Starting phenix.real_space_refine on Sun Aug 24 05:30:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ayv_43999/08_2025/9ayv_43999.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ayv_43999/08_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_43999/08_2025/9ayv_43999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ayv_43999/08_2025/9ayv_43999.map" model { file = "/net/cci-nas-00/data/ceres_data/9ayv_43999/08_2025/9ayv_43999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ayv_43999/08_2025/9ayv_43999.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.37, per 1000 atoms: 0.26 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: 1.90 Conformation dependent library (CDL) restraints added in 645.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.62 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: 3.05 Time building geometry restraints manager: 2.30 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 \ 507)) selection = (chain 'N' and (resid 33 through 387 or resid 403 through 507)) } ncs_group { reference = (chain 'B' and resid 521 through 701) selection = chain 'D' selection = (chain 'F' and resid 521 through 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: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.710 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.120 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (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 ARG 0.009 0.001 ARG D 617 TYR 0.044 0.003 TYR N 168 PHE 0.029 0.003 PHE C 53 TRP 0.063 0.003 TRP D 631 HIS 0.022 0.002 HIS D 585 Details of bonding type rmsd covalent geometry : bond 0.00637 (17342) covalent geometry : angle 0.94741 (23626) SS BOND : bond 0.00335 ( 31) SS BOND : angle 1.10103 ( 62) hydrogen bonds : bond 0.14635 ( 528) hydrogen bonds : angle 6.68057 ( 1422) link_ALPHA1-3 : bond 0.01271 ( 2) link_ALPHA1-3 : angle 3.70731 ( 6) 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_NAG-ASN : bond 0.00655 ( 58) link_NAG-ASN : angle 3.20466 ( 174) *********************** 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 : 0.608 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: 0.1306 time to fit residues: 74.9936 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 : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.103848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.089202 restraints weight = 56396.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.091391 restraints weight = 32919.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.092890 restraints weight = 22410.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.093955 restraints weight = 16872.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.094694 restraints weight = 13659.227| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17462 Z= 0.167 Angle : 0.711 9.149 23955 Z= 0.333 Chirality : 0.045 0.363 3005 Planarity : 0.004 0.051 2940 Dihedral : 9.719 82.116 4107 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.13 % Allowed : 2.89 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.20), residues: 1727 helix: 1.51 (0.25), residues: 437 sheet: 0.45 (0.24), residues: 409 loop : -0.50 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 617 TYR 0.029 0.002 TYR A 168 PHE 0.018 0.002 PHE C 201 TRP 0.031 0.002 TRP D 631 HIS 0.006 0.001 HIS N 240 Details of bonding type rmsd covalent geometry : bond 0.00366 (17342) covalent geometry : angle 0.66363 (23626) SS BOND : bond 0.00381 ( 31) SS BOND : angle 0.87428 ( 62) hydrogen bonds : bond 0.05135 ( 528) hydrogen bonds : angle 5.48961 ( 1422) link_ALPHA1-3 : bond 0.01616 ( 2) link_ALPHA1-3 : angle 2.09166 ( 6) link_ALPHA1-6 : bond 0.00718 ( 3) link_ALPHA1-6 : angle 1.45092 ( 9) link_BETA1-4 : bond 0.01027 ( 26) link_BETA1-4 : angle 3.19032 ( 78) link_NAG-ASN : bond 0.00388 ( 58) link_NAG-ASN : angle 2.16463 ( 174) *********************** 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 346 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 344 time to evaluate : 0.504 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: 0.8460 (m110) cc_final: 0.8189 (m110) REVERT: B 593 LEU cc_start: 0.9705 (mm) cc_final: 0.9426 (mm) REVERT: B 595 ILE cc_start: 0.9667 (tt) cc_final: 0.9356 (tt) REVERT: B 596 TRP cc_start: 0.9099 (m-10) cc_final: 0.8016 (m-90) REVERT: B 601 LYS cc_start: 0.8490 (mtpp) cc_final: 0.8237 (ttpt) REVERT: B 603 ILE cc_start: 0.9512 (mp) cc_final: 0.9269 (mp) REVERT: B 618 ASN cc_start: 0.8414 (t0) cc_final: 0.7995 (t0) REVERT: B 647 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8875 (mt-10) REVERT: B 653 GLN cc_start: 0.8295 (tm-30) cc_final: 0.7985 (tp-100) REVERT: D 585 HIS cc_start: 0.8115 (t-90) cc_final: 0.7861 (t70) REVERT: D 588 ARG cc_start: 0.9161 (ttp-170) cc_final: 0.8286 (ttt90) REVERT: D 646 LEU cc_start: 0.9179 (mt) cc_final: 0.8901 (mt) REVERT: F 530 MET cc_start: 0.8009 (mtt) cc_final: 0.7080 (mtt) REVERT: F 584 GLU cc_start: 0.8959 (tp30) cc_final: 0.8436 (tp30) REVERT: F 603 ILE cc_start: 0.9470 (mm) cc_final: 0.9257 (mm) REVERT: F 622 ILE cc_start: 0.8602 (pt) cc_final: 0.8314 (pt) REVERT: F 631 TRP cc_start: 0.9143 (t-100) cc_final: 0.8828 (t-100) REVERT: F 647 GLU cc_start: 0.9074 (pt0) cc_final: 0.8775 (pp20) REVERT: A 106 GLU cc_start: 0.7655 (pp20) cc_final: 0.7228 (pp20) REVERT: A 107 ASP cc_start: 0.8661 (m-30) cc_final: 0.8222 (m-30) REVERT: A 120 VAL cc_start: 0.8972 (t) cc_final: 0.8687 (m) REVERT: A 145 MET cc_start: 0.5228 (mmt) cc_final: 0.4909 (mmt) REVERT: A 171 ASP cc_start: 0.8097 (m-30) cc_final: 0.7860 (m-30) REVERT: A 176 ASP cc_start: 0.8123 (m-30) cc_final: 0.7897 (m-30) REVERT: A 206 ILE cc_start: 0.8993 (mm) cc_final: 0.8766 (tp) REVERT: A 216 ILE cc_start: 0.9273 (mm) cc_final: 0.9031 (mm) REVERT: A 309 TYR cc_start: 0.8633 (m-80) cc_final: 0.6820 (m-80) REVERT: A 322 ASN cc_start: 0.8370 (m110) cc_final: 0.7756 (p0) REVERT: A 358 ASP cc_start: 0.8634 (p0) cc_final: 0.8392 (p0) REVERT: A 417 TRP cc_start: 0.8281 (m-90) cc_final: 0.7730 (m-90) REVERT: A 472 TYR cc_start: 0.9007 (p90) cc_final: 0.8514 (p90) REVERT: C 95 MET cc_start: 0.9113 (ptm) cc_final: 0.7536 (ppp) REVERT: C 122 LEU cc_start: 0.9703 (mt) cc_final: 0.9451 (mt) REVERT: C 125 LEU cc_start: 0.9279 (tt) cc_final: 0.9028 (tt) REVERT: C 171 ASP cc_start: 0.8882 (m-30) cc_final: 0.8527 (m-30) REVERT: C 316 ILE cc_start: 0.9404 (mm) cc_final: 0.9151 (mt) REVERT: C 367 ASN cc_start: 0.9308 (t0) cc_final: 0.8956 (t0) REVERT: N 45 TRP cc_start: 0.8612 (p90) cc_final: 0.8333 (p90) REVERT: N 175 LEU cc_start: 0.8921 (tp) cc_final: 0.8661 (tp) REVERT: N 208 TYR cc_start: 0.8199 (m-80) cc_final: 0.7512 (m-80) REVERT: N 317 ARG cc_start: 0.6753 (ptp-170) cc_final: 0.5950 (tpt170) REVERT: N 358 ASP cc_start: 0.9064 (p0) cc_final: 0.8815 (p0) REVERT: N 416 MET cc_start: 0.8640 (ttm) cc_final: 0.6754 (ttm) REVERT: N 472 TYR cc_start: 0.8956 (p90) cc_final: 0.8739 (p90) outliers start: 2 outliers final: 1 residues processed: 345 average time/residue: 0.1193 time to fit residues: 63.3797 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 : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 91 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 114 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 563 GLN ** D 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN F 552 GLN F 554 ASN ** F 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 HIS C 85 HIS C 105 HIS C 194 GLN ** C 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.098065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.083604 restraints weight = 58227.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.085628 restraints weight = 34139.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.087072 restraints weight = 23384.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.088081 restraints weight = 17701.