Starting phenix.real_space_refine on Sun May 18 18:05:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ayv_43999/05_2025/9ayv_43999.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ayv_43999/05_2025/9ayv_43999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ayv_43999/05_2025/9ayv_43999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ayv_43999/05_2025/9ayv_43999.map" model { file = "/net/cci-nas-00/data/ceres_data/9ayv_43999/05_2025/9ayv_43999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ayv_43999/05_2025/9ayv_43999.cif" } resolution = 4.4 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 102 5.16 5 C 10591 2.51 5 N 2919 2.21 5 O 3449 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17061 Number of models: 1 Model: "" Number of chains: 36 Chain: "J" 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: "B" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1132 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain: "D" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1132 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain: "F" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1132 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain: "A" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3456 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 21, 'TRANS': 417} Chain breaks: 2 Chain: "C" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3486 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 21, 'TRANS': 421} Chain breaks: 2 Chain: "N" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3486 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 21, 'TRANS': 421} Chain breaks: 2 Chain: "H" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 484 Classifications: {'peptide': 97} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 96} Link IDs: {'TRANS': 96} Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 293 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 97} Unresolved non-hydrogen planarities: 97 Chain: "G" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 485 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'TRANS': 96} Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 291 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'UNK:plan-1': 97} Unresolved non-hydrogen planarities: 97 Chain: "E" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 545 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'TRANS': 108} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 109 Planarities with less than four sites: {'UNK:plan-1': 109} Unresolved non-hydrogen planarities: 109 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" 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: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 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: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 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: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 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: "N" 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 Time building chain proxies: 9.76, per 1000 atoms: 0.57 Number of scatterers: 17061 At special positions: 0 Unit cell: (136.895, 131.67, 158.84, 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 102 16.00 O 3449 8.00 N 2919 7.00 C 10591 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS F 561 " - pdb=" SG CYS N 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 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 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 209 " - pdb=" SG CYS A 238 " distance=2.03 Simple disulfide: pdb=" SG CYS A 219 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 321 " distance=2.03 Simple disulfide: pdb=" SG CYS A 368 " - pdb=" SG CYS A 435 " distance=2.03 Simple disulfide: pdb=" SG CYS A 375 " - pdb=" SG CYS A 408 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 187 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 209 " - pdb=" SG CYS C 238 " distance=2.03 Simple disulfide: pdb=" SG CYS C 219 " - pdb=" SG CYS C 230 " distance=2.04 Simple disulfide: pdb=" SG CYS C 287 " - pdb=" SG CYS C 321 " distance=2.03 Simple disulfide: pdb=" SG CYS C 368 " - pdb=" SG CYS C 435 " distance=2.03 Simple disulfide: pdb=" SG CYS C 375 " - pdb=" SG CYS C 408 " distance=2.03 Simple disulfide: pdb=" SG CYS N 54 " - pdb=" SG CYS N 73 " distance=2.03 Simple disulfide: pdb=" SG CYS N 119 " - pdb=" SG CYS N 196 " distance=2.03 Simple disulfide: pdb=" SG CYS N 126 " - pdb=" SG CYS N 187 " distance=2.03 Simple disulfide: pdb=" SG CYS N 131 " - pdb=" SG CYS N 148 " distance=2.03 Simple disulfide: pdb=" SG CYS N 209 " - pdb=" SG CYS N 238 " distance=2.03 Simple disulfide: pdb=" SG CYS N 219 " - pdb=" SG CYS N 230 " distance=2.03 Simple disulfide: pdb=" SG CYS N 287 " - pdb=" SG CYS N 321 " distance=2.03 Simple disulfide: pdb=" SG CYS N 368 " - pdb=" SG CYS N 435 " distance=2.03 Simple disulfide: pdb=" SG CYS N 375 " - pdb=" SG CYS N 408 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 4 " ALPHA1-6 " BMA T 3 " - " MAN T 5 " " BMA U 3 " - " MAN U 5 " " BMA W 3 " - " MAN W 4 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 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 b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A 501 " - " ASN A 133 " " NAG A 502 " - " ASN A 324 " " NAG A 503 " - " ASN A 382 " " NAG A 504 " - " ASN A 438 " " NAG A 505 " - " ASN A 130 " " NAG A 506 " - " ASN A 345 " " NAG A 507 " - " ASN A 292 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 501 " - " ASN C 324 " " NAG C 502 " - " ASN C 376 " " NAG C 503 " - " ASN C 438 " " NAG C 504 " - " ASN C 329 " " NAG C 505 " - " ASN C 88 " " NAG C 506 " - " ASN C 130 " " NAG C 507 " - " ASN C 188 " " NAG C 508 " - " ASN C 232 " " NAG C 509 " - " ASN C 267 " " NAG C 510 " - " ASN C 147 " " NAG C 511 " - " ASN C 280 " " NAG C 512 " - " ASN C 133 " " NAG C 513 " - " ASN C 382 " " NAG D 701 " - " ASN D 611 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG I 1 " - " ASN A 147 " " NAG K 1 " - " ASN A 151 " " NAG L 1 " - " ASN A 232 " " NAG M 1 " - " ASN A 253 " " NAG N 501 " - " ASN N 88 " " NAG N 502 " - " ASN N 130 " " NAG N 503 " - " ASN N 133 " " NAG N 504 " - " ASN N 147 " " NAG N 505 " - " ASN N 232 " " NAG N 506 " - " ASN N 292 " " NAG N 507 " - " ASN N 324 " " NAG N 508 " - " ASN N 329 " " NAG N 509 " - " ASN N 345 " " NAG N 510 " - " ASN N 382 " " NAG N 511 " - " ASN N 438 " " NAG N 512 " - " ASN N 451 " " NAG N 513 " - " ASN N 376 " " NAG O 1 " - " ASN A 376 " " NAG P 1 " - " ASN A 451 " " NAG Q 1 " - " ASN A 188 " " NAG R 1 " - " ASN A 221 " " NAG S 1 " - " ASN C 292 " " NAG T 1 " - " ASN C 138 " " NAG U 1 " - " ASN C 151 " " NAG V 1 " - " ASN C 221 " " NAG W 1 " - " ASN C 253 " " NAG X 1 " - " ASN C 345 " " NAG Y 1 " - " ASN C 451 " " NAG Z 1 " - " ASN N 151 " " NAG a 1 " - " ASN N 221 " " NAG b 1 " - " ASN N 253 " " NAG c 1 " - " ASN N 280 " " NAG d 1 " - " ASN N 188 " Time building additional restraints: 5.08 Conformation dependent library (CDL) restraints added in 1.7 seconds 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4076 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 40 sheets defined 30.0% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'B' and resid 534 through 542 removed outlier: 4.173A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 558 removed outlier: 5.070A pdb=" N GLN B 551 " --> pdb=" O GLY B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 568 Processing helix chain 'B' and resid 568 through 596 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 632 through 636 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'D' and resid 536 through 542 removed outlier: 3.509A pdb=" N ARG D 542 " --> pdb=" O THR D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 568 through 596 Processing helix chain 'D' and resid 611 through 615 Processing helix chain 'D' and resid 619 through 624 removed outlier: 3.672A pdb=" N ILE D 622 " --> pdb=" O LEU D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 662 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 537 through 558 removed outlier: 3.732A pdb=" N ALA F 541 " --> pdb=" O LEU F 537 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ILE F 548 " --> pdb=" O LEU F 544 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA F 558 " --> pdb=" O ASN F 554 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 568 Processing helix chain 'F' and resid 568 through 596 Processing helix chain 'F' and resid 618 through 623 removed outlier: 3.526A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 661 Processing helix