 0.97238 ( 3) link_ALPHA1-6 : bond 0.00686 ( 3) link_ALPHA1-6 : angle 1.34238 ( 9) link_BETA1-4 : bond 0.01118 ( 24) link_BETA1-4 : angle 3.59820 ( 72) link_ALPHA1-3 : bond 0.00854 ( 3) link_ALPHA1-3 : angle 3.07222 ( 9) hydrogen bonds : bond 0.04262 ( 562) hydrogen bonds : angle 5.62054 ( 1524) link_BETA1-6 : bond 0.00943 ( 2) link_BETA1-6 : angle 1.84557 ( 6) SS BOND : bond 0.00663 ( 30) SS BOND : angle 1.68591 ( 60) link_BETA1-3 : bond 0.00945 ( 1) link_BETA1-3 : angle 8.36316 ( 3) covalent geometry : bond 0.00319 (18984) covalent geometry : angle 0.71292 (25894) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 301 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6696 (m-70) cc_final: 0.6381 (m-70) REVERT: A 172 ASP cc_start: 0.8477 (m-30) cc_final: 0.8083 (m-30) REVERT: A 431 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8525 (mp10) REVERT: A 474 MET cc_start: 0.8941 (mmp) cc_final: 0.8583 (mmm) REVERT: B 543 ASN cc_start: 0.9209 (m110) cc_final: 0.8756 (t0) REVERT: B 584 GLU cc_start: 0.8488 (mt-10) cc_final: 0.7898 (mp0) REVERT: B 652 GLN cc_start: 0.8991 (tt0) cc_final: 0.8658 (tm-30) REVERT: B 656 ASN cc_start: 0.8889 (m110) cc_final: 0.8452 (m110) REVERT: C 39 TYR cc_start: 0.8712 (m-10) cc_final: 0.8336 (m-10) REVERT: C 80 ASN cc_start: 0.9127 (m-40) cc_final: 0.8759 (p0) REVERT: C 100 MET cc_start: 0.8821 (ptt) cc_final: 0.8547 (ptt) REVERT: C 142 MET cc_start: 0.9148 (mmm) cc_final: 0.8945 (mtp) REVERT: C 153 MET cc_start: 0.8718 (tpt) cc_final: 0.7982 (tpp) REVERT: C 249 HIS cc_start: 0.9313 (p-80) cc_final: 0.8816 (p90) REVERT: C 337 TRP cc_start: 0.8424 (t-100) cc_final: 0.7899 (t-100) REVERT: C 389 LEU cc_start: 0.9534 (mp) cc_final: 0.9248 (mp) REVERT: C 425 MET cc_start: 0.7736 (ppp) cc_final: 0.7364 (ppp) REVERT: D 536 THR cc_start: 0.9181 (p) cc_final: 0.8716 (t) REVERT: D 543 ASN cc_start: 0.8308 (t0) cc_final: 0.7976 (t0) REVERT: D 548 ILE cc_start: 0.8247 (pt) cc_final: 0.7729 (pt) REVERT: D 643 TYR cc_start: 0.9058 (m-10) cc_final: 0.8308 (m-80) REVERT: E 104 MET cc_start: 0.9010 (tmm) cc_final: 0.7583 (tmm) REVERT: E 108 ILE cc_start: 0.9528 (tt) cc_final: 0.9263 (mm) REVERT: E 153 MET cc_start: 0.7732 (tpt) cc_final: 0.7423 (tmm) REVERT: E 160 LYS cc_start: 0.8968 (mmtt) cc_final: 0.8436 (mtmt) REVERT: E 215 ILE cc_start: 0.9373 (mm) cc_final: 0.9114 (mm) REVERT: E 265 LEU cc_start: 0.8554 (tp) cc_final: 0.8240 (tp) REVERT: E 316 TYR cc_start: 0.7785 (m-80) cc_final: 0.6828 (m-80) REVERT: E 476 ASP cc_start: 0.9210 (m-30) cc_final: 0.8977 (p0) REVERT: F 628 TRP cc_start: 0.8964 (m100) cc_final: 0.8255 (m100) REVERT: F 647 GLU cc_start: 0.9189 (pt0) cc_final: 0.8841 (pp20) REVERT: F 650 GLN cc_start: 0.9280 (tp40) cc_final: 0.8782 (tm-30) REVERT: F 651 ASN cc_start: 0.9231 (m110) cc_final: 0.8481 (m110) REVERT: F 656 ASN cc_start: 0.9072 (t0) cc_final: 0.8840 (m-40) outliers start: 1 outliers final: 0 residues processed: 302 average time/residue: 0.3311 time to fit residues: 154.4868 Evaluate side-chains 231 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 82 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 65 optimal weight: 0.3980 chunk 17 optimal weight: 20.0000 chunk 78 optimal weight: 0.8980 chunk 231 optimal weight: 30.0000 chunk 175 optimal weight: 0.