Starting phenix.real_space_refine on Sun Jun 15 11:53:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ayv_43999/06_2025/9ayv_43999.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ayv_43999/06_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_43999/06_2025/9ayv_43999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ayv_43999/06_2025/9ayv_43999.map" model { file = "/net/cci-nas-00/data/ceres_data/9ayv_43999/06_2025/9ayv_43999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ayv_43999/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 11.98, per 1000 atoms: 0.70 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: 5.56 Conformation dependent library (CDL) restraints added in 1.9 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: 2.27 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: 5.20 Time building geometry restraints manager: 6.43 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: 3.800 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: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 42.400 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.290 ------------------------------------------------------------------------------- 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 : 1.898 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: 0.2867 time to fit residues: 163.4511 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 : 1.759 ------------------------------------------------------------------------------- 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 = 33)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.089146 restraints weight = 56127.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.091310 restraints weight = 32900.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.092811 restraints weight = 22440.753| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 3.08909 ( 78) link_ALPHA1-3 : bond 0.01653 ( 2) link_ALPHA1-3 : angle 1.94632 ( 6) hydrogen bonds : bond 0.05009 ( 528) hydrogen bonds : angle 5.44743 ( 1422) SS BOND : bond 0.00332 ( 31) SS BOND : angle 0.83369 ( 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 : 1.737 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: 0.8468 (m110) cc_final: 0.8207 (m110) REVERT: B 593 LEU cc_start: 0.9697 (mm) cc_final: 0.9426 (mm) REVERT: B 595 ILE cc_start: 0.9679 (tt) cc_final: 0.9382 (tt) REVERT: B 596 TRP cc_start: 0.9101 (m-10) cc_final: 0.8099 (m-90) REVERT: B 601 LYS cc_start: 0.8502 (mtpp) cc_final: 0.8242 (ttpt) REVERT: B 603 ILE cc_start: 0.9516 (mp) cc_final: 0.9260 (mp) REVERT: B 618 ASN cc_start: 0.8405 (t0) cc_final: 0.7978 (t0) REVERT: B 647 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8854 (mt-10) REVERT: B 653 GLN cc_start: 0.8324 (tm-30) cc_final: 0.8014 (tp-100) REVERT: D 585 HIS cc_start: 0.8102 (t-90) cc_final: 0.7850 (t70) REVERT: D 588 ARG cc_start: 0.9144 (ttp-170) cc_final: 0.8291 (ttt90) REVERT: D 646 LEU cc_start: 0.9179 (mt) cc_final: 0.8880 (mt) REVERT: F 530 MET cc_start: 0.8077 (mtt) cc_final: 0.7127 (mtt) REVERT: F 584 GLU cc_start: 0.8894 (tp30) cc_final: 0.8569 (tp30) REVERT: F 622 ILE cc_start: 0.8582 (pt) cc_final: 0.8279 (pt) REVERT: F 631 TRP cc_start: 0.9159 (t-100) cc_final: 0.8835 (t-100) REVERT: F 647 GLU cc_start: 0.9109 (pt0) cc_final: 0.8782 (pp20) REVERT: A 106 GLU cc_start: 0.7670 (pp20) cc_final: 0.7243 (pp20) REVERT: A 107 ASP cc_start: 0.8667 (m-30) cc_final: 0.8234 (m-30) REVERT: A 120 VAL cc_start: 0.8995 (t) cc_final: 0.8717 (m) REVERT: A 171 ASP cc_start: 0.8195 (m-30) cc_final: 0.7906 (m-30) REVERT: A 176 ASP cc_start: 0.8198 (m-30) cc_final: 0.7966 (m-30) REVERT: A 206 ILE cc_start: 0.8998 (mm) cc_final: 0.8767 (tp) REVERT: A 216 ILE cc_start: 0.9310 (mm) cc_final: 0.9062 (mm) REVERT: A 309 TYR cc_start: 0.8674 (m-80) cc_final: 0.6830 (m-80) REVERT: A 322 ASN cc_start: 0.8336 (m110) cc_final: 0.7753 (p0) REVERT: A 358 ASP cc_start: 0.8623 (p0) cc_final: 0.8371 (p0) REVERT: A 417 TRP cc_start: 0.8306 (m-90) cc_final: 0.7734 (m-90) REVERT: A 472 TYR cc_start: 0.9008 (p90) cc_final: 0.8510 (p90) REVERT: C 95 MET cc_start: 0.9114 (ptm) cc_final: 0.7508 (ppp) REVERT: C 122 LEU cc_start: 0.9711 (mt) cc_final: 0.9463 (mt) REVERT: C 125 LEU cc_start: 0.9275 (tt) cc_final: 0.9014 (tt) REVERT: C 171 ASP cc_start: 0.8884 (m-30) cc_final: 0.8544 (m-30) REVERT: C 316 ILE cc_start: 0.9409 (mm) cc_final: 0.9151 (mt) REVERT: C 422 GLN cc_start: 0.9289 (mp10) cc_final: 0.9086 (mp10) REVERT: N 45 TRP cc_start: 0.8615 (p90) cc_final: 0.8335 (p90) REVERT: N 175 LEU cc_start: 0.8923 (tp) cc_final: 0.8670 (tp) REVERT: N 208 TYR cc_start: 0.8204 (m-80) cc_final: 0.7543 (m-80) REVERT: N 317 ARG cc_start: 0.6753 (ptp-170) cc_final: 0.5937 (tpt170) REVERT: N 358 ASP cc_start: 0.9070 (p0) cc_final: 0.8804 (p0) REVERT: N 416 MET cc_start: 0.8631 (ttm) cc_final: 0.6820 (ttm) REVERT: N 472 TYR cc_start: 0.8915 (p90) cc_final: 0.8705 (p90) outliers start: 2 outliers final: 1 residues processed: 347 average time/residue: 0.2678 time to fit residues: 142.9049 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 : 1.678 ------------------------------------------------------------------------------- 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: 0.4980 chunk 45 optimal weight: 0.0770 chunk 75 optimal weight: 0.1980 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: 3.9990 chunk 15 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 chunk 169 optimal weight: 6.9990 overall best weight: 2.3542 ------------------------------------------------------------------------------- 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 99 ASN A 220 ASN A 278 HIS N 342 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.101982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.087306 restraints weight = 57000.