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.088808 restraints weight = 14389.547| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 17462 Z= 0.266 Angle : 0.833 10.230 23955 Z= 0.390 Chirality : 0.048 0.343 3005 Planarity : 0.005 0.051 2940 Dihedral : 8.017 66.149 4107 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.13 % Allowed : 3.34 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.20), residues: 1727 helix: 1.06 (0.24), residues: 459 sheet: 0.54 (0.25), residues: 384 loop : -0.71 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 617 TYR 0.054 0.003 TYR C 208 PHE 0.027 0.002 PHE C 201 TRP 0.051 0.003 TRP N 96 HIS 0.008 0.002 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00576 (17342) covalent geometry : angle 0.79490 (23626) SS BOND : bond 0.00796 ( 31) SS BOND : angle 1.11317 ( 62) hydrogen bonds : bond 0.05073 ( 528) hydrogen bonds : angle 5.58768 ( 1422) link_ALPHA1-3 : bond 0.01728 ( 2) link_ALPHA1-3 : angle 1.05210 ( 6) link_ALPHA1-6 : bond 0.00935 ( 3) link_ALPHA1-6 : angle 1.91475 ( 9) link_BETA1-4 : bond 0.00959 ( 26) link_BETA1-4 : angle 3.04316 ( 78) link_NAG-ASN : bond 0.00562 ( 58) link_NAG-ASN : angle 2.21945 ( 174) *********************** 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 317 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 315 time to evaluate : 0.677 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 603 ILE cc_start: 0.9506 (mp) cc_final: 0.9293 (mp) REVERT: B 647 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8923 (mt-10) REVERT: B 654 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8570 (mm-30) REVERT: D 534 SER cc_start: 0.8647 (m) cc_final: 0.8241 (p) REVERT: D 539 VAL cc_start: 0.9494 (t) cc_final: 0.9280 (p) REVERT: D 585 HIS cc_start: 0.8276 (t-90) cc_final: 0.8050 (t70) REVERT: D 588 ARG cc_start: 0.9232 (ttp-170) cc_final: 0.8478 (ttt90) REVERT: D 601 LYS cc_start: 0.9214 (mtmm) cc_final: 0.8930 (mtpp) REVERT: D 638 TYR cc_start: 0.8006 (m-80) cc_final: 0.7727 (m-80) REVERT: D 648 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8299 (tm-30) REVERT: F 584 GLU cc_start: 0.9125 (tp30) cc_final: 0.8619 (tp30) REVERT: F 631 TRP cc_start: 0.9117 (t-100) cc_final: 0.8914 (t-100) REVERT: F 647 GLU cc_start: 0.9105 (pt0) cc_final: 0.8747 (pp20) REVERT: A 120 VAL cc_start: 0.8996 (t) cc_final: 0.8782 (m) REVERT: A 145 MET cc_start: 0.6109 (mmt) cc_final: 0.5814 (mmt) REVERT: A 176 ASP cc_start: 0.8442 (m-30) cc_final: 0.8141 (m-30) REVERT: A 216 ILE cc_start: 0.9292 (mm) cc_final: 0.9043 (mm) REVERT: A 293 LYS cc_start: 0.8102 (mtmt) cc_final: 0.7649 (mtpt) REVERT: A 309 TYR cc_start: 0.8838 (m-80) cc_final: 0.7002 (m-80) REVERT: A 322 ASN cc_start: 0.8481 (m110) cc_final: 0.7893 (p0) REVERT: A 358 ASP cc_start: 0.8454 (p0) cc_final: 0.8240 (p0) REVERT: C 43 PRO cc_start: 0.9638 (Cg_endo) cc_final: 0.9400 (Cg_exo) REVERT: C 51 THR cc_start: 0.9023 (m) cc_final: 0.8572 (t) REVERT: C 93 PHE cc_start: 0.8096 (m-10) cc_final: 0.7884 (m-10) REVERT: C 95 MET cc_start: 0.9281 (ptm) cc_final: 0.8819 (tmm) REVERT: C 166 LEU cc_start: 0.9537 (mt) cc_final: 0.9318 (mt) REVERT: C 300 ILE cc_start: 0.9600 (pt) cc_final: 0.9331 (tt) REVERT: C 322 ASN cc_start: 0.9083 (t0) cc_final: 0.8242 (p0) REVERT: C 422 GLN cc_start: 0.9347 (mp10) cc_final: 0.9130 (mp10) REVERT: C 462 ASP cc_start: 0.8512 (t0) cc_final: 0.7782 (t0) REVERT: C 467 TRP cc_start: 0.9204 (m-90) cc_final: 0.8858 (m-90) REVERT: N 80 ASN cc_start: 0.8800 (m-40) cc_final: 0.8566 (m-40) REVERT: N 175 LEU cc_start: 0.8886 (tp) cc_final: 0.8527 (tp) REVERT: N 208 TYR cc_start: 0.8264 (m-80) cc_final: 0.7679 (m-80) REVERT: N 317 ARG cc_start: 0.7228 (ptp-170) cc_final: 0.6121 (tpt-90) REVERT: N 358 ASP cc_start: 0.9143 (p0) cc_final: 0.8866 (p0) REVERT: N 469 SER cc_start: 0.9173 (t) cc_final: 0.8831 (p) REVERT: N 472 TYR cc_start: 0.8830 (p90) cc_final: 0.8613 (p90) outliers start: 2 outliers final: 1 residues processed: 315 average time/residue: 0.1287 time to fit residues: 62.2709 Evaluate side-chains 239 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 50 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN D 540 GLN D 564 HIS F 552 GLN ** F 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN A 181 GLN A 278 HIS ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 342 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.098764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.084159 restraints weight = 57391.