chain 'A' and resid 68 through 73 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.217A 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 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 186 through 189 Processing helix chain 'A' and resid 324 through 344 removed outlier: 3.628A pdb=" N HIS A 342 " --> pdb=" O GLN A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 415 through 419 removed outlier: 3.763A pdb=" N ARG A 419 " --> pdb=" O MET A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 472 removed outlier: 3.544A pdb=" N SER A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLU A 470 " --> pdb=" O ASN A 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.110A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 189 Processing helix chain 'C' and resid 325 through 343 removed outlier: 3.888A pdb=" N LYS C 341 " --> pdb=" O LYS C 337 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N HIS C 342 " --> pdb=" O GLN C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 363 Processing helix chain 'C' and resid 415 through 419 removed outlier: 3.550A pdb=" N ARG C 419 " --> pdb=" O MET C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 469 removed outlier: 4.162A pdb=" N ASN C 466 " --> pdb=" O ASP C 462 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP C 467 " --> pdb=" O MET C 463 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 73 Processing helix chain 'N' and resid 96 through 98 No H-bonds generated for 'chain 'N' and resid 96 through 98' Processing helix chain 'N' and resid 99 through 116 Processing helix chain 'N' and resid 122 through 126 Processing helix chain 'N' and resid 137 through 139 No H-bonds generated for 'chain 'N' and resid 137 through 139' Processing helix chain 'N' and resid 186 through 189 Processing helix chain 'N' and resid 325 through 344 Processing helix chain 'N' and resid 358 through 363 Processing helix chain 'N' and resid 377 through 380 Processing helix chain 'N' and resid 415 through 419 removed outlier: 3.708A pdb=" N ARG N 419 " --> pdb=" O MET N 416 " (cutoff:3.500A) Processing helix chain 'N' and resid 463 through 471 removed outlier: 3.818A pdb=" N GLU N 470 " --> pdb=" O ASN N 466 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'J' and resid 13 through 14 removed outlier: 3.583A pdb=" N UNK J 13 " --> pdb=" O UNK J 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 29 through 30 removed outlier: 3.557A pdb=" N UNK J 29 " --> pdb=" O UNK J 85 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 34 through 35 removed outlier: 3.707A pdb=" N UNK J 79 " --> pdb=" O UNK J 35 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 45 through 47 Processing sheet with id=AA6, first strand: chain 'J' and resid 62 through 63 Processing sheet with id=AA7, first strand: chain 'B' and resid 603 through 609 removed outlier: 5.231A pdb=" N VAL C 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 603 through 609 removed outlier: 8.245A pdb=" N CYS D 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N TYR A 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N THR D 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL A 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL D 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 603 through 609 removed outlier: 8.159A pdb=" N CYS F 604 " --> pdb=" O TYR N 40 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N TYR N 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N THR F 606 " --> pdb=" O VAL N 38 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N VAL N 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N VAL F 608 " --> pdb=" O VAL N 36 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AB2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AB3, first strand: chain 'A' and resid 66 through 67 removed outlier: 6.764A pdb=" N ARG A 66 " --> pdb=" O SER A 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'A' and resid 130 through 136 removed outlier: 7.251A pdb=" N MET A 145 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 11.266A pdb=" N ALA A 136 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 9.808A pdb=" N GLU A 143 " --> pdb=" O ALA A 136 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 172 through 174 Processing sheet with id=AB7, first strand: chain 'A' and resid 193 through 194 removed outlier: 6.583A pdb=" N THR A 193 " --> pdb=" O TYR A 425 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 250 through 252 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 250 through 252 current: chain 'A' and resid 275 through 289 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 320 through 323 current: chain 'A' and resid 371 through 375 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 371 through 375 current: chain 'A' and resid 453 through 457 Processing sheet with id=AB9, first strand: chain 'A' and resid 293 through 301 removed outlier: 4.164A pdb=" N GLN A 311 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N THR A 296 " --> pdb=" O TYR A 309 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N TYR A 309 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE A 298 " --> pdb=" O TYR A 307 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N TYR A 307 " --> pdb=" O ILE A 298 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILE A 300 " --> pdb=" O TRP A 305 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N TRP A 305 " --> pdb=" O ILE A 300 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AC2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AC4, first strand: chain 'C' and resid 160 through 168 removed outlier: 10.036A pdb=" N GLU C 143 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 9.905A pdb=" N ALA C 136 " --> pdb=" O GLU C 143 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N MET C 145 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA C 134 " --> pdb=" O MET C 145 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 193 through 194 removed outlier: 6.683A pdb=" N THR C 193 " --> pdb=" O TYR C 425 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 250 through 252 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 250 through 252 current: chain 'C' and resid 275 through 301 removed outlier: 7.688A pdb=" N ASN C 292 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N VAL C 312 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N THR C 294 " --> pdb=" O GLY C 310 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLN C 304 " --> pdb=" O ILE C 300 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 304 through 313 current: chain 'C' and resid 371 through 375 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 371 through 375 current: chain 'C' and resid 453 through 457 Processing sheet with id=AC7, first strand: chain 'N' and resid 45 through 47 Processing sheet with id=AC8, first strand: chain 'N' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'N' and resid 91 through 94 Processing sheet with id=AD1, first strand: chain 'N' and resid 160 through 168 removed outlier: 6.894A pdb=" N MET N 145 " --> pdb=" O ALA N 134 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA N 134 " --> pdb=" O MET N 145 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 193 through 194 removed outlier: 6.716A pdb=" N THR N 193 " --> pdb=" O TYR N 425 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 250 through 252 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 250 through 252 current: chain 'N' and resid 275 through 301 removed outlier: 7.506A pdb=" N ASN N 292 " --> pdb=" O VAL N 312 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL N 312 " --> pdb=" O ASN N 292 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR N 294 " --> pdb=" O GLY N 310 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLN N 304 " --> pdb=" O ILE N 300 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 304 through 312 current: chain 'N' and resid 371 through 375 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 371 through 375 current: chain 'N' and resid 453 through 458 Processing sheet with id=AD4, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AD5, first strand: chain 'H' and resid 42 through 43 removed outlier: 6.634A pdb=" N UNK H 33 " --> pdb=" O UNK H 96 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 45 through 46 Processing sheet with id=AD7, first strand: chain 'G' and resid 10 through 11 Processing sheet with id=AD8, first strand: chain 'G' and resid 20 through 21 Processing sheet with id=AD9, first strand: chain 'G' and resid 30 through 31 removed outlier: 3.575A pdb=" N UNK G 43 " --> pdb=" O UNK G 31 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 2 through 3 Processing sheet with id=AE2, first strand: chain 'E' and resid 14 through 18 Processing sheet with id=AE3, first strand: chain 'E' and resid 41 through 43 Processing sheet with id=AE4, first strand: chain 'E' and resid 46 through 48 528 hydrogen bonds defined for protein. 