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.089447 restraints weight = 33486.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.090937 restraints weight = 22924.125| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17462 Z= 0.177 Angle : 0.689 9.042 23955 Z= 0.324 Chirality : 0.045 0.342 3005 Planarity : 0.004 0.044 2940 Dihedral : 7.545 67.881 4107 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.19 % Allowed : 2.57 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.20), residues: 1727 helix: 1.46 (0.25), residues: 447 sheet: 0.42 (0.25), residues: 416 loop : -0.51 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP N 96 HIS 0.006 0.001 HIS C 240 PHE 0.019 0.002 PHE C 201 TYR 0.045 0.002 TYR C 208 ARG 0.007 0.001 ARG D 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 58) link_NAG-ASN : angle 2.03810 ( 174) link_ALPHA1-6 : bond 0.00888 ( 3) link_ALPHA1-6 : angle 1.67012 ( 9) link_BETA1-4 : bond 0.00941 ( 26) link_BETA1-4 : angle 2.85189 ( 78) link_ALPHA1-3 : bond 0.01730 ( 2) link_ALPHA1-3 : angle 1.13228 ( 6) hydrogen bonds : bond 0.04641 ( 528) hydrogen bonds : angle 5.20685 ( 1422) SS BOND : bond 0.00925 ( 31) SS BOND : angle 0.88991 ( 62) covalent geometry : bond 0.00382 (17342) covalent geometry : angle 0.64807 (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 329 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 326 time to evaluate : 1.721 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: B 543 ASN cc_start: 0.8547 (m110) cc_final: 0.8288 (m110) REVERT: B 601 LYS cc_start: 0.8554 (mtpp) cc_final: 0.8307 (ttmm) REVERT: B 647 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8915 (mt-10) REVERT: B 653 GLN cc_start: 0.8510 (tm-30) cc_final: 0.8073 (tp-100) REVERT: D 534 SER cc_start: 0.8427 (m) cc_final: 0.8113 (p) REVERT: D 535 MET cc_start: 0.9297 (mpp) cc_final: 0.8999 (mmm) REVERT: D 585 HIS cc_start: 0.8213 (t-90) cc_final: 0.7847 (t70) REVERT: D 588 ARG cc_start: 0.9210 (ttp-170) cc_final: 0.8660 (tpt90) REVERT: D 648 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8274 (tm-30) REVERT: F 622 ILE cc_start: 0.8602 (pt) cc_final: 0.8188 (pt) REVERT: F 631 TRP cc_start: 0.9100 (t-100) cc_final: 0.8871 (t-100) REVERT: F 647 GLU cc_start: 0.9111 (pt0) cc_final: 0.8844 (mt-10) REVERT: A 120 VAL cc_start: 0.9006 (t) cc_final: 0.8762 (m) REVERT: A 171 ASP cc_start: 0.8114 (m-30) cc_final: 0.7861 (m-30) REVERT: A 176 ASP cc_start: 0.8220 (m-30) cc_final: 0.7931 (m-30) REVERT: A 206 ILE cc_start: 0.9107 (mm) cc_final: 0.8903 (tp) REVERT: A 216 ILE cc_start: 0.9310 (mm) cc_final: 0.9092 (mm) REVERT: A 309 TYR cc_start: 0.8820 (m-80) cc_final: 0.7017 (m-80) REVERT: A 322 ASN cc_start: 0.8416 (m110) cc_final: 0.7793 (p0) REVERT: A 358 ASP cc_start: 0.8504 (p0) cc_final: 0.8257 (p0) REVERT: A 417 TRP cc_start: 0.8427 (m-90) cc_final: 0.7761 (m-90) REVERT: A 472 TYR cc_start: 0.8933 (p90) cc_final: 0.8492 (p90) REVERT: C 35 TRP cc_start: 0.7996 (m100) cc_final: 0.7265 (m100) REVERT: C 95 MET cc_start: 0.9229 (ptm) cc_final: 0.7662 (ppp) REVERT: C 122 LEU cc_start: 0.9695 (mt) cc_final: 0.9485 (mt) REVERT: C 171 ASP cc_start: 0.8991 (m-30) cc_final: 0.8681 (m-30) REVERT: C 300 ILE cc_start: 0.9531 (pt) cc_final: 0.9288 (tt) REVERT: C 358 ASP cc_start: 0.8696 (t0) cc_final: 0.8474 (t70) REVERT: C 422 GLN cc_start: 0.9302 (mp10) cc_final: 0.9078 (mp10) REVERT: C 467 TRP cc_start: 0.9142 (m-90) cc_final: 0.8765 (m-90) REVERT: N 45 TRP cc_start: 0.8679 (p90) cc_final: 0.8276 (p90) REVERT: N 104 MET cc_start: 0.9224 (tpp) cc_final: 0.9005 (tpp) REVERT: N 175 LEU cc_start: 0.8836 (tp) cc_final: 0.8539 (tp) REVERT: N 208 TYR cc_start: 0.8194 (m-80) cc_final: 0.7362 (m-80) REVERT: N 317 ARG cc_start: 0.6938 (ptp-170) cc_final: 0.5913 (tpt170) REVERT: N 358 ASP cc_start: 0.9111 (p0) cc_final: 0.8869 (p0) REVERT: N 416 MET cc_start: 0.8521 (ttm) cc_final: 0.6415 (ttm) REVERT: N 472 TYR cc_start: 0.8879 (p90) cc_final: 0.8579 (p90) outliers start: 3 outliers final: 1 residues processed: 327 average time/residue: 0.2763 time to fit residues: 137.7431 Evaluate side-chains 242 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 241 time to evaluate : 1.638 ------------------------------------------------------------------------------- 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: 7.9990 chunk 63 optimal weight: 9.9990 chunk 170 optimal weight: 6.9990 chunk 144 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 204 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 187 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 552 GLN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 GLN ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 GLN C 85 HIS ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 HIS ** C 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 85 HIS N 412 GLN N 466 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.092110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.077862 restraints weight = 58995.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.079783 restraints weight = 34923.