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.086327 restraints weight = 33180.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.087826 restraints weight = 22410.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.088810 restraints weight = 16812.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.089582 restraints weight = 13677.376| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17462 Z= 0.162 Angle : 0.688 10.162 23955 Z= 0.323 Chirality : 0.044 0.312 3005 Planarity : 0.004 0.042 2940 Dihedral : 7.192 56.760 4107 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.13 % Allowed : 2.19 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.20), residues: 1727 helix: 1.56 (0.24), residues: 443 sheet: 0.57 (0.25), residues: 396 loop : -0.64 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 66 TYR 0.032 0.002 TYR C 208 PHE 0.026 0.002 PHE C 201 TRP 0.022 0.002 TRP N 96 HIS 0.017 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00354 (17342) covalent geometry : angle 0.64944 (23626) SS BOND : bond 0.00274 ( 31) SS BOND : angle 0.69780 ( 62) hydrogen bonds : bond 0.04470 ( 528) hydrogen bonds : angle 5.17873 ( 1422) link_ALPHA1-3 : bond 0.01686 ( 2) link_ALPHA1-3 : angle 0.89433 ( 6) link_ALPHA1-6 : bond 0.00827 ( 3) link_ALPHA1-6 : angle 1.33813 ( 9) link_BETA1-4 : bond 0.00849 ( 26) link_BETA1-4 : angle 2.72331 ( 78) link_NAG-ASN : bond 0.00321 ( 58) link_NAG-ASN : angle 2.07480 ( 174) *********************** 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 319 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 317 time to evaluate : 0.628 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: 0.9152 (mt-10) cc_final: 0.8878 (mt-10) REVERT: B 654 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8694 (mm-30) REVERT: D 534 SER cc_start: 0.8688 (m) cc_final: 0.8276 (p) REVERT: D 601 LYS cc_start: 0.9133 (mtmm) cc_final: 0.8910 (mtpp) REVERT: D 622 ILE cc_start: 0.7544 (tp) cc_final: 0.6938 (tp) REVERT: D 638 TYR cc_start: 0.7973 (m-80) cc_final: 0.7772 (m-80) REVERT: D 654 GLU cc_start: 0.8274 (mt-10) cc_final: 0.8068 (mt-10) REVERT: F 584 GLU cc_start: 0.9047 (tp30) cc_final: 0.8661 (tp30) REVERT: F 647 GLU cc_start: 0.9055 (pt0) cc_final: 0.8581 (mt-10) REVERT: A 106 GLU cc_start: 0.8075 (pp20) cc_final: 0.7845 (pp20) REVERT: A 176 ASP cc_start: 0.8278 (m-30) cc_final: 0.7993 (m-30) REVERT: A 216 ILE cc_start: 0.9295 (mm) cc_final: 0.8999 (mm) REVERT: A 293 LYS cc_start: 0.7964 (mtmt) cc_final: 0.7516 (mtpt) REVERT: A 309 TYR cc_start: 0.8432 (m-80) cc_final: 0.7110 (m-80) REVERT: A 322 ASN cc_start: 0.8296 (m110) cc_final: 0.7766 (p0) REVERT: A 358 ASP cc_start: 0.8527 (p0) cc_final: 0.8303 (p0) REVERT: A 417 TRP cc_start: 0.8370 (m-90) cc_final: 0.7665 (m-90) REVERT: A 472 TYR cc_start: 0.8901 (p90) cc_final: 0.8571 (p90) REVERT: C 51 THR cc_start: 0.8968 (m) cc_final: 0.8559 (t) REVERT: C 95 MET cc_start: 0.9274 (ptm) cc_final: 0.8478 (ppp) REVERT: C 139 SER cc_start: 0.9329 (m) cc_final: 0.9085 (p) REVERT: C 166 LEU cc_start: 0.9480 (mt) cc_final: 0.9209 (mt) REVERT: C 300 ILE cc_start: 0.9579 (pt) cc_final: 0.9367 (tt) REVERT: C 322 ASN cc_start: 0.9021 (t0) cc_final: 0.8426 (p0) REVERT: C 422 GLN cc_start: 0.9308 (mp10) cc_final: 0.9094 (mp10) REVERT: N 175 LEU cc_start: 0.8801 (tp) cc_final: 0.8436 (tp) REVERT: N 208 TYR cc_start: 0.8397 (m-80) cc_final: 0.7565 (m-80) REVERT: N 317 ARG cc_start: 0.7163 (ptp-170) cc_final: 0.5965 (tpt170) REVERT: N 358 ASP cc_start: 0.9139 (p0) cc_final: 0.8896 (p0) REVERT: N 416 MET cc_start: 0.8680 (ttm) cc_final: 0.6422 (ttm) REVERT: N 469 SER cc_start: 0.9139 (t) cc_final: 0.8909 (p) REVERT: N 472 TYR cc_start: 0.8855 (p90) cc_final: 0.8622 (p90) outliers start: 2 outliers final: 0 residues processed: 318 average time/residue: 0.1328 time to fit residues: 64.5908 Evaluate side-chains 248 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 191 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 196 optimal weight: 9.9990 chunk 204 optimal weight: 10.0000 chunk 193 optimal weight: 20.0000 chunk 172 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 147 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 HIS ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 HIS ** C 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 85 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.094189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.080055 restraints weight = 59430.