1422 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.91 Time building geometry restraints manager: 5.77 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: 5529 1.34 - 1.47: 4154 1.47 - 1.59: 7527 1.59 - 1.72: 0 1.72 - 1.84: 132 Bond restraints: 17342 Sorted by residual: bond pdb=" C3 BMA T 3 " pdb=" O3 BMA T 3 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" N VAL N 173 " pdb=" CA VAL N 173 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.14e-02 7.69e+03 1.01e+01 bond pdb=" C1 BMA T 3 " pdb=" C2 BMA T 3 " ideal model delta sigma weight residual 1.519 1.581 -0.062 2.00e-02 2.50e+03 9.56e+00 bond pdb=" C1 NAG Y 2 " pdb=" O5 NAG Y 2 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.05e+00 bond pdb=" C1 NAG C 506 " pdb=" O5 NAG C 506 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.87e+00 ... (remaining 17337 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 21800 1.66 - 3.31: 1548 3.31 - 4.97: 228 4.97 - 6.63: 42 6.63 - 8.29: 8 Bond angle restraints: 23626 Sorted by residual: angle pdb=" CA GLY A 357 " pdb=" C GLY A 357 " pdb=" O GLY A 357 " ideal model delta sigma weight residual 121.76 117.90 3.86 8.70e-01 1.32e+00 1.97e+01 angle pdb=" N GLU A 330 " pdb=" CA GLU A 330 " pdb=" CB GLU A 330 " ideal model delta sigma weight residual 110.28 116.58 -6.30 1.55e+00 4.16e-01 1.65e+01 angle pdb=" C ALA A 257 " pdb=" CA ALA A 257 " pdb=" CB ALA A 257 " ideal model delta sigma weight residual 116.63 112.36 4.27 1.16e+00 7.43e-01 1.35e+01 angle pdb=" CA GLU A 330 " pdb=" CB GLU A 330 " pdb=" CG GLU A 330 " ideal model delta sigma weight residual 114.10 121.27 -7.17 2.00e+00 2.50e-01 1.29e+01 angle pdb=" CA ARG B 557 " pdb=" CB ARG B 557 " pdb=" CG ARG B 557 " ideal model delta sigma weight residual 114.10 121.06 -6.96 2.00e+00 2.50e-01 1.21e+01 ... (remaining 23621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.42: 10953 22.42 - 44.83: 481 44.83 - 67.25: 66 67.25 - 89.66: 60 89.66 - 112.08: 25 Dihedral angle restraints: 11585 sinusoidal: 5324 harmonic: 6261 Sorted by residual: dihedral pdb=" CB CYS N 126 " pdb=" SG CYS N 126 " pdb=" SG CYS N 187 " pdb=" CB CYS N 187 " ideal model delta sinusoidal sigma weight residual 93.00 157.04 -64.04 1 1.00e+01 1.00e-02 5.40e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 187 " pdb=" CB CYS A 187 " ideal model delta sinusoidal sigma weight residual 93.00 154.33 -61.33 1 1.00e+01 1.00e-02 4.99e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 187 " pdb=" CB CYS C 187 " ideal model delta sinusoidal sigma weight residual 93.00 150.35 -57.35 1 1.00e+01 1.00e-02 4.42e+01 ... (remaining 11582 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 2893 0.124 - 0.249: 101 0.249 - 0.373: 8 0.373 - 0.498: 2 0.498 - 0.622: 1 Chirality restraints: 3005 Sorted by residual: 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 -2.02 -0.38 2.00e-02 2.50e+03 3.58e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-02 2.50e+03 3.25e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.58e+01 ... (remaining 3002 not shown) Planarity restraints: 2998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " -0.316 2.00e-02 2.50e+03 2.70e-01 9.12e+02 pdb=" C7 NAG K 2 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " -0.177 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " 0.472 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 2 " -0.305 2.00e-02 2.50e+03 2.57e-01 8.27e+02 pdb=" C7 NAG I 2 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG I 2 " -0.188 2.00e-02 2.50e+03 pdb=" N2 NAG I 2 " 0.442 2.00e-02 2.50e+03 pdb=" O7 NAG I 2 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 2 " 0.300 2.00e-02 2.50e+03 2.54e-01 8.09e+02 pdb=" C7 NAG a 2 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG a 2 " 0.182 2.00e-02 2.50e+03 pdb=" N2 NAG a 2 " -0.439 2.00e-02 2.50e+03 pdb=" O7 NAG a 2 " 0.035 2.00e-02 2.50e+03 ... (remaining 2995 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 85 2.53 - 3.12: 13568 3.12 - 3.72: 25670 3.72 - 4.31: 35301 4.31 - 4.90: 56588 Nonbonded interactions: 131212 Sorted by model distance: nonbonded pdb=" ND2 ASN N 188 " pdb=" O7 NAG d 1 " model vdw 1.938 3.120 nonbonded pdb=" OG1 THR A 154 " pdb=" OE1 GLU A 155 " model vdw 2.047 3.040 nonbonded pdb=" OG SER A 469 " pdb=" OE1 GLU A 470 " model vdw 2.108 3.040 nonbonded pdb=" O3 NAG b 2 " pdb=" O5 BMA b 3 " model vdw 2.129 3.040 nonbonded pdb=" OD1 ASN D 607 " pdb=" OG SER D 649 " model vdw 2.210 3.040 ... (remaining 131207 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' selection = (chain 'C' and (resid 33 through 57 or resid 65 through 387 or resid 403 through \ 493 or resid 501 through 507)) selection = (chain 'N' and (resid 33 through 387 or resid 403 through 493 or resid 501 throu \ gh 507)) } ncs_group { reference = (chain 'B' and (resid 521 through 662 or resid 701)) selection = chain 'D' selection = (chain 'F' and (resid 521 through 662 or resid 701)) } ncs_group { reference = (chain 'E' and (resid 13 through 86 or (resid 87 and (name N or name CA or name \ C or name O )) or resid 88 through 109)) selection = (chain 'G' and (resid 1 through 74 or (resid 75 and (name N or name CA or name C \ or name O )) or resid 76 through 97)) selection = chain 'H' selection = (chain 'J' and (resid 6 through 79 or (resid 80 and (name N or name CA or name C \ or name O )) or resid 81 through 102)) } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'b' } ncs_group { reference = chain 'T' selection = chain 'U' } 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: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 37.670 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.100 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 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 : 0.006 0.070 17462 Z= 0.318 Angle : 1.014 20.372 23955 Z= 0.503 Chirality : 0.058 0.622 3005 Planarity : 0.012 0.270 2940 Dihedral : 14.683 112.079 7416 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.06 % Allowed : 0.26 % Favored : 99.68 % 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: 0.07 (0.19), residues: 1727 helix: 1.09 (0.24), residues: 427 sheet: 0.48 (0.26), residues: 346 loop : -0.58 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP D 631 HIS 0.022 0.002 HIS D 585 PHE 0.029 0.003 PHE C 53 TYR 0.044 0.003 TYR N 168 ARG 0.009 0.001 ARG D 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00655 ( 58) link_NAG-ASN : angle 3.20466 ( 174) link_ALPHA1-6 : bond 0.00504 ( 3) link_ALPHA1-6 : angle 1.94371 ( 9) link_BETA1-4 : bond 0.01361 ( 26) link_BETA1-4 : angle 4.28931 ( 78) link_ALPHA1-3 : bond 0.01271 ( 2) link_ALPHA1-3 : angle 3.70731 ( 6) hydrogen bonds : bond 0.14635 ( 528) hydrogen bonds : angle 6.68057 ( 1422) SS BOND : bond 0.00335 ( 31) SS BOND : angle 1.10103 ( 62) covalent geometry : bond 0.00637 (17342) covalent geometry : angle 0.94741 (23626) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 376 time to evaluate : 1.652 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: B 593 LEU cc_start: 0.9721 (mm) cc_final: 0.9291 (mm) REVERT: B 595 ILE cc_start: 0.9671 (tt) cc_final: 0.9370 (tt) REVERT: B 596 TRP cc_start: 0.9108 (m-10) cc_final: 0.7829 (m-90) REVERT: B 618 ASN cc_start: 0.8581 (t0) cc_final: 0.8268 (t0) REVERT: D 535 MET cc_start: 0.9458 (mpp) cc_final: 0.9225 (mpp) REVERT: D 588 ARG cc_start: 0.9203 (ttp-170) cc_final: 0.8523 (tpt90) REVERT: D 622 ILE cc_start: 0.7732 (tp) cc_final: 0.7205 (tp) REVERT: A 176 ASP cc_start: 0.8091 (m-30) cc_final: 0.7813 (m-30) REVERT: A 240 HIS cc_start: 0.7301 (p-80) cc_final: 0.6987 (p90) REVERT: A 309 TYR cc_start: 0.8296 (m-80) cc_final: 0.6981 (m-80) REVERT: A 322 ASN cc_start: 0.8549 (m-40) cc_final: 0.7741 (p0) REVERT: A 472 TYR cc_start: 0.8807 (p90) cc_final: 0.8344 (p90) REVERT: C 95 MET cc_start: 0.9051 (ptm) cc_final: 0.7120 (ppp) REVERT: C 122 LEU cc_start: 0.9646 (mt) cc_final: 0.9413 (mt) REVERT: C 125 LEU cc_start: 0.9215 (tt) cc_final: 0.8951 (tt) REVERT: C 166 LEU cc_start: 0.9355 (mt) cc_final: 0.9029 (mt) REVERT: C 171 ASP cc_start: 0.8780 (m-30) cc_final: 0.7680 (m-30) REVERT: C 288 THR cc_start: 0.9447 (t) cc_final: 0.9160 (m) REVERT: C 367 ASN cc_start: 0.9165 (t0) cc_final: 0.8923 (t0) REVERT: C 413 ILE cc_start: 0.9259 (mt) cc_final: 0.8443 (mt) REVERT: C 422 GLN cc_start: 0.9218 (mp10) cc_final: 0.8969 (mp10) REVERT: N 45 TRP cc_start: 0.8678 (p90) cc_final: 0.8311 (p90) REVERT: N 78 ASP cc_start: 0.7915 (t0) cc_final: 0.7702 (t0) REVERT: N 206 ILE cc_start: 0.9389 (mm) cc_final: 0.9076 (mm) REVERT: N 208 TYR cc_start: 0.8442 (m-80) cc_final: 0.7986 (m-80) REVERT: N 309 TYR cc_start: 0.8547 (m-80) cc_final: 0.7805 (m-80) REVERT: N 317 ARG cc_start: 0.6972 (ptp-170) cc_final: 0.5840 (tpt170) REVERT: N 340 ARG cc_start: 0.8494 (mmt90) cc_final: 0.8268 (mtp180) REVERT: N 358 ASP cc_start: 0.9063 (p0) cc_final: 0.8840 (p0) REVERT: N 416 MET cc_start: 0.8770 (ttm) cc_final: 0.6901 (ttm) outliers start: 1 outliers final: 0 residues processed: 377 average time/residue: 0.2753 time to fit residues: 156.2430 Evaluate side-chains 265 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 178 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 191 optimal weight: 9.