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.081119 restraints weight = 24182.686| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.072 17462 Z= 0.458 Angle : 1.154 13.607 23955 Z= 0.537 Chirality : 0.057 0.326 3005 Planarity : 0.006 0.056 2940 Dihedral : 9.219 58.644 4107 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.32 % Allowed : 6.05 % Favored : 93.63 % 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: -0.67 (0.19), residues: 1727 helix: 0.51 (0.24), residues: 452 sheet: 0.21 (0.25), residues: 394 loop : -1.26 (0.19), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP N 96 HIS 0.014 0.003 HIS D 564 PHE 0.036 0.003 PHE C 201 TYR 0.037 0.004 TYR N 208 ARG 0.011 0.001 ARG A 488 Details of bonding type rmsd link_NAG-ASN : bond 0.01019 ( 58) link_NAG-ASN : angle 2.84461 ( 174) link_ALPHA1-6 : bond 0.00759 ( 3) link_ALPHA1-6 : angle 1.59850 ( 9) link_BETA1-4 : bond 0.01138 ( 26) link_BETA1-4 : angle 3.41110 ( 78) link_ALPHA1-3 : bond 0.01354 ( 2) link_ALPHA1-3 : angle 0.94671 ( 6) hydrogen bonds : bond 0.06083 ( 528) hydrogen bonds : angle 6.40362 ( 1422) SS BOND : bond 0.00946 ( 31) SS BOND : angle 1.55779 ( 62) covalent geometry : bond 0.00995 (17342) covalent geometry : angle 1.11566 (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 272 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 267 time to evaluate : 1.691 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 605 CYS cc_start: 0.8932 (p) cc_final: 0.8329 (t) REVERT: B 647 GLU cc_start: 0.9190 (mt-10) cc_final: 0.8976 (mt-10) REVERT: D 530 MET cc_start: 0.7391 (ptt) cc_final: 0.6681 (ptt) REVERT: D 534 SER cc_start: 0.8933 (m) cc_final: 0.8602 (p) REVERT: D 535 MET cc_start: 0.9401 (mpp) cc_final: 0.9177 (mpp) REVERT: D 601 LYS cc_start: 0.9324 (mtmm) cc_final: 0.9068 (mtpp) REVERT: D 603 ILE cc_start: 0.9430 (mm) cc_final: 0.9103 (pt) REVERT: D 622 ILE cc_start: 0.7899 (tp) cc_final: 0.7662 (tp) REVERT: D 648 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8237 (tm-30) REVERT: D 654 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8315 (mt-10) REVERT: F 543 ASN cc_start: 0.8495 (m-40) cc_final: 0.8150 (m-40) REVERT: F 561 CYS cc_start: 0.6900 (m) cc_final: 0.6697 (m) REVERT: F 589 ASP cc_start: 0.9212 (m-30) cc_final: 0.8867 (m-30) REVERT: F 610 TRP cc_start: 0.8637 (t-100) cc_final: 0.8258 (t-100) REVERT: A 104 MET cc_start: 0.9372 (ptm) cc_final: 0.8777 (ttp) REVERT: A 107 ASP cc_start: 0.8914 (m-30) cc_final: 0.8639 (m-30) REVERT: A 176 ASP cc_start: 0.8585 (m-30) cc_final: 0.8228 (m-30) REVERT: A 209 CYS cc_start: 0.6654 (m) cc_final: 0.6452 (m) REVERT: A 216 ILE cc_start: 0.9365 (mm) cc_final: 0.9139 (mm) REVERT: A 322 ASN cc_start: 0.8366 (m-40) cc_final: 0.7932 (p0) REVERT: A 358 ASP cc_start: 0.8570 (p0) cc_final: 0.8351 (p0) REVERT: C 51 THR cc_start: 0.9145 (m) cc_final: 0.8878 (t) REVERT: C 95 MET cc_start: 0.9357 (ptm) cc_final: 0.8964 (tmm) REVERT: C 100 MET cc_start: 0.9123 (mmm) cc_final: 0.8797 (tpp) REVERT: C 367 ASN cc_start: 0.9441 (t0) cc_final: 0.9147 (t0) REVERT: N 95 MET cc_start: 0.9107 (ptt) cc_final: 0.8801 (ptt) REVERT: N 100 MET cc_start: 0.9173 (mtp) cc_final: 0.8965 (tpp) REVERT: N 171 ASP cc_start: 0.8661 (m-30) cc_final: 0.8356 (m-30) REVERT: N 208 TYR cc_start: 0.8379 (m-80) cc_final: 0.8089 (m-80) REVERT: N 317 ARG cc_start: 0.6722 (ptp-170) cc_final: 0.5730 (tpt170) REVERT: N 358 ASP cc_start: 0.9061 (p0) cc_final: 0.8784 (p0) REVERT: N 469 SER cc_start: 0.9456 (t) cc_final: 0.9069 (p) outliers start: 5 outliers final: 5 residues processed: 272 average time/residue: 0.2873 time to fit residues: 119.9100 Evaluate side-chains 226 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 221 time to evaluate : 1.616 ------------------------------------------------------------------------------- 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: 7.9990 chunk 194 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 107 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 9 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 chunk 126 optimal weight: 20.0000 chunk 105 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN ** D 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 HIS ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 552 GLN A 99 ASN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 GLN ** C 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.095863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.081622 restraints weight = 58486.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.083613 restraints weight = 34407.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.085035 restraints weight = 23653.463| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17462 Z= 0.237 Angle : 0.828 12.517 23955 Z= 0.387 Chirality : 0.049 0.556 3005 Planarity : 0.004 0.058 2940 Dihedral : 8.110 54.047 4107 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.13 % Allowed : 1.86 % Favored : 98.01 % 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: -0.40 (0.20), residues: 1727 helix: 1.17 (0.24), residues: 435 sheet: 0.17 (0.25), residues: 386 loop : -1.20 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP N 96 HIS 0.025 0.002 HIS A 364 PHE 0.030 0.002 PHE C 201 TYR 0.029 0.002 TYR N 309 ARG 0.005 0.001 ARG C 157 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 58) link_NAG-ASN : angle 2.48019 ( 174) link_ALPHA1-6 : bond 0.00924 ( 3) link_ALPHA1-6 : angle 1.40980 ( 9) link_BETA1-4 : bond 0.00959 ( 26) link_BETA1-4 : angle 2.87724 ( 78) link_ALPHA1-3 : bond 0.01711 ( 2) link_ALPHA1-3 : angle 1.07558 ( 6) hydrogen bonds : bond 0.04973 ( 528) hydrogen bonds : angle 5.66729 ( 1422) SS BOND : bond 0.00433 ( 31) SS BOND : angle 1.24174 ( 62) covalent geometry : bond 0.00518 (17342) covalent geometry : angle 0.78625 (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 298 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 296 time to evaluate : 1.991 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 647 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8912 (mt-10) REVERT: B 654 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8948 (mm-30) REVERT: D 601 LYS cc_start: 0.9242 (mtmm) cc_final: 0.9035 (mtpp) REVERT: D 603 ILE cc_start: 0.9380 (mm) cc_final: 0.9118 (pt) REVERT: D 648 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8289 (tm-30) REVERT: D 654 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8139 (mt-10) REVERT: F 610 TRP cc_start: 0.8599 (t-100) cc_final: 0.8261 (t-100) REVERT: F 650 GLN cc_start: 0.9092 (tm-30) cc_final: 0.8520 (tm-30) REVERT: A 176 ASP cc_start: 0.8569 (m-30) cc_final: 0.8207 (m-30) REVERT: A 185 ILE cc_start: 0.9265 (tp) cc_final: 0.8926 (mm) REVERT: A 216 ILE cc_start: 0.9406 (mm) cc_final: 0.9072 (mm) REVERT: A 322 ASN cc_start: 0.8263 (m-40) cc_final: 0.7932 (p0) REVERT: A 417 TRP cc_start: 0.8532 (m-90) cc_final: 0.7840 (m-90) REVERT: A 472 TYR cc_start: 0.9088 (p90) cc_final: 0.8727 (p90) REVERT: C 51 THR cc_start: 0.9063 (m) cc_final: 0.8676 (t) REVERT: C 74 CYS cc_start: 0.8877 (p) cc_final: 0.8625 (p) REVERT: C 95 MET cc_start: 0.9347 (ptm) cc_final: 0.8976 (tmm) REVERT: C 100 MET cc_start: 0.8982 (mmm) cc_final: 0.8656 (tpp) REVERT: C 281 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8332 (mm-30) REVERT: C 300 ILE cc_start: 0.9649 (pt) cc_final: 0.9445 (tt) REVERT: C 422 GLN cc_start: 0.9398 (mp10) cc_final: 0.9106 (mp10) REVERT: C 492 ARG cc_start: 0.8787 (tpt-90) cc_final: 0.8359 (tpp-160) REVERT: N 171 ASP cc_start: 0.8774 (m-30) cc_final: 0.8497 (m-30) REVERT: N 175 LEU cc_start: 0.8887 (tp) cc_final: 0.8560 (tp) REVERT: N 208 TYR cc_start: 0.8318 (m-80) cc_final: 0.7673 (m-80) REVERT: N 309 TYR cc_start: 0.8721 (m-10) cc_final: 0.8494 (m-10) REVERT: N 358 ASP cc_start: 0.9120 (p0) cc_final: 0.8834 (p0) REVERT: N 416 MET cc_start: 0.8653 (ttm) cc_final: 0.6583 (ttm) REVERT: N 469 SER cc_start: 0.9302 (t) cc_final: 0.8980 (p) REVERT: N 480 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8091 (mm-30) outliers start: 2 outliers final: 0 residues processed: 298 average time/residue: 0.3419 time to fit residues: 157.9777 Evaluate side-chains 238 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 1.722 ------------------------------------------------------------------------------- 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: 9.9990 chunk 12 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 203 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 138 optimal weight: 0.9990 chunk 194 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 178 optimal weight: 8.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN ** D 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 HIS F 630 GLN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** 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 = 0.3287 r_free = 0.3287 target = 0.095192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.080991 restraints weight = 58641.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.082955 restraints weight = 34729.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.084314 restraints weight = 24058.062| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 17462 Z= 0.253 Angle : 0.832 9.208 23955 Z= 0.389 Chirality : 0.048 0.480 3005 Planarity : 0.004 0.045 2940 Dihedral : 8.048 56.961 4107 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.06 % Allowed : 2.38 % Favored : 97.56 % 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: -0.42 (0.20), residues: 1727 helix: 1.19 (0.25), residues: 440 sheet: 0.15 (0.25), residues: 396 loop : -1.26 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP N 96 HIS 0.007 0.002 HIS D 585 PHE 0.025 0.002 PHE C 201 TYR 0.020 0.002 TYR N 208 ARG 0.004 0.001 ARG F 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00505 ( 58) link_NAG-ASN : angle 2.38308 ( 174) link_ALPHA1-6 : bond 0.00934 ( 3) link_ALPHA1-6 : angle 1.39466 ( 9) link_BETA1-4 : bond 0.00928 ( 26) link_BETA1-4 : angle 2.86165 ( 78) link_ALPHA1-3 : bond 0.01747 ( 2) link_ALPHA1-3 : angle 1.13806 ( 6) hydrogen bonds : bond 0.04765 ( 528) hydrogen bonds : angle 5.59390 ( 1422) SS BOND : bond 0.00517 ( 31) SS BOND : angle 1.23753 ( 62) covalent geometry : bond 0.00552 (17342) covalent geometry : angle 0.79190 (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 280 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 279 time to evaluate : 1.648 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: B 647 GLU cc_start: 0.9186 (mt-10) cc_final: 0.8888 (mt-10) REVERT: D 603 ILE cc_start: 0.9409 (mm) cc_final: 0.9050 (pt) REVERT: D 648 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8399 (tp30) REVERT: D 654 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8265 (mt-10) REVERT: F 538 THR cc_start: 0.8724 (p) cc_final: 0.7750 (p) REVERT: F 610 TRP cc_start: 0.8667 (t-100) cc_final: 0.8370 (t-100) REVERT: F 650 GLN cc_start: 0.9143 (tm-30) cc_final: 0.8533 (tm-30) REVERT: A 176 ASP cc_start: 0.8615 (m-30) cc_final: 0.8250 (m-30) REVERT: A 185 ILE cc_start: 0.9289 (tp) cc_final: 0.8970 (mm) REVERT: A 216 ILE cc_start: 0.9391 (mm) cc_final: 0.9062 (mm) REVERT: A 322 ASN cc_start: 0.8237 (m-40) cc_final: 0.7895 (p0) REVERT: A 417 TRP cc_start: 0.8502 (m-90) cc_final: 0.7916 (m-90) REVERT: A 472 TYR cc_start: 0.9131 (p90) cc_final: 0.8766 (p90) REVERT: C 51 THR cc_start: 0.9018 (m) cc_final: 0.8689 (t) REVERT: C 74 CYS cc_start: 0.8844 (p) cc_final: 0.8595 (p) REVERT: C 93 PHE cc_start: 0.8405 (m-10) cc_final: 0.8072 (m-10) REVERT: C 95 MET cc_start: 0.9366 (ptm) cc_final: 0.9008 (tmm) REVERT: C 100 MET cc_start: 0.8997 (mmm) cc_final: 0.8659 (tpp) REVERT: C 166 LEU cc_start: 0.9589 (mt) cc_final: 0.9378 (mt) REVERT: C 281 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8321 (mm-30) REVERT: C 467 TRP cc_start: 0.9029 (m-90) cc_final: 0.8794 (m-90) REVERT: C 492 ARG