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.081967 restraints weight = 35461.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.083325 restraints weight = 24691.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.084217 restraints weight = 18987.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.084879 restraints weight = 15765.221| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 17462 Z= 0.364 Angle : 0.977 10.369 23955 Z= 0.457 Chirality : 0.052 0.302 3005 Planarity : 0.005 0.049 2940 Dihedral : 8.331 57.954 4107 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.19), residues: 1727 helix: 0.93 (0.24), residues: 440 sheet: 0.21 (0.25), residues: 400 loop : -1.15 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 579 TYR 0.028 0.003 TYR C 208 PHE 0.040 0.003 PHE C 201 TRP 0.034 0.003 TRP N 96 HIS 0.017 0.003 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00786 (17342) covalent geometry : angle 0.94103 (23626) SS BOND : bond 0.00694 ( 31) SS BOND : angle 1.29992 ( 62) hydrogen bonds : bond 0.05477 ( 528) hydrogen bonds : angle 5.98703 ( 1422) link_ALPHA1-3 : bond 0.01447 ( 2) link_ALPHA1-3 : angle 0.88419 ( 6) link_ALPHA1-6 : bond 0.00859 ( 3) link_ALPHA1-6 : angle 1.46252 ( 9) link_BETA1-4 : bond 0.01128 ( 26) link_BETA1-4 : angle 3.10472 ( 78) link_NAG-ASN : bond 0.00779 ( 58) link_NAG-ASN : angle 2.49625 ( 174) *********************** 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 280 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.528 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 557 ARG cc_start: 0.8577 (tmm160) cc_final: 0.8351 (tmm-80) REVERT: B 647 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8925 (mt-10) REVERT: D 534 SER cc_start: 0.8887 (m) cc_final: 0.8527 (p) REVERT: D 535 MET cc_start: 0.9332 (mpp) cc_final: 0.9117 (mpp) REVERT: D 591 GLN cc_start: 0.9270 (tm-30) cc_final: 0.8648 (tp-100) REVERT: D 601 LYS cc_start: 0.9237 (mtmm) cc_final: 0.8930 (mtpp) REVERT: D 603 ILE cc_start: 0.9426 (mm) cc_final: 0.9092 (pt) REVERT: D 622 ILE cc_start: 0.7774 (tp) cc_final: 0.7508 (tp) REVERT: D 654 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8196 (mt-10) REVERT: F 530 MET cc_start: 0.7704 (mtm) cc_final: 0.7380 (mpp) REVERT: F 543 ASN cc_start: 0.8470 (m-40) cc_final: 0.8108 (m110) REVERT: F 610 TRP cc_start: 0.8560 (t-100) cc_final: 0.8214 (t-100) REVERT: A 106 GLU cc_start: 0.8341 (pp20) cc_final: 0.7926 (pp20) REVERT: A 107 ASP cc_start: 0.8852 (m-30) cc_final: 0.8439 (m-30) REVERT: A 176 ASP cc_start: 0.8502 (m-30) cc_final: 0.8150 (m-30) REVERT: A 216 ILE cc_start: 0.9368 (mm) cc_final: 0.9100 (mm) REVERT: A 322 ASN cc_start: 0.8429 (m-40) cc_final: 0.8015 (p0) REVERT: A 472 TYR cc_start: 0.9072 (p90) cc_final: 0.8754 (p90) REVERT: C 51 THR cc_start: 0.9108 (m) cc_final: 0.8777 (t) REVERT: C 95 MET cc_start: 0.9355 (ptm) cc_final: 0.8995 (tmm) REVERT: C 100 MET cc_start: 0.9085 (mmm) cc_final: 0.8695 (tpp) REVERT: C 271 ASN cc_start: 0.8080 (p0) cc_final: 0.7627 (p0) REVERT: C 281 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8450 (mm-30) REVERT: C 467 TRP cc_start: 0.9183 (m-90) cc_final: 0.8785 (m-90) REVERT: C 492 ARG cc_start: 0.8682 (tpt-90) cc_final: 0.8256 (tpp-160) REVERT: N 95 MET cc_start: 0.8998 (ptt) cc_final: 0.8738 (ptt) REVERT: N 171 ASP cc_start: 0.8613 (m-30) cc_final: 0.8306 (m-30) REVERT: N 208 TYR cc_start: 0.8321 (m-80) cc_final: 0.7742 (m-80) REVERT: N 317 ARG cc_start: 0.6894 (ptp-170) cc_final: 0.5798 (tpt170) REVERT: N 358 ASP cc_start: 0.9119 (p0) cc_final: 0.8824 (p0) REVERT: N 469 SER cc_start: 0.9364 (t) cc_final: 0.8972 (p) REVERT: N 480 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8131 (mm-30) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.1171 time to fit residues: 50.8052 Evaluate side-chains 241 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 82 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN D 552 GLN ** D 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 HIS D 585 HIS ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.098566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.084392 restraints weight = 57356.