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 HIS ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 ASN ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.080917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.069128 restraints weight = 86638.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.070971 restraints weight = 52409.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.072240 restraints weight = 35931.533| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.5440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 19113 Z= 0.212 Angle : 0.840 16.443 26251 Z= 0.393 Chirality : 0.049 0.423 3354 Planarity : 0.004 0.045 3234 Dihedral : 7.784 59.055 4593 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.06 % Allowed : 0.38 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.19), residues: 1767 helix: 0.22 (0.24), residues: 447 sheet: -0.71 (0.25), residues: 397 loop : -1.13 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP B 614 HIS 0.007 0.001 HIS A 249 PHE 0.030 0.002 PHE E 210 TYR 0.052 0.002 TYR B 643 ARG 0.010 0.001 ARG B 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00604 ( 65) link_NAG-ASN : angle 2.88495 ( 195) link_ALPHA1-4 : bond 0.01753 ( 1) link_ALPHA1-4 : angle 0.82231 ( 3) link_ALPHA1-6 : bond 0.00647 ( 3) link_ALPHA1-6 : angle 1.40491 ( 9) link_BETA1-4 : bond 0.01034 ( 24) link_BETA1-4 : angle 3.64416 ( 72) link_ALPHA1-3 : bond 0.00726 ( 3) link_ALPHA1-3 : angle 3.28329 ( 9) hydrogen bonds : bond 0.04434 ( 562) hydrogen bonds : angle 5.83737 ( 1524) link_BETA1-6 : bond 0.00786 ( 2) link_BETA1-6 : angle 1.92870 ( 6) SS BOND : bond 0.00521 ( 30) SS BOND : angle 1.41753 ( 60) link_BETA1-3 : bond 0.00591 ( 1) link_BETA1-3 : angle 7.49362 ( 3) covalent geometry : bond 0.00459 (18984) covalent geometry : angle 0.77357 (25894) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 284 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6786 (m-70) cc_final: 0.6454 (m-70) REVERT: A 163 LYS cc_start: 0.9192 (tttt) cc_final: 0.8967 (ttpt) REVERT: A 172 ASP cc_start: 0.8447 (m-30) cc_final: 0.8079 (m-30) REVERT: A 431 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8533 (mp10) REVERT: A 474 MET cc_start: 0.8992 (mmp) cc_final: 0.8728 (mmm) REVERT: B 543 ASN cc_start: 0.9228 (m110) cc_final: 0.8863 (t0) REVERT: B 584 GLU cc_start: 0.8584 (mt-10) cc_final: 0.7990 (mp0) REVERT: B 652 GLN cc_start: 0.9013 (tt0) cc_final: 0.8669 (tm-30) REVERT: B 656 ASN cc_start: 0.8978 (m110) cc_final: 0.8517 (m110) REVERT: C 80 ASN cc_start: 0.9133 (m-40) cc_final: 0.8479 (p0) REVERT: C 100 MET cc_start: 0.8883 (ptt) cc_final: 0.8613 (ptt) REVERT: C 142 MET cc_start: 0.9135 (mmm) cc_final: 0.8923 (mtt) REVERT: C 153 MET cc_start: 0.8736 (tpt) cc_final: 0.8231 (tpp) REVERT: D 536 THR cc_start: 0.9174 (p) cc_final: 0.8768 (t) REVERT: D 543 ASN cc_start: 0.8509 (t0) cc_final: 0.8146 (t0) REVERT: D 548 ILE cc_start: 0.8302 (pt) cc_final: 