cc_start: 0.8740 (tpt-90) cc_final: 0.8384 (tpp-160) REVERT: N 171 ASP cc_start: 0.8745 (m-30) cc_final: 0.8360 (m-30) REVERT: N 208 TYR cc_start: 0.8204 (m-80) cc_final: 0.7577 (m-80) REVERT: N 358 ASP cc_start: 0.9118 (p0) cc_final: 0.8805 (p0) REVERT: N 416 MET cc_start: 0.8669 (ttm) cc_final: 0.6695 (ttm) REVERT: N 469 SER cc_start: 0.9332 (t) cc_final: 0.9000 (p) REVERT: N 480 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8067 (mm-30) outliers start: 1 outliers final: 1 residues processed: 280 average time/residue: 0.2711 time to fit residues: 116.4668 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 : 1.647 ------------------------------------------------------------------------------- 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: 9.9990 chunk 72 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 56 optimal weight: 0.3980 chunk 46 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 8 optimal weight: 20.0000 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 618 ASN F 637 ASN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 GLN ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.097462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.083228 restraints weight = 58601.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.085260 restraints weight = 34831.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.086644 restraints weight = 24016.195| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17462 Z= 0.155 Angle : 0.716 8.834 23955 Z= 0.339 Chirality : 0.046 0.345 3005 Planarity : 0.004 0.040 2940 Dihedral : 7.492 59.173 4107 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.06 % Allowed : 1.41 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % 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: -0.13 (0.20), residues: 1727 helix: 1.47 (0.25), residues: 429 sheet: 0.34 (0.26), residues: 390 loop : -1.06 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP N 96 HIS 0.012 0.001 HIS D 585 PHE 0.017 0.001 PHE C 53 TYR 0.026 0.002 TYR C 208 ARG 0.007 0.000 ARG F 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00309 ( 58) link_NAG-ASN : angle 2.01876 ( 174) link_ALPHA1-6 : bond 0.00986 ( 3) link_ALPHA1-6 : angle 1.30331 ( 9) link_BETA1-4 : bond 0.00842 ( 26) link_BETA1-4 : angle 2.64432 ( 78) link_ALPHA1-3 : bond 0.01668 ( 2) link_ALPHA1-3 : angle 1.38578 ( 6) hydrogen bonds : bond 0.04379 ( 528) hydrogen bonds : angle 5.24609 ( 1422) SS BOND : bond 0.00275 ( 31) SS BOND : angle 1.20353 ( 62) covalent geometry : bond 0.00346 (17342) covalent geometry : angle 0.67978 (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 308 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 307 time to evaluate : 1.635 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: B 603 ILE cc_start: 0.9553 (mt) cc_final: 0.9299 (mm) REVERT: B 647 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8811 (mt-10) REVERT: D 534 SER cc_start: 0.8884 (m) cc_final: 0.8517 (p) REVERT: D 634 GLU cc_start: 0.9235 (mm-30) cc_final: 0.8932 (tm-30) REVERT: D 638 TYR cc_start: 0.8052 (m-80) cc_final: 0.7759 (m-80) REVERT: D 647 GLU cc_start: 0.8535 (tp30) cc_final: 0.7893 (tp30) REVERT: D 651 ASN cc_start: 0.8754 (m-40) cc_final: 0.8488 (m-40) REVERT: D 654 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8163 (mt-10) REVERT: F 610 TRP cc_start: 0.8593 (t-100) cc_final: 0.8317 (t-100) REVERT: F 622 ILE cc_start: 0.8716 (pt) cc_final: 0.8389 (pt) REVERT: F 628 TRP cc_start: 0.9087 (m100) cc_final: 0.8508 (m100) REVERT: F 650 GLN cc_start: 0.9172 (tm-30) cc_final: 0.8579 (tm-30) REVERT: F 657 GLU cc_start: 0.9347 (tp30) cc_final: 0.8985 (tp30) REVERT: A 106 GLU cc_start: 0.8128 (pp20) cc_final: 0.7763 (pp20) REVERT: A 107 ASP cc_start: 0.8665 (m-30) cc_final: 0.8407 (m-30) REVERT: A 176 ASP cc_start: 0.8445 (m-30) cc_final: 0.8132 (m-30) REVERT: A 185 ILE cc_start: 0.9220 (tp) cc_final: 0.8924 (mm) REVERT: A 309 TYR cc_start: 0.8498 (m-80) cc_final: 0.7340 (m-80) REVERT: A 322 ASN cc_start: 0.8280 (m-40) cc_final: 0.7978 (p0) REVERT: A 417 TRP cc_start: 0.8353 (m-90) cc_final: 0.7612 (m-90) REVERT: A 472 TYR cc_start: 0.9118 (p90) cc_final: 0.8827 (p90) REVERT: C 51 THR cc_start: 0.8897 (m) cc_final: 0.8581 (t) REVERT: C 74 CYS cc_start: 0.8766 (p) cc_final: 0.8436 (p) REVERT: C 93 PHE cc_start: 0.8138 (m-10) cc_final: 0.7844 (m-10) REVERT: C 95 MET cc_start: 0.9339 (ptm) cc_final: 0.8804 (ppp) REVERT: C 135 THR cc_start: 0.9369 (p) cc_final: 0.9130 (p) REVERT: C 166 LEU cc_start: 0.9596 (mt) cc_final: 0.9383 (mt) REVERT: C 281 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8259 (mm-30) REVERT: C 422 GLN cc_start: 0.9365 (mp10) cc_final: 0.9161 (mp10) REVERT: C 492 ARG cc_start: 0.8761 (tpt-90) cc_final: 0.8384 (tpp-160) REVERT: N 104 MET cc_start: 0.9379 (tpp) cc_final: 0.8790 (tpp) REVERT: N 171 ASP cc_start: 0.8723 (m-30) cc_final: 0.8519 (m-30) REVERT: N 175 LEU cc_start: 0.8728 (tp) cc_final: 0.8407 (tp) REVERT: N 208 TYR cc_start: 0.8238 (m-80) cc_final: 0.7181 (m-80) REVERT: N 358 ASP cc_start: 0.9152 (p0) cc_final: 0.8879 (p0) REVERT: N 469 SER cc_start: 0.9234 (t) cc_final: 0.9012 (p) REVERT: N 480 GLU cc_start: 0.8452 (mm-30) cc_final: 0.7751 (mp0) outliers start: 1 outliers final: 0 residues processed: 308 average time/residue: 0.2974 time to fit residues: 142.7058 Evaluate side-chains 255 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 1.625 ------------------------------------------------------------------------------- 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: 0.6980 chunk 52 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 103 optimal weight: 0.0670 chunk 139 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 chunk 161 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 35 optimal weight: 0.1980 overall best weight: 1.3920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 HIS D 585 HIS F 625 ASN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 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 = 0.3357 r_free = 0.3357 target = 0.098294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.084404 restraints weight = 58258.