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.086396 restraints weight = 34000.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.087801 restraints weight = 23473.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.088785 restraints weight = 17945.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.089430 restraints weight = 14674.382| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17462 Z= 0.154 Angle : 0.727 13.919 23955 Z= 0.339 Chirality : 0.045 0.284 3005 Planarity : 0.003 0.042 2940 Dihedral : 7.402 53.162 4107 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.13 % Allowed : 1.61 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.20), residues: 1727 helix: 1.48 (0.25), residues: 436 sheet: 0.40 (0.25), residues: 400 loop : -0.96 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 66 TYR 0.018 0.002 TYR N 309 PHE 0.020 0.001 PHE C 201 TRP 0.045 0.002 TRP N 96 HIS 0.015 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00339 (17342) covalent geometry : angle 0.68186 (23626) SS BOND : bond 0.00295 ( 31) SS BOND : angle 0.99061 ( 62) hydrogen bonds : bond 0.04499 ( 528) hydrogen bonds : angle 5.24969 ( 1422) link_ALPHA1-3 : bond 0.01761 ( 2) link_ALPHA1-3 : angle 1.24931 ( 6) link_ALPHA1-6 : bond 0.00989 ( 3) link_ALPHA1-6 : angle 1.31736 ( 9) link_BETA1-4 : bond 0.00845 ( 26) link_BETA1-4 : angle 2.67575 ( 78) link_NAG-ASN : bond 0.00333 ( 58) link_NAG-ASN : angle 2.42605 ( 174) *********************** 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 330 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 328 time to evaluate : 0.613 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 595 ILE cc_start: 0.9637 (tt) cc_final: 0.9435 (tt) REVERT: B 596 TRP cc_start: 0.9140 (m-10) cc_final: 0.8145 (m-90) REVERT: B 645 LEU cc_start: 0.9520 (mt) cc_final: 0.9309 (mt) REVERT: B 647 GLU cc_start: 0.9168 (mt-10) cc_final: 0.8875 (mt-10) REVERT: B 654 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8706 (mm-30) REVERT: D 540 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8204 (tm-30) REVERT: D 585 HIS cc_start: 0.8618 (t-90) cc_final: 0.8320 (t70) REVERT: D 595 ILE cc_start: 0.9314 (tt) cc_final: 0.9104 (tt) REVERT: D 622 ILE cc_start: 0.7714 (tp) cc_final: 0.7493 (tp) REVERT: D 634 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8807 (tm-30) REVERT: D 654 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8088 (mt-10) REVERT: F 549 VAL cc_start: 0.7303 (p) cc_final: 0.6687 (p) REVERT: F 584 GLU cc_start: 0.8969 (tp30) cc_final: 0.8639 (tp30) REVERT: F 610 TRP cc_start: 0.8544 (t-100) cc_final: 0.8272 (t-100) REVERT: F 647 GLU cc_start: 0.9101 (pt0) cc_final: 0.8710 (mt-10) REVERT: A 106 GLU cc_start: 0.8188 (pp20) cc_final: 0.7955 (pp20) REVERT: A 176 ASP cc_start: 0.8491 (m-30) cc_final: 0.8172 (m-30) REVERT: A 182 TYR cc_start: 0.7859 (m-80) cc_final: 0.7646 (m-10) REVERT: A 185 ILE cc_start: 0.9218 (tp) cc_final: 0.8894 (mm) REVERT: A 216 ILE cc_start: 0.9352 (mm) cc_final: 0.9092 (mm) REVERT: A 309 TYR cc_start: 0.8378 (m-80) cc_final: 0.7090 (m-80) REVERT: A 322 ASN cc_start: 0.8325 (m-40) cc_final: 0.7976 (p0) REVERT: A 417 TRP cc_start: 0.8344 (m-90) cc_final: 0.7571 (m-90) REVERT: A 472 TYR cc_start: 0.9020 (p90) cc_final: 0.8576 (p90) REVERT: C 95 MET cc_start: 0.9359 (ptm) cc_final: 0.8748 (ppp) REVERT: C 112 TRP cc_start: 0.8622 (m100) cc_final: 0.8412 (m100) REVERT: C 135 THR cc_start: 0.9382 (p) cc_final: 0.9139 (p) REVERT: C 171 ASP cc_start: 0.8881 (m-30) cc_final: 0.8612 (m-30) REVERT: C 271 ASN cc_start: 0.7873 (p0) cc_final: 0.7437 (p0) REVERT: C 281 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8330 (mm-30) REVERT: C 422 GLN cc_start: 0.9319 (mp10) cc_final: 0.9064 (mp10) REVERT: C 492 ARG cc_start: 0.8717 (tpt-90) cc_final: 0.8340 (tpp-160) REVERT: N 104 MET cc_start: 0.9378 (tpp) cc_final: 0.8842 (tpp) REVERT: N 171 ASP cc_start: 0.8719 (m-30) cc_final: 0.8404 (m-30) REVERT: N 175 LEU cc_start: 0.8827 (tp) cc_final: 0.8516 (tp) REVERT: N 208 TYR cc_start: 0.8237 (m-80) cc_final: 0.7279 (m-80) REVERT: N 358 ASP cc_start: 0.9151 (p0) cc_final: 0.8885 (p0) REVERT: N 410 ILE cc_start: 0.9336 (mm) cc_final: 0.8987 (mm) REVERT: N 416 MET cc_start: 0.8624 (ttm) cc_final: 0.6502 (ttm) REVERT: N 469 SER cc_start: 0.9178 (t) cc_final: 0.8977 (p) REVERT: N 480 GLU cc_start: 0.8459 (mm-30) cc_final: 0.7785 (mp0) outliers start: 2 outliers final: 0 residues processed: 330 average time/residue: 0.1209 time to fit residues: 61.7105 Evaluate side-chains 248 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 195 optimal weight: 20.0000 chunk 176 optimal weight: 0.9980 chunk 189 optimal weight: 20.0000 chunk 50 optimal weight: 0.9980 chunk 3 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 202 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 overall best weight: 4.9986 ------------------------------------------------------------------------------- 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 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 637 ASN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 HIS N 466 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.094545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.080443 restraints weight = 58449.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.082381 restraints weight = 34926.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.083499 restraints weight = 24268.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.084545 restraints weight = 19386.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.085237 restraints weight = 15820.309| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 17462 Z= 0.313 Angle : 0.893 10.511 23955 Z= 0.417 Chirality : 0.049 0.278 3005 Planarity : 0.004 0.041 2940 Dihedral : 8.019 57.025 4107 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.56 % Favored : 94.38 % Rotamer: Outliers : 0.13 % Allowed : 1.67 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.20), residues: 1727 helix: 1.33 (0.25), residues: 426 sheet: 0.22 (0.25), residues: 392 loop : -1.15 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 617 TYR 0.040 0.003 TYR C 208 PHE 0.029 0.002 PHE C 201 TRP 0.041 0.003 TRP A 35 HIS 0.018 0.002 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00689 (17342) covalent geometry : angle 0.85382 (23626) SS BOND : bond 0.00547 ( 31) SS BOND : angle 1.66974 ( 62) hydrogen bonds : bond 0.04959 ( 528) hydrogen bonds : angle 5.64989 ( 1422) link_ALPHA1-3 : bond 0.01691 ( 2) link_ALPHA1-3 : angle 1.09957 ( 6) link_ALPHA1-6 : bond 0.00912 ( 3) link_ALPHA1-6 : angle 1.42191 ( 9) link_BETA1-4 : bond 0.01025 ( 26) link_BETA1-4 : angle 2.89100 ( 78) link_NAG-ASN : bond 0.00668 ( 58) link_NAG-ASN : angle 2.45159 ( 174) *********************** 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 286 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 284 time to evaluate : 0.615 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 603 ILE cc_start: 0.9585 (mt) cc_final: 0.9306 (mt) REVERT: B 638 TYR cc_start: 0.8460 (m-80) cc_final: 0.7792 (m-80) REVERT: B 647 GLU cc_start: 0.9209 (mt-10) cc_final: 0.8632 (mp0) REVERT: D 540 GLN cc_start: 0.8837 (tm-30) cc_final: 0.8308 (tm-30) REVERT: D 588 ARG cc_start: 0.9160 (ttp-170) cc_final: 0.8827 (ttp-170) REVERT: D 591 GLN cc_start: 0.9246 (tm-30) cc_final: 0.8776 (tp-100) REVERT: D 603 ILE cc_start: 0.9407 (mm) cc_final: 0.9108 (pt) REVERT: D 622 ILE cc_start: 0.7976 (tp) cc_final: 0.7578 (tp) REVERT: D 634 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8849 (tm-30) REVERT: D 654 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8224 (mt-10) REVERT: F 610 TRP cc_start: 0.8515 (t-100) cc_final: 0.8245 (t-100) REVERT: A 106 GLU cc_start: 0.8428 (pp20) cc_final: 0.8024 (pp20) REVERT: A 107 ASP