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN B 591 GLN D 540 GLN D 562 GLN D 585 HIS F 552 GLN ** F 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 HIS A 278 HIS A 322 ASN A 466 ASN C 105 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.103730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.089146 restraints weight = 56127.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.091321 restraints weight = 32861.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.092835 restraints weight = 22420.663| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17462 Z= 0.166 Angle : 0.704 8.760 23955 Z= 0.330 Chirality : 0.045 0.356 3005 Planarity : 0.004 0.054 2940 Dihedral : 9.473 80.187 4107 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.13 % Allowed : 2.77 % Favored : 97.11 % 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: 0.26 (0.20), residues: 1727 helix: 1.44 (0.25), residues: 443 sheet: 0.30 (0.24), residues: 435 loop : -0.52 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 631 HIS 0.005 0.001 HIS N 240 PHE 0.015 0.001 PHE C 201 TYR 0.028 0.002 TYR A 168 ARG 0.010 0.001 ARG D 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 58) link_NAG-ASN : angle 2.12114 ( 174) link_ALPHA1-6 : bond 0.00754 ( 3) link_ALPHA1-6 : angle 1.47572 ( 9) link_BETA1-4 : bond 0.01027 ( 26) link_BETA1-4 : angle 3.08910 ( 78) link_ALPHA1-3 : bond 0.01653 ( 2) link_ALPHA1-3 : angle 1.94634 ( 6) hydrogen bonds : bond 0.05009 ( 528) hydrogen bonds : angle 5.44743 ( 1422) SS BOND : bond 0.00332 ( 31) SS BOND : angle 0.83371 ( 62) covalent geometry : bond 0.00361 (17342) covalent geometry : angle 0.65951 (23626) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 346 time to evaluate : 1.599 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: B 543 ASN cc_start: 0.8475 (m110) cc_final: 0.8215 (m110) REVERT: B 593 LEU cc_start: 0.9698 (mm) cc_final: 0.9427 (mm) REVERT: B 595 ILE cc_start: 0.9677 (tt) cc_final: 0.9377 (tt) REVERT: B 596 TRP cc_start: 0.9100 (m-10) cc_final: 0.8092 (m-90) REVERT: B 601 LYS cc_start: 0.8502 (mtpp) cc_final: 0.8241 (ttpt) REVERT: B 603 ILE cc_start: 0.9518 (mp) cc_final: 0.9262 (mp) REVERT: B 618 ASN cc_start: 0.8404 (t0) cc_final: 0.7977 (t0) REVERT: B 647 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8862 (mt-10) REVERT: B 653 GLN cc_start: 0.8328 (tm-30) cc_final: 0.8017 (tp-100) REVERT: D 585 HIS cc_start: 0.8112 (t-90) cc_final: 0.7859 (t70) REVERT: D 588 ARG cc_start: 0.9152 (ttp-170) cc_final: 0.8288 (ttt90) REVERT: D 646 LEU cc_start: 0.9180 (mt) cc_final: 0.8882 (mt) REVERT: F 530 MET cc_start: 0.8080 (mtt) cc_final: 0.7128 (mtt) REVERT: F 584 GLU cc_start: 0.8907 (tp30) cc_final: 0.8581 (tp30) REVERT: F 622 ILE cc_start: 0.8580 (pt) cc_final: 0.8275 (pt) REVERT: F 631 TRP cc_start: 0.9167 (t-100) cc_final: 0.8842 (t-100) REVERT: F 647 GLU cc_start: 0.9115 (pt0) cc_final: 0.8786 (pp20) REVERT: A 106 GLU cc_start: 0.7671 (pp20) cc_final: 0.7246 (pp20) REVERT: A 107 ASP cc_start: 0.8673 (m-30) cc_final: 0.8240 (m-30) REVERT: A 120 VAL cc_start: 0.8996 (t) cc_final: 0.8720 (m) REVERT: A 171 ASP cc_start: 0.8194 (m-30) cc_final: 0.7906 (m-30) REVERT: A 176 ASP cc_start: 0.8199 (m-30) cc_final: 0.7965 (m-30) REVERT: A 206 ILE cc_start: 0.8996 (mm) cc_final: 0.8763 (tp) REVERT: A 216 ILE cc_start: 0.9306 (mm) cc_final: 0.9057 (mm) REVERT: A 309 TYR cc_start: 0.8673 (m-80) cc_final: 0.6827 (m-80) REVERT: A 322 ASN cc_start: 0.8331 (m110) cc_final: 0.7747 (p0) REVERT: A 358 ASP cc_start: 0.8628 (p0) cc_final: 0.8377 (p0) REVERT: A 417 TRP cc_start: 0.8306 (m-90) cc_final: 0.7730 (m-90) REVERT: A 472 TYR cc_start: 0.9006 (p90) cc_final: 0.8510 (p90) REVERT: C 95 MET cc_start: 0.9117 (ptm) cc_final: 0.7507 (ppp) REVERT: C 122 LEU cc_start: 0.9712 (mt) cc_final: 0.9465 (mt) REVERT: C 125 LEU cc_start: 0.9277 (tt) cc_final: 0.9017 (tt) REVERT: C 171 ASP cc_start: 0.8885 (m-30) cc_final: 0.8546 (m-30) REVERT: C 316 ILE cc_start: 0.9410 (mm) cc_final: 0.9152 (mt) REVERT: C 422 GLN cc_start: 0.9289 (mp10) cc_final: 0.9083 (mp10) REVERT: N 45 TRP cc_start: 0.8618 (p90) cc_final: 0.8336 (p90) REVERT: N 175 LEU cc_start: 0.8926 (tp) cc_final: 0.8674 (tp) REVERT: N 208 TYR cc_start: 0.8206 (m-80) cc_final: 0.7550 (m-80) REVERT: N 317 ARG cc_start: 0.6752 (ptp-170) cc_final: 0.5934 (tpt170) REVERT: N 358 ASP cc_start: 0.9067 (p0) cc_final: 0.8801 (p0) REVERT: N 416 MET cc_start: 0.8632 (ttm) cc_final: 0.6821 (ttm) REVERT: N 472 TYR cc_start: 0.8917 (p90) cc_final: 0.8708 (p90) outliers start: 2 outliers final: 1 residues processed: 347 average time/residue: 0.2711 time to fit residues: 143.5163 Evaluate side-chains 253 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 252 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 130 optimal weight: 0.0370 chunk 45 optimal weight: 0.0370 chunk 75 optimal weight: 0.8980 chunk 6 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 204 optimal weight: 10.0000 chunk 164 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 169 optimal weight: 6.9990 overall best weight: 1.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 552 GLN F 554 ASN ** F 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN A 278 HIS N 342 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.103163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.088488 restraints weight = 56760.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.090671 restraints weight = 33301.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.092197 restraints weight = 22686.484| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17462 Z= 0.149 Angle : 0.660 9.016 23955 Z= 0.311 Chirality : 0.044 0.340 3005 Planarity : 0.004 0.044 2940 Dihedral : 7.464 68.028 4107 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.19 % Allowed : 2.38 % 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: 0.39 (0.20), residues: 1727 helix: 1.48 (0.25), residues: 447 sheet: 0.46 (0.25), residues: 426 loop : -0.47 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP N 96 HIS 0.006 0.001 HIS C 240 PHE 0.017 0.001 PHE C 201 TYR 0.041 0.002 TYR C 208 ARG 0.006 0.000 ARG D 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 58) link_NAG-ASN : angle 2.02843 ( 174) link_ALPHA1-6 : bond 0.00917 ( 3) link_ALPHA1-6 : angle 1.65097 ( 9) link_BETA1-4 : bond 0.00890 ( 26) link_BETA1-4 : angle 2.81770 ( 78) link_ALPHA1-3 : bond 0.01726 ( 2) link_ALPHA1-3 : angle 1.16904 ( 6) hydrogen bonds : bond 0.04575 ( 528) hydrogen bonds : angle 5.13080 ( 1422) SS BOND : bond 0.00263 ( 31) SS BOND : angle 0.73328 ( 62) covalent geometry : bond 0.00324 (17342) covalent geometry : angle 0.61877 (23626) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 329 time to evaluate : 1.755 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: B 543 ASN cc_start: 0.8531 (m110) cc_final: 0.8293 (m110) REVERT: B 601 LYS cc_start: 0.8528 (mtpp) cc_final: 0.8300 (ttmm) REVERT: B 647 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8926 (mt-10) REVERT: B 653 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8021 (tp-100) REVERT: D 534 SER cc_start: 0.8373 (m) cc_final: 0.8053 (p) REVERT: D 585 HIS cc_start: 0.8200 (t-90) cc_final: 0.7794 (t70) REVERT: D 588 ARG cc_start: 0.9205 (ttp-170) cc_final: 0.8653 (tpt90) REVERT: D 648 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8253 (tm-30) REVERT: F 584 GLU cc_start: 0.8922 (tp30) cc_final: 0.8530 (tp30) REVERT: F 622 ILE cc_start: 0.8588 (pt) cc_final: 0.8204 (pt) REVERT: F 631 TRP cc_start: 0.9090 (t-100) cc_final: 0.8881 (t-100) REVERT: F 647 GLU cc_start: 0.9098 (pt0) cc_final: 0.8797 (mt-10) REVERT: A 120 VAL cc_start: 0.8980 (t) cc_final: 0.8778 (m) REVERT: A 171 ASP cc_start: 0.8072 (m-30) cc_final: 0.7819 (m-30) REVERT: A 176 ASP cc_start: 0.8235 (m-30) cc_final: 0.7954 (m-30) REVERT: A 206 ILE cc_start: 0.9099 (mm) cc_final: 0.8898 (tp) REVERT: A 309 TYR cc_start: 0.8796 (m-80) cc_final: 0.7068 (m-80) REVERT: A 322 ASN cc_start: 0.8403 (m110) cc_final: 0.7775 (p0) REVERT: A 358 ASP cc_start: 0.8493 (p0) cc_final: 0.8245 (p0) REVERT: A 417 TRP cc_start: 0.8362 (m-90) cc_final: 0.7880 (m-90) REVERT: A 472 TYR cc_start: 0.8912 (p90) cc_final: 0.8493 (p90) REVERT: C 95 MET cc_start: 0.9190 (ptm) cc_final: 0.7682 (ppp) REVERT: C 122 LEU cc_start: 0.9685 (mt) cc_final: 0.9459 (mt) REVERT: C 171 ASP cc_start: 0.8958 (m-30) cc_final: 0.8656 (m-30) REVERT: C 422 GLN cc_start: 0.9289 (mp10) cc_final: 0.9077 (mp10) REVERT: C 467 TRP cc_start: 0.9115 (m-90) cc_final: 0.8733 (m-90) REVERT: N 104 MET cc_start: 0.9194 (tpp) cc_final: 0.8978 (tpp) REVERT: N 175 LEU cc_start: 0.8805 (tp) cc_final: 0.8534 (tp) REVERT: N 208 TYR cc_start: 0.8233 (m-80) cc_final: 0.7398 (m-80) REVERT: N 317 ARG cc_start: 0.6837 (ptp-170) cc_final: 0.5851 (tpt170) REVERT: N 358 ASP cc_start: 0.9104 (p0) cc_final: 0.8869 (p0) REVERT: N 416 MET cc_start: 0.8524 (ttm) cc_final: 0.6426 (ttm) REVERT: N 472 TYR cc_start: 0.8890 (p90) cc_final: 0.8565 (p90) outliers start: 3 outliers final: 1 residues processed: 330 average time/residue: 0.2686 time to fit residues: 135.2790 Evaluate side-chains 246 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 245 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 27 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 170 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 204 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 187 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN D 552 GLN ** D 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 HIS ** D 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 GLN A 220 ASN ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS C 278 HIS ** C 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 412 GLN N 466 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.094967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.080535 restraints weight = 58230.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.082521 restraints weight = 34576.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.083895 restraints weight = 23962.494| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 17462 Z= 0.373 Angle : 0.961 12.034 23955 Z= 0.450 Chirality : 0.051 0.337 3005 Planarity : 0.005 0.056 2940 Dihedral : 8.240 57.941 4107 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.13 % Allowed : 4.50 % Favored : 95.37 % 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: -0.12 (0.19), residues: 1727 helix: 1.04 (0.24), residues: 452 sheet: 0.39 (0.25), residues: 395 loop : -0.88 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP N 96 HIS 0.010 0.002 HIS D 564 PHE 0.027 0.003 PHE C 201 TYR 0.030 0.003 TYR N 208 ARG 0.010 0.001 ARG A 488 Details of bonding type rmsd link_NAG-ASN : bond 0.00754 ( 58) link_NAG-ASN : angle 2.41994 ( 174) link_ALPHA1-6 : bond 0.00723 ( 3) link_ALPHA1-6 : angle 1.48257 ( 9) link_BETA1-4 : bond 0.01002 ( 26) link_BETA1-4 : angle 3.13597 ( 78) link_ALPHA1-3 : bond 0.01643 ( 2) link_ALPHA1-3 : angle 0.91387 ( 6) hydrogen bonds : bond 0.05316 ( 528) hydrogen bonds : angle 5.86037 ( 1422) SS BOND : bond 0.00643 ( 31) SS BOND : angle 1.23796 ( 62) covalent geometry : bond 0.00819 (17342) covalent geometry : angle 0.92518 (23626) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 284 time to evaluate : 1.886 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: B 601 LYS cc_start: 0.8623 (mtpp) cc_final: 0.8344 (ttpt) REVERT: B 603 ILE cc_start: 0.9529 (mp) cc_final: 0.9176 (mt) REVERT: B 647 GLU cc_start: 0.9151 (mt-10) cc_final: 0.8903 (mt-10) REVERT: B 654 GLU cc_start: 0.9236 (mm-30) cc_final: 0.8749 (mm-30) REVERT: D 534 SER cc_start: 0.8826 (m) cc_final: 0.8406 (p) REVERT: D 535 MET cc_start: 0.9398 (mpp) cc_final: 0.9159 (mpp) REVERT: D 601 LYS cc_start: 0.9263 (mtmm) cc_final: 0.9001 (mtpp) REVERT: D 654 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8232 (mt-10) REVERT: F 530 MET cc_start: 0.7341 (mtt) cc_final: 0.7076 (mtm) REVERT: F 543 ASN cc_start: 0.8379 (m-40) cc_final: 0.8102 (m-40) REVERT: F 610 TRP cc_start: 0.8601 (t-100) cc_final: 0.8284 (t-100) REVERT: A 99 ASN cc_start: 0.9067 (t0) cc_final: 0.8840 (t0) REVERT: A 104 MET cc_start: 0.9518 (ptp) cc_final: 0.9279 (ptp) REVERT: A 107 ASP cc_start: 0.8867 (m-30) cc_final: 0.8507 (m-30) REVERT: A 145 MET cc_start: 0.6165 (mmt) cc_final: 0.5088 (mmt) REVERT: A 176 ASP cc_start: 0.8527 (m-30) cc_final: 0.8170 (m-30) REVERT: A 185 ILE cc_start: 0.9291 (tt) cc_final: 0.9091 (tp) REVERT: A 216 ILE cc_start: 0.9352 (mm) cc_final: 0.9119 (mm) REVERT: A 322 ASN cc_start: 0.8421 (m110) cc_final: 0.7883 (p0) REVERT: C 51 THR cc_start: 0.9061 (m) cc_final: 0.8721 (t) REVERT: C 74 CYS cc_start: 0.8977 (p) cc_final: 0.8721 (p) REVERT: C 93 PHE cc_start: 0.8488 (m-10) cc_final: 0.8166 (m-10) REVERT: C 95 MET cc_start: 0.9382 (ptm) cc_final: 0.8945 (tmm) REVERT: C 316 ILE cc_start: 0.9475 (mm) cc_final: 0.9265 (mt) REVERT: C 462 ASP cc_start: 0.8660 (t0) cc_final: 0.7837 (t0) REVERT: C 465 ASP cc_start: 0.9088 (m-30) cc_final: 0.8866 (m-30) REVERT: N 100 MET cc_start: 0.9110 (mtp) cc_final: 0.8821 (tpp) REVERT: N 156 LEU cc_start: 0.9006 (mp) cc_final: 0.8388 (tt) REVERT: N 171 ASP cc_start: 0.8722 (m-30) cc_final: 0.8374 (m-30) REVERT: N 175 LEU cc_start: 0.8926 (tp) cc_final: 0.8539 (tp) REVERT: N 208 TYR cc_start: 0.8307 (m-80) cc_final: 0.7745 (m-80) REVERT: N 209 CYS cc_start: 0.5433 (m) cc_final: 0.5024 (m) REVERT: N 317 ARG cc_start: 0.6718 (ptp-170) cc_final: 0.5899 (tpt170) REVERT: N 358 ASP cc_start: 0.9127 (p0) cc_final: 0.8864 (p0) REVERT: N 469 SER cc_start: 0.9286 (t) cc_final: 0.8939 (p) outliers start: 2 outliers final: 0 residues processed: 286 average time/residue: 0.2821 time to fit residues: 121.4036 Evaluate side-chains 222 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 68 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 9 optimal weight: 20.0000 chunk 142 optimal weight: 0.1980 chunk 126 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 564 HIS A 99 ASN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.099293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.085038 restraints weight = 57902.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.087106 restraints weight = 34254.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.088558 restraints weight = 23536.881| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17462 Z= 0.161 Angle : 0.714 12.768 23955 Z= 0.336 Chirality : 0.046 0.378 3005 Planarity : 0.004 0.041 2940 Dihedral : 7.260 52.862 4107 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.06 % Allowed : 1.48 % Favored : 98.46 % 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: 0.16 (0.20), residues: 1727 helix: 1.63 (0.25), residues: 435 sheet: 0.38 (0.25), residues: 407 loop : -0.80 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP N 96 HIS 0.018 0.001 HIS A 364 PHE 0.011 0.001 PHE C 53 TYR 0.026 0.002 TYR N 309 ARG 0.009 0.000 ARG C 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 58) link_NAG-ASN : angle 2.22553 ( 174) link_ALPHA1-6 : bond 0.00921 ( 3) link_ALPHA1-6 : angle 1.33232 ( 9) link_BETA1-4 : bond 0.00882 ( 26) link_BETA1-4 : angle 2.68511 ( 78) link_ALPHA1-3 : bond 0.01770 ( 2) link_ALPHA1-3 : angle 1.11175 ( 6) hydrogen bonds : bond 0.04550 ( 528) hydrogen bonds : angle 5.16204 ( 1422) SS BOND : bond 0.00360 ( 31) SS BOND : angle 0.89247 ( 62) covalent geometry : bond 0.00351 (17342) covalent geometry : angle 0.67370 (23626) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 313 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 595 ILE cc_start: 0.9672 (tt) cc_final: 0.9452 (tt) REVERT: B 596 TRP cc_start: 0.9207 (m-10) cc_final: 0.8343 (m-90) REVERT: B 601 LYS cc_start: 0.8541 (mtpp) cc_final: 0.8282 (ttpt) REVERT: B 603 ILE cc_start: 0.9477 (mp) cc_final: 0.9222 (mp) REVERT: B 647 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8866 (mt-10) REVERT: B 654 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8743 (mm-30) REVERT: D 534 SER cc_start: 0.8813 (m) cc_final: 0.8525 (p) REVERT: D 535 MET cc_start: 0.9354 (mpp) cc_final: 0.9130 (mpp) REVERT: D 588 ARG cc_start: 0.9155 (ttp-170) cc_final: 0.8366 (ttt90) REVERT: F 610 TRP cc_start: 0.8588 (t-100) cc_final: 0.8326 (t-100) REVERT: F 647 GLU cc_start: 0.9088 (pt0) cc_final: 0.8780 (pt0) REVERT: A 99 ASN cc_start: 0.8988 (OUTLIER) cc_final: 0.8763 (t0) REVERT: A 168 