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.086416 restraints weight = 35069.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.087788 restraints weight = 24260.358| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17462 Z= 0.139 Angle : 0.695 12.698 23955 Z= 0.327 Chirality : 0.045 0.311 3005 Planarity : 0.004 0.066 2940 Dihedral : 7.044 54.287 4107 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.06 % Allowed : 0.96 % Favored : 98.97 % 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: -0.01 (0.20), residues: 1727 helix: 1.54 (0.25), residues: 429 sheet: 0.49 (0.27), residues: 368 loop : -0.98 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP N 96 HIS 0.004 0.001 HIS A 364 PHE 0.012 0.001 PHE C 53 TYR 0.037 0.002 TYR A 182 ARG 0.010 0.000 ARG C 264 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 58) link_NAG-ASN : angle 2.20400 ( 174) link_ALPHA1-6 : bond 0.00961 ( 3) link_ALPHA1-6 : angle 1.28530 ( 9) link_BETA1-4 : bond 0.00823 ( 26) link_BETA1-4 : angle 2.54048 ( 78) link_ALPHA1-3 : bond 0.01765 ( 2) link_ALPHA1-3 : angle 1.49916 ( 6) hydrogen bonds : bond 0.04207 ( 528) hydrogen bonds : angle 5.12739 ( 1422) SS BOND : bond 0.00327 ( 31) SS BOND : angle 1.05131 ( 62) covalent geometry : bond 0.00310 (17342) covalent geometry : angle 0.65507 (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 302 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 301 time to evaluate : 1.721 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 647 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8770 (mt-10) REVERT: D 534 SER cc_start: 0.8767 (m) cc_final: 0.8447 (p) REVERT: D 535 MET cc_start: 0.9355 (mpp) cc_final: 0.9129 (mpp) REVERT: D 588 ARG cc_start: 0.9078 (ttp-170) cc_final: 0.8500 (tpt90) REVERT: D 591 GLN cc_start: 0.9141 (tm-30) cc_final: 0.8859 (tp-100) REVERT: D 634 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8943 (tm-30) REVERT: D 638 TYR cc_start: 0.8018 (m-80) cc_final: 0.7754 (m-80) REVERT: D 647 GLU cc_start: 0.8693 (tp30) cc_final: 0.8018 (tp30) REVERT: D 651 ASN cc_start: 0.8781 (m-40) cc_final: 0.8397 (m-40) REVERT: D 654 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7956 (mt-10) REVERT: F 610 TRP cc_start: 0.8541 (t-100) cc_final: 0.8279 (t-100) REVERT: F 614 TRP cc_start: 0.6240 (m100) cc_final: 0.5977 (m100) REVERT: F 623 TRP cc_start: 0.7885 (m100) cc_final: 0.7444 (m-10) REVERT: F 626 MET cc_start: 0.5114 (pmm) cc_final: 0.3780 (ppp) REVERT: F 650 GLN cc_start: 0.9134 (tm-30) cc_final: 0.8651 (tm-30) REVERT: F 657 GLU cc_start: 0.9289 (tp30) cc_final: 0.9014 (tp30) REVERT: A 106 GLU cc_start: 0.8091 (pp20) cc_final: 0.7583 (pp20) REVERT: A 107 ASP cc_start: 0.8596 (m-30) cc_final: 0.8327 (m-30) REVERT: A 176 ASP cc_start: 0.8405 (m-30) cc_final: 0.8051 (m-30) REVERT: A 185 ILE cc_start: 0.9220 (tp) cc_final: 0.8903 (mm) REVERT: A 309 TYR cc_start: 0.8805 (m-80) cc_final: 0.7306 (m-80) REVERT: A 322 ASN cc_start: 0.8298 (m-40) cc_final: 0.8001 (p0) REVERT: A 417 TRP cc_start: 0.8382 (m-90) cc_final: 0.7705 (m-90) REVERT: A 472 TYR cc_start: 0.9133 (p90) cc_final: 0.8885 (p90) REVERT: C 51 THR cc_start: 0.8891 (m) cc_final: 0.8581 (t) REVERT: C 93 PHE cc_start: 0.8157 (m-10) cc_final: 0.7823 (m-10) REVERT: C 95 MET cc_start: 0.9266 (ptm) cc_final: 0.8794 (ppp) REVERT: C 166 LEU cc_start: 0.9612 (mt) cc_final: 0.9358 (mt) REVERT: C 171 ASP cc_start: 0.8687 (m-30) cc_final: 0.8341 (m-30) REVERT: C 281 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8226 (mm-30) REVERT: C 422 GLN cc_start: 0.9378 (mp10) cc_final: 0.9139 (mp10) REVERT: C 467 TRP cc_start: 0.8905 (m-90) cc_final: 0.8676 (m-90) REVERT: C 492 ARG cc_start: 0.8701 (tpt-90) cc_final: 0.8373 (tpp-160) REVERT: N 100 MET cc_start: 0.8791 (tpp) cc_final: 0.8554 (tpp) REVERT: N 104 MET cc_start: 0.9321 (tpp) cc_final: 0.8673 (tpp) REVERT: N 171 ASP cc_start: 0.8750 (m-30) cc_final: 0.8500 (m-30) REVERT: N 175 LEU cc_start: 0.8670 (tp) cc_final: 0.8349 (tp) REVERT: N 208 TYR cc_start: 0.8177 (m-80) cc_final: 0.7353 (m-80) REVERT: N 358 ASP cc_start: 0.9181 (p0) cc_final: 0.8917 (p0) REVERT: N 424 MET cc_start: 0.7969 (ttp) cc_final: 0.7486 (ttp) REVERT: N 480 GLU cc_start: 0.8491 (mm-30) cc_final: 0.7855 (mp0) outliers start: 1 outliers final: 0 residues processed: 302 average time/residue: 0.3000 time to fit residues: 141.5963 Evaluate side-chains 247 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 2.037 ------------------------------------------------------------------------------- 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: 8.9990 chunk 208 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 111 optimal weight: 0.3980 chunk 38 optimal weight: 9.9990 chunk 101 optimal weight: 0.0050 chunk 2 optimal weight: 30.0000 chunk 23 optimal weight: 5.9990 chunk 175 optimal weight: 0.1980 overall best weight: 2.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN ** D 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 HIS D 585 HIS F 630 GLN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 342 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.097997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.083979 restraints weight = 57681.