0.7829 (pt) REVERT: D 643 TYR cc_start: 0.9069 (m-10) cc_final: 0.8328 (m-80) REVERT: E 108 ILE cc_start: 0.9625 (tt) cc_final: 0.9231 (mm) REVERT: E 143 ARG cc_start: 0.7741 (mmt90) cc_final: 0.7169 (mtp-110) REVERT: E 153 MET cc_start: 0.7887 (tpt) cc_final: 0.7370 (tmm) REVERT: E 160 LYS cc_start: 0.8934 (mmtt) cc_final: 0.7967 (ttpt) REVERT: E 316 TYR cc_start: 0.7750 (m-80) cc_final: 0.6798 (m-80) REVERT: F 530 MET cc_start: 0.7991 (ttt) cc_final: 0.7686 (ttt) REVERT: F 579 ARG cc_start: 0.9363 (ttm110) cc_final: 0.9129 (ttm170) REVERT: F 647 GLU cc_start: 0.9236 (pt0) cc_final: 0.8904 (pp20) REVERT: F 650 GLN cc_start: 0.9376 (tp40) cc_final: 0.8851 (tm-30) REVERT: F 651 ASN cc_start: 0.9263 (m110) cc_final: 0.8572 (m110) REVERT: F 656 ASN cc_start: 0.9085 (t0) cc_final: 0.8850 (m-40) outliers start: 1 outliers final: 0 residues processed: 285 average time/residue: 0.3106 time to fit residues: 136.1071 Evaluate side-chains 226 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 147 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 chunk 178 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 166 optimal weight: 0.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 HIS ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN D 658 GLN ** E 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 ASN ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.082447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.070541 restraints weight = 85198.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.072411 restraints weight = 51570.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.073663 restraints weight = 35389.491| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19113 Z= 0.145 Angle : 0.769 16.311 26251 Z= 0.360 Chirality : 0.047 0.429 3354 Planarity : 0.004 0.047 3234 Dihedral : 7.427 57.989 4593 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.06 % Allowed : 0.44 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.20), residues: 1767 helix: 0.38 (0.25), residues: 446 sheet: -0.63 (0.25), residues: 406 loop : -1.17 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 426 HIS 0.009 0.001 HIS C 105 PHE 0.022 0.002 PHE E 210 TYR 0.040 0.002 TYR B 643 ARG 0.010 0.001 ARG B 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00539 ( 65) link_NAG-ASN : angle 2.80425 ( 195) link_ALPHA1-4 : bond 0.01535 ( 1) link_ALPHA1-4 : angle 0.94377 ( 3) link_ALPHA1-6 : bond 0.00714 ( 3) link_ALPHA1-6 : angle 1.31594 ( 9) link_BETA1-4 : bond 0.01105 ( 24) link_BETA1-4 : angle 3.51815 ( 72) link_ALPHA1-3 : bond 0.00932 ( 3) link_ALPHA1-3 : angle 2.96200 ( 9) hydrogen bonds : bond 0.04141 ( 562) hydrogen bonds : angle 5.62720 ( 1524) link_BETA1-6 : bond 0.00936 ( 2) link_BETA1-6 : angle 1.79845 ( 6) SS BOND : bond 0.00359 ( 30) SS BOND : angle 1.34820 ( 60) link_BETA1-3 : bond 0.00523 ( 1) link_BETA1-3 : angle 7.40638 ( 3) covalent geometry : bond 0.00316 (18984) covalent geometry : angle 0.70095 (25894) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5428.73 seconds wall clock time: 98 minutes 11.37 seconds (5891.37 seconds total)