TYR cc_start: 0.8735 (m-10) cc_final: 0.8527 (m-10) REVERT: A 176 ASP cc_start: 0.8434 (m-30) cc_final: 0.8129 (m-30) REVERT: A 185 ILE cc_start: 0.9244 (tt) cc_final: 0.9040 (tp) REVERT: A 208 TYR cc_start: 0.8276 (m-10) cc_final: 0.8072 (m-10) REVERT: A 293 LYS cc_start: 0.8053 (mtmt) cc_final: 0.7673 (mtpt) REVERT: A 309 TYR cc_start: 0.8833 (m-80) cc_final: 0.7133 (m-80) REVERT: A 322 ASN cc_start: 0.8278 (m110) cc_final: 0.7802 (p0) REVERT: A 417 TRP cc_start: 0.8389 (m-90) cc_final: 0.7527 (m-90) REVERT: A 472 TYR cc_start: 0.8977 (p90) cc_final: 0.8567 (p90) REVERT: C 51 THR cc_start: 0.8952 (m) cc_final: 0.8602 (t) REVERT: C 74 CYS cc_start: 0.8912 (p) cc_final: 0.8551 (p) REVERT: C 93 PHE cc_start: 0.8244 (m-10) cc_final: 0.7794 (m-10) REVERT: C 95 MET cc_start: 0.9321 (ptm) cc_final: 0.8596 (ppp) REVERT: C 171 ASP cc_start: 0.8734 (m-30) cc_final: 0.8525 (m-30) REVERT: C 281 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8305 (mm-30) REVERT: C 300 ILE cc_start: 0.9679 (pt) cc_final: 0.9441 (tt) REVERT: C 322 ASN cc_start: 0.9047 (t0) cc_final: 0.8491 (p0) REVERT: C 422 GLN cc_start: 0.9363 (mp10) cc_final: 0.9083 (mp10) REVERT: C 467 TRP cc_start: 0.9024 (m-90) cc_final: 0.8771 (m-90) REVERT: N 171 ASP cc_start: 0.8756 (m-30) cc_final: 0.8521 (m-30) REVERT: N 175 LEU cc_start: 0.8701 (tp) cc_final: 0.8333 (tp) REVERT: N 208 TYR cc_start: 0.8317 (m-80) cc_final: 0.7403 (m-80) REVERT: N 317 ARG cc_start: 0.6775 (ptp-170) cc_final: 0.5811 (tpt170) REVERT: N 358 ASP cc_start: 0.9130 (p0) cc_final: 0.8886 (p0) REVERT: N 416 MET cc_start: 0.8701 (ttm) cc_final: 0.6561 (ttm) REVERT: N 469 SER cc_start: 0.9149 (t) cc_final: 0.8939 (p) REVERT: N 480 GLU cc_start: 0.8417 (mm-30) cc_final: 0.7767 (mp0) outliers start: 1 outliers final: 0 residues processed: 313 average time/residue: 0.2761 time to fit residues: 131.8721 Evaluate side-chains 247 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 246 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 201 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 203 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 178 optimal weight: 9.9990 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 HIS ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 HIS A 322 ASN ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.096004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.081723 restraints weight = 59067.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.083675 restraints weight = 35426.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.085054 restraints weight = 24662.984| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 17462 Z= 0.286 Angle : 0.850 8.706 23955 Z= 0.398 Chirality : 0.048 0.363 3005 Planarity : 0.004 0.047 2940 Dihedral : 7.734 57.385 4107 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.06 % Allowed : 2.83 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.20), residues: 1727 helix: 1.55 (0.25), residues: 434 sheet: 0.24 (0.25), residues: 406 loop : -1.09 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 35 HIS 0.007 0.002 HIS D 564 PHE 0.015 0.002 PHE A 93 TYR 0.019 0.002 TYR C 208 ARG 0.006 0.001 ARG C 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00589 ( 58) link_NAG-ASN : angle 2.26843 ( 174) link_ALPHA1-6 : bond 0.00910 ( 3) link_ALPHA1-6 : angle 1.41817 ( 9) link_BETA1-4 : bond 0.00944 ( 26) link_BETA1-4 : angle 2.85312 ( 78) link_ALPHA1-3 : bond 0.01723 ( 2) link_ALPHA1-3 : angle 1.04051 ( 6) hydrogen bonds : bond 0.04921 ( 528) hydrogen bonds : angle 5.51922 ( 1422) SS BOND : bond 0.00546 ( 31) SS BOND : angle 1.34933 ( 62) covalent geometry : bond 0.00627 (17342) covalent geometry : angle 0.81391 (23626) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 289 time to evaluate : 1.580 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: B 601 LYS cc_start: 0.8582 (mtpp) cc_final: 0.8327 (ttpt) REVERT: B 603 ILE cc_start: 0.9507 (mp) cc_final: 0.9138 (mt) REVERT: B 634 GLU cc_start: 0.9097 (mp0) cc_final: 0.8882 (mp0) REVERT: B 647 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8872 (mt-10) REVERT: D 534 SER cc_start: 0.8948 (m) cc_final: 0.8532 (p) REVERT: D 535 MET cc_start: 0.9389 (mpp) cc_final: 0.9178 (mpp) REVERT: D 603 ILE cc_start: 0.9381 (mm) cc_final: 0.9072 (pt) REVERT: D 638 TYR cc_start: 0.8097 (m-10) cc_final: 0.7829 (m-10) REVERT: F 601 LYS cc_start: 0.8818 (mtmt) cc_final: 0.8574 (mtmm) REVERT: F 610 TRP cc_start: 0.8654 (t-100) cc_final: 0.8336 (t-100) REVERT: F 647 GLU cc_start: 0.9159 (pt0) cc_final: 0.8900 (pp20) REVERT: A 107 ASP cc_start: 0.8970 (m-30) cc_final: 0.7960 (m-30) REVERT: A 171 ASP cc_start: 0.8351 (m-30) cc_final: 0.8146 (m-30) REVERT: A 176 ASP cc_start: 0.8573 (m-30) cc_final: 0.8220 (m-30) REVERT: A 309 TYR cc_start: 0.8825 (m-80) cc_final: 0.7164 (m-80) REVERT: A 322 ASN cc_start: 0.8346 (m-40) cc_final: 0.7939 (p0) REVERT: A 358 ASP cc_start: 0.8827 (p0) cc_final: 0.8604 (p0) REVERT: A 417 TRP cc_start: 0.8537 (m-90) cc_final: 0.7889 (m-90) REVERT: A 472 TYR cc_start: 0.8986 (p90) cc_final: 0.8612 (p90) REVERT: C 51 THR cc_start: 0.8967 (m) cc_final: 0.8677 (t) REVERT: C 74 CYS cc_start: 0.8844 (p) cc_final: 0.8616 (p) REVERT: C 93 PHE cc_start: 0.8252 (m-10) cc_final: 0.7942 (m-10) REVERT: C 95 MET cc_start: 0.9357 (ptm) cc_final: 0.8992 (tmm) REVERT: C 112 TRP cc_start: 0.8322 (m100) cc_final: 0.7316 (m100) REVERT: C 281 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8296 (mm-30) REVERT: C 300 ILE cc_start: 0.9662 (pt) cc_final: 0.9454 (tt) REVERT: C 422 GLN cc_start: 0.9408 (mp10) cc_final: 0.9116 (mp10) REVERT: C 462 ASP cc_start: 0.8616 (t0) cc_final: 0.7433 (t0) REVERT: C 492 ARG cc_start: 0.8771 (tpt-90) cc_final: 0.8400 (tpp-160) REVERT: N 171 ASP cc_start: 0.8693 (m-30) cc_final: 0.8402 (m-30) REVERT: N 175 LEU cc_start: 0.8860 (tp) cc_final: 0.8493 (tp) REVERT: N 208 TYR cc_start: 0.8226 (m-80) cc_final: 0.7501 (m-80) REVERT: N 358 ASP cc_start: 0.9146 (p0) cc_final: 0.8865 (p0) REVERT: N 416 MET cc_start: 0.8623 (ttm) cc_final: 0.6698 (ttm) REVERT: N 469 SER cc_start: 0.9300 (t) cc_final: 0.8997 (p) REVERT: N 480 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8051 (mm-30) outliers start: 1 outliers final: 1 residues processed: 290 average time/residue: 0.2872 time to fit residues: 128.6724 Evaluate side-chains 236 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 41 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 56 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 563 GLN D 564 HIS ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 342 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.097342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.083139 restraints weight = 58740.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.085147 restraints weight = 34902.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.086563 restraints weight = 24033.785| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 17462 Z= 0.184 Angle : 0.746 14.982 23955 Z= 0.349 Chirality : 0.046 0.419 3005 Planarity : 0.004 0.041 2940 Dihedral : 7.380 53.538 4107 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.20), residues: 1727 helix: 1.71 (0.25), residues: 428 sheet: 0.25 (0.25), residues: 405 loop : -1.02 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP N 96 HIS 0.010 0.001 HIS D 585 PHE 0.014 0.001 PHE C 53 TYR 0.014 0.002 TYR D 643 ARG 0.005 0.001 ARG C 157 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 58) link_NAG-ASN : angle 2.34723 ( 174) link_ALPHA1-6 : bond 0.00952 ( 3) link_ALPHA1-6 : angle 1.32328 ( 9) link_BETA1-4 : bond 0.00824 ( 26) link_BETA1-4 : angle 2.67179 ( 78) link_ALPHA1-3 : bond 0.01690 ( 2) link_ALPHA1-3 : angle 1.22822 ( 6) hydrogen bonds : bond 0.04477 ( 528) hydrogen bonds : angle 5.31759 ( 1422) SS BOND : bond 0.00349 ( 31) SS BOND : angle 1.28312 ( 62) covalent geometry : bond 0.00411 (17342) covalent geometry : angle 0.70311 (23626) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 1.618 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: B 596 TRP cc_start: 0.9182 (m-10) cc_final: 0.8180 (m-90) REVERT: B 601 LYS cc_start: 0.8584 (mtpp) cc_final: 0.8326 (ttpt) REVERT: B 603 ILE cc_start: 0.9482 (mp) cc_final: 0.9125 (mt) REVERT: B 634 GLU cc_start: 0.9070 (mp0) cc_final: 0.8758 (mp0) REVERT: B 647 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8792 (mt-10) REVERT: D 534 SER cc_start: 0.8908 (m) cc_final: 0.8560 (p) REVERT: D 603 ILE cc_start: 0.9367 (mm) cc_final: 0.9035 (pt) REVERT: D 634 GLU cc_start: 0.9181 (mm-30) cc_final: 0.8953 (tm-30) REVERT: D 638 TYR cc_start: 0.8117 (m-10) cc_final: 0.7737 (m-10) REVERT: D 654 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8100 (mt-10) REVERT: F 610 TRP cc_start: 0.8603 (t-100) cc_final: 0.8320 (t-100) REVERT: F 647 GLU cc_start: 0.9050 (pt0) cc_final: 0.8763 (pt0) REVERT: A 107 ASP cc_start: 0.8843 (m-30) cc_final: 0.7902 (m-30) REVERT: A 171 ASP cc_start: 0.8342 (m-30) cc_final: 0.8136 (m-30) REVERT: A 176 ASP cc_start: 0.8543 (m-30) cc_final: 0.8199 (m-30) REVERT: A 309 TYR cc_start: 0.8754 (m-80) cc_final: 0.7353 (m-80) REVERT: A 322 ASN cc_start: 0.8371 (m-40) cc_final: 0.7968 (p0) REVERT: A 358 ASP cc_start: 0.8775 (p0) cc_final: 0.8530 (p0) REVERT: A 417 TRP cc_start: 0.8398 (m-90) cc_final: 0.7625 (m-90) REVERT: A 472 TYR cc_start: 0.9038 (p90) cc_final: 0.8581 (p90) REVERT: C 51 THR cc_start: 0.8959 (m) cc_final: 0.8639 (t) REVERT: C 74 CYS cc_start: 0.8797 (p) cc_final: 0.8500 (p) REVERT: C 93 PHE cc_start: 0.8221 (m-10) cc_final: 0.7952 (m-10) REVERT: C 95 MET cc_start: 0.9324 (ptm) cc_final: 0.8784 (ppp) REVERT: C 201 PHE cc_start: 0.8206 (m-10) cc_final: 0.7933 (m-10) REVERT: C 271 ASN cc_start: 0.7923 (p0) cc_final: 0.7509 (p0) REVERT: C 281 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8279 (mm-30) REVERT: C 422 GLN cc_start: 0.9385 (mp10) cc_final: 0.9146 (mp10) REVERT: C 440 THR cc_start: 0.9216 (p) cc_final: 0.8949 (t) REVERT: C 462 ASP cc_start: 0.8548 (t0) cc_final: 0.7391 (t0) REVERT: C 467 TRP cc_start: 0.8894 (m-90) cc_final: 0.8674 (m-90) REVERT: C 492 ARG cc_start: 0.8727 (tpt-90) cc_final: 0.8389 (tpp-160) REVERT: N 104 MET cc_start: 0.9346 (tpp) cc_final: 0.8777 (tpp) REVERT: N 171 ASP cc_start: 0.8712 (m-30) cc_final: 0.8432 (m-30) REVERT: N 175 LEU cc_start: 0.8772 (tp) cc_final: 0.8448 (tp) REVERT: N 208 TYR cc_start: 0.8146 (m-80) cc_final: 0.7280 (m-80) REVERT: N 358 ASP cc_start: 0.9149 (p0) cc_final: 0.8894 (p0) REVERT: N 469 SER cc_start: 0.9236 (t) cc_final: 0.9015 (p) REVERT: N 480 GLU cc_start: 0.8438 (mm-30) cc_final: 0.7785 (mp0) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.2733 time to fit residues: 128.7373 Evaluate side-chains 233 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 124 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 103 optimal weight: 0.0770 chunk 139 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 119 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 overall best weight: 1.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 HIS D 585 HIS F 637 ASN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 GLN A 466 ASN ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 342 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.099445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.085253 restraints weight = 57819.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.087320 restraints weight = 34410.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.088735 restraints weight = 23707.616| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17462 Z= 0.143 Angle : 0.699 11.295 23955 Z= 0.330 Chirality : 0.045 0.311 3005 Planarity : 0.003 0.039 2940 Dihedral : 7.001 54.664 4107 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.06 % Allowed : 1.16 % Favored : 98.78 % 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: 0.09 (0.20), residues: 1727 helix: 1.79 (0.25), residues: 417 sheet: 0.31 (0.25), residues: 405 loop : -0.90 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 631 HIS 0.006 0.001 HIS A 364 PHE 0.012 0.001 PHE C 53 TYR 0.014 0.001 TYR D 638 ARG 0.007 0.000 ARG F 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00316 ( 58) link_NAG-ASN : angle 2.20191 ( 174) link_ALPHA1-6 : bond 0.00971 ( 3) link_ALPHA1-6 : angle 1.28692 ( 9) link_BETA1-4 : bond 0.00826 ( 26) link_BETA1-4 : angle 2.54571 ( 78) link_ALPHA1-3 : bond 0.01717 ( 2) link_ALPHA1-3 : angle 1.39611 ( 6) hydrogen bonds : bond 0.04300 ( 528) hydrogen bonds : angle 5.12511 ( 1422) SS BOND : bond 0.00342 ( 31) SS BOND : angle 0.89544 ( 62) covalent geometry : bond 0.00316 (17342) covalent geometry : angle 0.65935 (23626) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 311 time to evaluate : 1.738 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: B 601 LYS cc_start: 0.8623 (mtpp) cc_final: 0.8356 (ttpt) REVERT: B 603 ILE cc_start: 0.9491 (mp) cc_final: 0.9155 (mt) REVERT: B 634 GLU cc_start: 0.8981 (mp0) cc_final: 0.8753 (mp0) REVERT: B 647 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8856 (mt-10) REVERT: D 534 SER cc_start: 0.8887 (m) cc_final: 0.8494 (p) REVERT: D 634 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8895 (tm-30) REVERT: D 654 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8164 (mt-10) REVERT: F 610 TRP cc_start: 0.8581 (t-100) cc_final: 0.8310 (t-100) REVERT: F 614 TRP cc_start: 0.6304 (m100) cc_final: 0.5962 (m100) REVERT: F 647 GLU cc_start: 0.9103 (pt0) cc_final: 0.8761 (pt0) REVERT: A 171 ASP cc_start: 0.8308 (m-30) cc_final: 0.8068 (m-30) REVERT: A 176 ASP cc_start: 0.8501 (m-30) cc_final: 0.8208 (m-30) REVERT: A 182 TYR cc_start: 0.7802 (m-80) cc_final: 0.7594 (m-10) REVERT: A 309 TYR cc_start: 0.8764 (m-80) cc_final: 0.7116 (m-80) REVERT: A 322 ASN cc_start: 0.8323 (m-40) cc_final: 0.7976 (p0) REVERT: A 358 ASP cc_start: 0.8762 (p0) cc_final: 0.8529 (p0) REVERT: A 417 TRP cc_start: 0.8312 (m-90) cc_final: 0.7557 (m-90) REVERT: A 472 TYR cc_start: 0.9049 (p90) cc_final: 0.8602 (p90) REVERT: C 47 ASP cc_start: 0.8030 (m-30) cc_final: 0.7445 (m-30) REVERT: C 51 THR cc_start: 0.8967 (m) cc_final: 0.8605 (t) REVERT: C 74 CYS cc_start: 0.8767 (p) cc_final: 0.8489 (p) REVERT: C 93 PHE cc_start: 0.8460 (m-10) cc_final: 0.7965 (m-10) REVERT: C 95 MET cc_start: 0.9324 (ptm) cc_final: 0.8791 (ppp) REVERT: C 171 ASP cc_start: 0.8636 (m-30) cc_final: 0.8365 (m-30) REVERT: C 271 ASN cc_start: 0.7897 (p0) cc_final: 0.7482 (p0) REVERT: C 281 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8229 (mm-30) REVERT: C 322 ASN cc_start: 0.9001 (t0) cc_final: 0.8536 (p0) REVERT: C 422 GLN cc_start: 0.9371 (mp10) cc_final: 0.9125 (mp10) REVERT: C 424 MET cc_start: 0.8289 (ttm) cc_final: 0.8057 (ttm) REVERT: C 462 ASP cc_start: 0.8552 (t0) cc_final: 0.7345 (t0) REVERT: C 492 ARG cc_start: 0.8737 (tpt-90) cc_final: 0.8362 (tpp-160) REVERT: N 171 ASP cc_start: 0.8789 (m-30) cc_final: 0.8560 (m-30) REVERT: N 175 LEU cc_start: 0.8749 (tp) cc_final: 0.8420 (tp) REVERT: N 208 TYR cc_start: 0.8025 (m-80) cc_final: 0.7494 (m-80) REVERT: N 358 ASP cc_start: 0.9144 (p0) cc_final: 0.8892 (p0) REVERT: N 424 MET cc_start: 0.8017 (ttp) cc_final: 0.7487 (ttp) REVERT: N 469 SER cc_start: 0.9190 (t) cc_final: 0.8968 (p) REVERT: N 480 GLU cc_start: 0.8442 (mm-30) cc_final: 0.7751 (mp0) outliers start: 1 outliers final: 0 residues processed: 312 average time/residue: 0.2657 time to fit residues: 128.1240 Evaluate side-chains 249 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 72 optimal weight: 6.9990 chunk 208 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 111 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 chunk 2 optimal weight: 30.0000 chunk 23 optimal weight: 5.9990 chunk 175 optimal weight: 0.8980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 HIS ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 625 ASN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 ASN N 342 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.097996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.084153 restraints weight = 58909.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.086108 restraints weight = 35817.