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.085971 restraints weight = 34423.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.087368 restraints weight = 23745.304| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17462 Z= 0.180 Angle : 0.729 11.393 23955 Z= 0.344 Chirality : 0.046 0.398 3005 Planarity : 0.004 0.043 2940 Dihedral : 7.074 55.236 4107 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.06 % Allowed : 0.45 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 1727 helix: 1.47 (0.25), residues: 429 sheet: 0.44 (0.26), residues: 378 loop : -1.02 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP N 96 HIS 0.006 0.001 HIS D 585 PHE 0.013 0.001 PHE C 201 TYR 0.017 0.002 TYR A 182 ARG 0.004 0.000 ARG N 492 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 58) link_NAG-ASN : angle 2.20099 ( 174) link_ALPHA1-6 : bond 0.00917 ( 3) link_ALPHA1-6 : angle 1.32424 ( 9) link_BETA1-4 : bond 0.00817 ( 26) link_BETA1-4 : angle 2.56128 ( 78) link_ALPHA1-3 : bond 0.01781 ( 2) link_ALPHA1-3 : angle 1.42469 ( 6) hydrogen bonds : bond 0.04236 ( 528) hydrogen bonds : angle 5.23061 ( 1422) SS BOND : bond 0.00362 ( 31) SS BOND : angle 0.99154 ( 62) covalent geometry : bond 0.00402 (17342) covalent geometry : angle 0.69115 (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 299 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 298 time to evaluate : 1.739 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 647 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8516 (mp0) REVERT: D 530 MET cc_start: 0.7447 (ptt) cc_final: 0.6788 (ptt) REVERT: D 534 SER cc_start: 0.8757 (m) cc_final: 0.8442 (p) REVERT: D 535 MET cc_start: 0.9391 (mpp) cc_final: 0.9072 (mmm) REVERT: D 540 GLN cc_start: 0.8504 (tp40) cc_final: 0.8262 (tp40) REVERT: D 591 GLN cc_start: 0.9230 (tm-30) cc_final: 0.8799 (tp-100) REVERT: D 634 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8991 (tm-30) REVERT: D 638 TYR cc_start: 0.8096 (m-80) cc_final: 0.7772 (m-80) REVERT: D 647 GLU cc_start: 0.8689 (tp30) cc_final: 0.7984 (tp30) REVERT: D 651 ASN cc_start: 0.8781 (m-40) cc_final: 0.8427 (m-40) REVERT: D 654 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7992 (mt-10) REVERT: F 610 TRP cc_start: 0.8602 (t-100) cc_final: 0.8317 (t-100) REVERT: F 623 TRP cc_start: 0.7911 (m100) cc_final: 0.7546 (m-10) REVERT: F 626 MET cc_start: 0.3771 (pmm) cc_final: 0.3268 (ppp) REVERT: F 650 GLN cc_start: 0.9104 (tm-30) cc_final: 0.8714 (tm-30) REVERT: A 106 GLU cc_start: 0.8096 (pp20) cc_final: 0.7641 (pp20) REVERT: A 107 ASP cc_start: 0.8622 (m-30) cc_final: 0.8367 (m-30) REVERT: A 176 ASP cc_start: 0.8266 (m-30) cc_final: 0.7896 (m-30) REVERT: A 304 GLN cc_start: 0.9165 (mm-40) cc_final: 0.8707 (mm110) REVERT: A 309 TYR cc_start: 0.8801 (m-80) cc_final: 0.7204 (m-80) REVERT: A 322 ASN cc_start: 0.8347 (m-40) cc_final: 0.8038 (p0) REVERT: A 417 TRP cc_start: 0.8454 (m-90) cc_final: 0.7784 (m-90) REVERT: A 472 TYR cc_start: 0.9141 (p90) cc_final: 0.8895 (p90) REVERT: C 51 THR cc_start: 0.8940 (m) cc_final: 0.8608 (t) REVERT: C 93 PHE cc_start: 0.8384 (m-10) cc_final: 0.8001 (m-10) REVERT: C 95 MET cc_start: 0.9319 (ptm) cc_final: 0.8795 (ppp) REVERT: C 112 TRP cc_start: 0.8857 (m100) cc_final: 0.8165 (m100) REVERT: C 166 LEU cc_start: 0.9612 (mt) cc_final: 0.9349 (mt) REVERT: C 281 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8283 (mm-30) REVERT: C 306 PHE cc_start: 0.8678 (t80) cc_final: 0.8453 (t80) REVERT: C 492 ARG cc_start: 0.8724 (tpt-90) cc_final: 0.8386 (tpp-160) REVERT: N 100 MET cc_start: 0.8856 (tpp) cc_final: 0.8600 (tpp) REVERT: N 171 ASP cc_start: 0.8762 (m-30) cc_final: 0.8491 (m-30) REVERT: N 175 LEU cc_start: 0.8729 (tp) cc_final: 0.8387 (tp) REVERT: N 208 TYR cc_start: 0.8140 (m-80) cc_final: 0.7497 (m-80) REVERT: N 358 ASP cc_start: 0.9189 (p0) cc_final: 0.8938 (p0) REVERT: N 480 GLU cc_start: 0.8444 (mm-30) cc_final: 0.7764 (mp0) outliers start: 1 outliers final: 0 residues processed: 299 average time/residue: 0.2952 time to fit residues: 135.2254 Evaluate side-chains 252 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 1.639 ------------------------------------------------------------------------------- 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: 3.9990 chunk 82 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 131 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 161 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 120 optimal weight: 0.6980 chunk 105 optimal weight: 7.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 342 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.099393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.085417 restraints weight = 57942.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.087426 restraints weight = 34931.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.088825 restraints weight = 24186.428| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17462 Z= 0.125 Angle : 0.675 10.391 23955 Z= 0.321 Chirality : 0.045 0.283 3005 Planarity : 0.003 0.040 2940 Dihedral : 6.646 54.080 4107 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.06 % Allowed : 0.13 % 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: 0.02 (0.20), residues: 1727 helix: 1.57 (0.25), residues: 428 sheet: 0.52 (0.26), residues: 380 loop : -0.99 (0.21), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP N 96 HIS 0.010 0.001 HIS D 585 PHE 0.010 0.001 PHE C 53 TYR 0.014 0.001 TYR A 182 ARG 0.004 0.000 ARG F 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00282 ( 58) link_NAG-ASN : angle 1.96875 ( 174) link_ALPHA1-6 : bond 0.00906 ( 3) link_ALPHA1-6 : angle 1.24564 ( 9) link_BETA1-4 : bond 0.00774 ( 26) link_BETA1-4 : angle 2.43074 ( 78) link_ALPHA1-3 : bond 0.01578 ( 2) link_ALPHA1-3 : angle 1.65576 ( 6) hydrogen bonds : bond 0.04047 ( 528) hydrogen bonds : angle 5.01207 ( 1422) SS BOND : bond 0.00521 ( 31) SS BOND : angle 1.44865 ( 62) covalent geometry : bond 0.00279 (17342) covalent geometry : angle 0.63787 (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 319 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 318 time to evaluate : 1.857 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 634 GLU cc_start: 0.8956 (mp0) cc_final: 0.8688 (mp0) REVERT: B 638 TYR cc_start: 0.8297 (m-80) cc_final: 0.7783 (m-80) REVERT: B 647 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8810 (mt-10) REVERT: D 534 SER cc_start: 0.8731 (m) cc_final: 0.8471 (p) REVERT: D 535 MET cc_start: 0.9375 (mpp) cc_final: 0.8980 (mmm) REVERT: D 580 VAL cc_start: 0.9224 (t) cc_final: 0.8926 (t) REVERT: D 581 LEU cc_start: 0.9482 (tp) cc_final: 0.8908 (tp) REVERT: D 584 GLU cc_start: 0.9342 (mt-10) cc_final: 0.9126 (mt-10) REVERT: D 588 ARG cc_start: 0.8845 (ttp-170) cc_final: 0.8247 (tpt90) REVERT: D 634 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8931 (tm-30) REVERT: D 638 TYR cc_start: 0.7996 (m-80) cc_final: 0.7675 (m-80) REVERT: D 647 GLU cc_start: 0.8716 (tp30) cc_final: 0.8053 (tp30) REVERT: D 651 ASN cc_start: 0.8732 (m-40) cc_final: 0.8326 (m-40) REVERT: D 654 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7931 (mt-10) REVERT: F 575 GLN cc_start: 0.8855 (mm110) cc_final: 0.8592 (mm110) REVERT: F 610 TRP cc_start: 0.8537 (t-100) cc_final: 0.8304 (t-100) REVERT: F 614 TRP cc_start: 0.6091 (m100) cc_final: 0.5760 (m100) REVERT: F 650 GLN cc_start: 0.9024 (tm-30) cc_final: 0.8620 (tm-30) REVERT: A 106 GLU cc_start: 0.8020 (pp20) cc_final: 0.7533 (pp20) REVERT: A 107 ASP cc_start: 0.8593 (m-30) cc_final: 0.8392 (m-30) REVERT: A 176 ASP cc_start: 0.8254 (m-30) cc_final: 0.7873 (m-30) REVERT: A 304 GLN cc_start: 0.9153 (mm-40) cc_final: 0.8719 (mm110) REVERT: A 309 TYR cc_start: 0.8887 (m-80) cc_final: 0.7617 (m-80) REVERT: A 322 ASN cc_start: 0.8275 (m-40) cc_final: 0.7991 (p0) REVERT: A 417 TRP cc_start: 0.8350 (m-90) cc_final: 0.7649 (m-90) REVERT: A 472 TYR cc_start: 0.9132 (p90) cc_final: 0.8922 (p90) REVERT: A 492 ARG cc_start: 0.8927 (ptp-110) cc_final: 0.8201 (mtt90) REVERT: C 51 THR cc_start: 0.8933 (m) cc_final: 0.8642 (t) REVERT: C 93 PHE cc_start: 0.8241 (m-10) cc_final: 0.7861 (m-10) REVERT: C 95 MET cc_start: 0.9285 (ptm) cc_final: 0.8777 (ppp) REVERT: C 112 TRP cc_start: 0.8822 (m100) cc_final: 0.7968 (m100) REVERT: C 139 SER cc_start: 0.9110 (m) cc_final: 0.8747 (p) REVERT: C 166 LEU cc_start: 0.9558 (mt) cc_final: 0.9313 (mt) REVERT: C 171 ASP cc_start: 0.8738 (m-30) cc_final: 0.8376 (m-30) REVERT: C 281 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8257 (mm-30) REVERT: C 322 ASN cc_start: 0.8950 (t0) cc_final: 0.8542 (p0) REVERT: C 467 TRP cc_start: 0.8872 (m-90) cc_final: 0.8553 (m-90) REVERT: C 492 ARG cc_start: 0.8694 (tpt-90) cc_final: 0.8405 (tpp-160) REVERT: N 66 ARG cc_start: 0.8201 (mmm160) cc_final: 0.7768 (mmm160) REVERT: N 104 MET cc_start: 0.9449 (tpp) cc_final: 0.8869 (tpp) REVERT: N 171 ASP cc_start: 0.8736 (m-30) cc_final: 0.8508 (m-30) REVERT: N 175 LEU cc_start: 0.8615 (tp) cc_final: 0.8291 (tp) REVERT: N 208 TYR cc_start: 0.8215 (m-80) cc_final: 0.7713 (m-80) REVERT: N 307 TYR cc_start: 0.8523 (m-80) cc_final: 0.8307 (m-10) REVERT: N 358 ASP cc_start: 0.9204 (p0) cc_final: 0.8960 (p0) REVERT: N 480 GLU cc_start: 0.8506 (mm-30) cc_final: 0.7849 (mp0) outliers start: 1 outliers final: 0 residues processed: 319 average time/residue: 0.3512 time to fit residues: 172.9060 Evaluate side-chains 258 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 1.688 ------------------------------------------------------------------------------- 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: 2.9990 chunk 89 optimal weight: 0.3980 chunk 178 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 183 optimal weight: 20.0000 chunk 189 optimal weight: 20.0000 chunk 169 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 208 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 658 GLN ** D 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.096167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.082187 restraints weight = 58729.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.084048 restraints weight = 35932.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.085363 restraints weight = 25307.130| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 17462 Z= 0.260 Angle : 0.819 10.853 23955 Z= 0.387 Chirality : 0.048 0.345 3005 Planarity : 0.004 0.051 2940 Dihedral : 7.444 56.180 4107 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -0.22 (0.20), residues: 1727 helix: 1.34 (0.25), residues: 430 sheet: 0.25 (0.26), residues: 394 loop : -1.09 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP N 96 HIS 0.006 0.001 HIS A 85 PHE 0.029 0.002 PHE A 306 TYR 0.021 0.003 TYR N 208 ARG 0.005 0.001 ARG F 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00558 ( 58) link_NAG-ASN : angle 2.26678 ( 174) link_ALPHA1-6 : bond 0.00892 ( 3) link_ALPHA1-6 : angle 1.37719 ( 9) link_BETA1-4 : bond 0.00876 ( 26) link_BETA1-4 : angle 2.68331 ( 78) link_ALPHA1-3 : bond 0.01715 ( 2) link_ALPHA1-3 : angle 1.34980 ( 6) hydrogen bonds : bond 0.04653 ( 528) hydrogen bonds : angle 5.40565 ( 1422) SS BOND : bond 0.00469 ( 31) SS BOND : angle 1.79191 ( 62) covalent geometry : bond 0.00573 (17342) covalent geometry : angle 0.78043 (23626) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5221.93 seconds wall clock time: 92 minutes 54.22 seconds (5574.22 seconds total)