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.087467 restraints weight = 25036.488| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17462 Z= 0.201 Angle : 0.749 10.487 23955 Z= 0.353 Chirality : 0.047 0.423 3005 Planarity : 0.004 0.039 2940 Dihedral : 7.197 55.752 4107 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.20), residues: 1727 helix: 1.75 (0.25), residues: 423 sheet: 0.38 (0.26), residues: 390 loop : -0.97 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP N 96 HIS 0.011 0.001 HIS D 585 PHE 0.018 0.002 PHE C 201 TYR 0.020 0.002 TYR C 208 ARG 0.006 0.001 ARG F 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00401 ( 58) link_NAG-ASN : angle 2.27735 ( 174) link_ALPHA1-6 : bond 0.00955 ( 3) link_ALPHA1-6 : angle 1.34761 ( 9) link_BETA1-4 : bond 0.00873 ( 26) link_BETA1-4 : angle 2.59412 ( 78) link_ALPHA1-3 : bond 0.01793 ( 2) link_ALPHA1-3 : angle 1.33587 ( 6) hydrogen bonds : bond 0.04413 ( 528) hydrogen bonds : angle 5.20866 ( 1422) SS BOND : bond 0.00380 ( 31) SS BOND : angle 1.13992 ( 62) covalent geometry : bond 0.00446 (17342) covalent geometry : angle 0.70941 (23626) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 1.802 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: B 601 LYS cc_start: 0.8627 (mtpp) cc_final: 0.8414 (ttpt) REVERT: B 603 ILE cc_start: 0.9494 (mp) cc_final: 0.9173 (mt) REVERT: B 634 GLU cc_start: 0.9083 (mp0) cc_final: 0.8721 (mp0) REVERT: B 647 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8768 (mt-10) REVERT: D 534 SER cc_start: 0.8876 (m) cc_final: 0.8524 (p) REVERT: D 535 MET cc_start: 0.9429 (mpp) cc_final: 0.9192 (mpp) REVERT: D 588 ARG cc_start: 0.8901 (ttp-170) cc_final: 0.8391 (tpt90) REVERT: D 634 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8931 (tm-30) REVERT: D 654 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8110 (mt-10) REVERT: F 610 TRP cc_start: 0.8558 (t-100) cc_final: 0.8303 (t-100) REVERT: F 626 MET cc_start: 0.5717 (ppp) cc_final: 0.4745 (ppp) REVERT: F 647 GLU cc_start: 0.9101 (pt0) cc_final: 0.8779 (pt0) REVERT: A 107 ASP cc_start: 0.8934 (m-30) cc_final: 0.8062 (m-30) REVERT: A 176 ASP cc_start: 0.8535 (m-30) cc_final: 0.8222 (m-30) REVERT: A 293 LYS cc_start: 0.8371 (mtmt) cc_final: 0.7990 (mtpt) REVERT: A 304 GLN cc_start: 0.9138 (mm-40) cc_final: 0.8722 (mm110) REVERT: A 309 TYR cc_start: 0.8761 (m-80) cc_final: 0.7047 (m-80) REVERT: A 322 ASN cc_start: 0.8416 (m-40) cc_final: 0.8057 (p0) REVERT: A 358 ASP cc_start: 0.8726 (p0) cc_final: 0.8494 (p0) REVERT: A 472 TYR cc_start: 0.9092 (p90) cc_final: 0.8643 (p90) REVERT: C 51 THR cc_start: 0.8945 (m) cc_final: 0.8613 (t) REVERT: C 95 MET cc_start: 0.9307 (ptm) cc_final: 0.9039 (tmm) REVERT: C 143 GLU cc_start: 0.8316 (tp30) cc_final: 0.8060 (tp30) REVERT: C 171 ASP cc_start: 0.8629 (m-30) cc_final: 0.8364 (m-30) REVERT: C 281 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8287 (mm-30) REVERT: C 462 ASP cc_start: 0.8601 (t0) cc_final: 0.7391 (t0) REVERT: C 467 TRP cc_start: 0.8962 (m-90) cc_final: 0.8613 (m-90) REVERT: C 492 ARG cc_start: 0.8725 (tpt-90) cc_final: 0.8389 (tpp-160) REVERT: N 171 ASP cc_start: 0.8755 (m-30) cc_final: 0.8474 (m-30) REVERT: N 175 LEU cc_start: 0.8781 (tp) cc_final: 0.8454 (tp) REVERT: N 208 TYR cc_start: 0.8071 (m-80) cc_final: 0.7364 (m-80) REVERT: N 358 ASP cc_start: 0.9171 (p0) cc_final: 0.8921 (p0) REVERT: N 469 SER cc_start: 0.9248 (t) cc_final: 0.9035 (p) REVERT: N 480 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7797 (mp0) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.2651 time to fit residues: 118.4497 Evaluate side-chains 235 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 165 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 181 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 161 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 109 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 562 GLN D 585 HIS ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 ASN C 278 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.098718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.084813 restraints weight = 58192.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.086842 restraints weight = 34986.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.088205 restraints weight = 24226.955| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17462 Z= 0.135 Angle : 0.691 9.723 23955 Z= 0.327 Chirality : 0.045 0.292 3005 Planarity : 0.003 0.039 2940 Dihedral : 6.834 54.686 4107 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.20), residues: 1727 helix: 1.83 (0.26), residues: 417 sheet: 0.52 (0.26), residues: 382 loop : -0.88 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP N 96 HIS 0.008 0.001 HIS C 278 PHE 0.011 0.001 PHE C 53 TYR 0.021 0.002 TYR C 208 ARG 0.006 0.000 ARG A 264 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 58) link_NAG-ASN : angle 2.01136 ( 174) link_ALPHA1-6 : bond 0.00969 ( 3) link_ALPHA1-6 : angle 1.28163 ( 9) link_BETA1-4 : bond 0.00819 ( 26) link_BETA1-4 : angle 2.47433 ( 78) link_ALPHA1-3 : bond 0.01754 ( 2) link_ALPHA1-3 : angle 1.53436 ( 6) hydrogen bonds : bond 0.04162 ( 528) hydrogen bonds : angle 5.01956 ( 1422) SS BOND : bond 0.00283 ( 31) SS BOND : angle 1.31830 ( 62) covalent geometry : bond 0.00302 (17342) covalent geometry : angle 0.65482 (23626) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 1.598 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: B 601 LYS cc_start: 0.8618 (mtpp) cc_final: 0.8382 (ttpt) REVERT: B 603 ILE cc_start: 0.9464 (mp) cc_final: 0.9094 (mt) REVERT: B 634 GLU cc_start: 0.8971 (mp0) cc_final: 0.8706 (mp0) REVERT: B 647 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8766 (mt-10) REVERT: D 534 SER cc_start: 0.8885 (m) cc_final: 0.8475 (p) REVERT: D 588 ARG cc_start: 0.8933 (ttp-170) cc_final: 0.8388 (tpt90) REVERT: D 634 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8879 (tm-30) REVERT: F 575 GLN cc_start: 0.8925 (mm110) cc_final: 0.8710 (mm110) REVERT: F 610 TRP cc_start: 0.8531 (t-100) cc_final: 0.8308 (t-100) REVERT: F 614 TRP cc_start: 0.6183 (m100) cc_final: 0.5745 (m100) REVERT: F 626 MET cc_start: 0.5411 (ppp) cc_final: 0.4611 (ppp) REVERT: F 647 GLU cc_start: 0.9065 (pt0) cc_final: 0.8753 (pt0) REVERT: A 176 ASP cc_start: 0.8449 (m-30) cc_final: 0.8131 (m-30) REVERT: A 293 LYS cc_start: 0.8194 (mtmt) cc_final: 0.7882 (mtpt) REVERT: A 304 GLN cc_start: 0.9195 (mm-40) cc_final: 0.8740 (mm110) REVERT: A 309 TYR cc_start: 0.8752 (m-80) cc_final: 0.7105 (m-80) REVERT: A 322 ASN cc_start: 0.8390 (m-40) cc_final: 0.8038 (p0) REVERT: A 358 ASP cc_start: 0.8756 (p0) cc_final: 0.8503 (p0) REVERT: A 472 TYR cc_start: 0.9105 (p90) cc_final: 0.8705 (p90) REVERT: C 51 THR cc_start: 0.8924 (m) cc_final: 0.8578 (t) REVERT: C 95 MET cc_start: 0.9208 (ptm) cc_final: 0.8829 (ppp) REVERT: C 171 ASP cc_start: 0.8590 (m-30) cc_final: 0.8306 (m-30) REVERT: C 281 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8226 (mm-30) REVERT: C 322 ASN cc_start: 0.9008 (t0) cc_final: 0.8564 (p0) REVERT: C 462 ASP cc_start: 0.8564 (t0) cc_final: 0.7276 (t0) REVERT: C 467 TRP cc_start: 0.8932 (m-90) cc_final: 0.8520 (m-90) REVERT: C 492 ARG cc_start: 0.8728 (tpt-90) cc_final: 0.8388 (tpp-160) REVERT: N 104 MET cc_start: 0.9469 (tpp) cc_final: 0.8763 (tpp) REVERT: N 171 ASP cc_start: 0.8755 (m-30) cc_final: 0.8527 (m-30) REVERT: N 175 LEU cc_start: 0.8662 (tp) cc_final: 0.8316 (tp) REVERT: N 208 TYR cc_start: 0.8142 (m-80) cc_final: 0.7369 (m-80) REVERT: N 358 ASP cc_start: 0.9174 (p0) cc_final: 0.8938 (p0) REVERT: N 469 SER cc_start: 0.9229 (t) cc_final: 0.9022 (p) REVERT: N 480 GLU cc_start: 0.8467 (mm-30) cc_final: 0.7803 (mp0) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.2616 time to fit residues: 118.8488 Evaluate side-chains 242 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 51 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 178 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 183 optimal weight: 20.0000 chunk 189 optimal weight: 20.0000 chunk 169 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 208 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 658 GLN ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 ASN ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.094084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.080086 restraints weight = 58889.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.082029 restraints weight = 34899.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.083389 restraints weight = 24040.775| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 17462 Z= 0.337 Angle : 0.936 10.877 23955 Z= 0.441 Chirality : 0.051 0.438 3005 Planarity : 0.005 0.043 2940 Dihedral : 8.109 56.705 4107 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.20), residues: 1727 helix: 1.25 (0.24), residues: 418 sheet: 0.12 (0.26), residues: 405 loop : -1.22 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.004 TRP C 69 HIS 0.012 0.002 HIS A 364 PHE 0.033 0.002 PHE C 201 TYR 0.033 0.003 TYR C 208 ARG 0.005 0.001 ARG A 317 Details of bonding type rmsd link_NAG-ASN : bond 0.00744 ( 58) link_NAG-ASN : angle 2.53904 ( 174) link_ALPHA1-6 : bond 0.00922 ( 3) link_ALPHA1-6 : angle 1.44650 ( 9) link_BETA1-4 : bond 0.00985 ( 26) link_BETA1-4 : angle 2.89616 ( 78) link_ALPHA1-3 : bond 0.01845 ( 2) link_ALPHA1-3 : angle 1.19169 ( 6) hydrogen bonds : bond 0.05101 ( 528) hydrogen bonds : angle 5.74827 ( 1422) SS BOND : bond 0.00585 ( 31) SS BOND : angle 1.86804 ( 62) covalent geometry : bond 0.00743 (17342) covalent geometry : angle 0.89630 (23626) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4811.08 seconds wall clock time: 85 minutes 36.04 seconds (5136.04 seconds total)