cc_start: 0.8755 (m-30) cc_final: 0.8265 (m-30) REVERT: A 171 ASP cc_start: 0.8334 (m-30) cc_final: 0.8119 (m-30) REVERT: A 176 ASP cc_start: 0.8597 (m-30) cc_final: 0.8245 (m-30) REVERT: A 216 ILE cc_start: 0.9385 (mm) cc_final: 0.9143 (mm) REVERT: A 309 TYR cc_start: 0.8781 (m-80) cc_final: 0.7369 (m-80) REVERT: A 322 ASN cc_start: 0.8398 (m-40) cc_final: 0.8021 (p0) REVERT: A 417 TRP cc_start: 0.8522 (m-90) cc_final: 0.7937 (m-90) REVERT: A 472 TYR cc_start: 0.9098 (p90) cc_final: 0.8616 (p90) REVERT: A 492 ARG cc_start: 0.8127 (ttm110) cc_final: 0.7853 (mtt90) REVERT: C 51 THR cc_start: 0.8905 (m) cc_final: 0.8608 (t) REVERT: C 95 MET cc_start: 0.9369 (ptm) cc_final: 0.9028 (tmm) REVERT: C 281 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8397 (mm-30) REVERT: C 322 ASN cc_start: 0.9185 (t0) cc_final: 0.8279 (p0) REVERT: C 467 TRP cc_start: 0.9003 (m-90) cc_final: 0.8796 (m-90) REVERT: C 492 ARG cc_start: 0.8689 (tpt-90) cc_final: 0.8342 (tpp-160) REVERT: N 171 ASP cc_start: 0.8703 (m-30) cc_final: 0.8414 (m-30) REVERT: N 208 TYR cc_start: 0.8187 (m-80) cc_final: 0.7658 (m-80) REVERT: N 358 ASP cc_start: 0.9119 (p0) cc_final: 0.8835 (p0) REVERT: N 469 SER cc_start: 0.9367 (t) cc_final: 0.9053 (p) REVERT: N 480 GLU cc_start: 0.8427 (mm-30) cc_final: 0.7805 (mp0) outliers start: 2 outliers final: 0 residues processed: 286 average time/residue: 0.1239 time to fit residues: 54.7562 Evaluate side-chains 243 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 151 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 143 optimal weight: 0.0670 chunk 9 optimal weight: 20.0000 chunk 87 optimal weight: 7.9990 chunk 139 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 186 optimal weight: 20.0000 chunk 156 optimal weight: 1.9990 overall best weight: 1.3724 ------------------------------------------------------------------------------- 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 F 552 GLN ** F 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 637 ASN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.097653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.083338 restraints weight = 57919.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.085407 restraints weight = 34070.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.086832 restraints weight = 23347.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.087810 restraints weight = 17737.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.088511 restraints weight = 14547.794| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17462 Z= 0.147 Angle : 0.720 9.827 23955 Z= 0.343 Chirality : 0.046 0.445 3005 Planarity : 0.003 0.041 2940 Dihedral : 7.268 54.423 4107 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.13 % Allowed : 0.71 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.20), residues: 1727 helix: 1.46 (0.25), residues: 431 sheet: 0.32 (0.25), residues: 399 loop : -0.94 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 617 TYR 0.011 0.002 TYR C 309 PHE 0.012 0.001 PHE C 53 TRP 0.025 0.002 TRP B 631 HIS 0.009 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00325 (17342) covalent geometry : angle 0.68027 (23626) SS BOND : bond 0.00272 ( 31) SS BOND : angle 1.30624 ( 62) hydrogen bonds : bond 0.04478 ( 528) hydrogen bonds : angle 5.19999 ( 1422) link_ALPHA1-3 : bond 0.01770 ( 2) link_ALPHA1-3 : angle 1.47978 ( 6) link_ALPHA1-6 : bond 0.00974 ( 3) link_ALPHA1-6 : angle 1.30308 ( 9) link_BETA1-4 : bond 0.00826 ( 26) link_BETA1-4 : angle 2.58471 ( 78) link_NAG-ASN : bond 0.00325 ( 58) link_NAG-ASN : angle 2.17493 ( 174) *********************** 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 313 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 311 time to evaluate : 0.606 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 647 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8794 (mt-10) REVERT: B 661 LEU cc_start: 0.8688 (tp) cc_final: 0.8442 (tp) REVERT: D 530 MET cc_start: 0.6899 (pmm) cc_final: 0.5525 (pmm) REVERT: D 560 GLU cc_start: 0.8235 (mt-10) cc_final: 0.8028 (pt0) REVERT: D 588 ARG cc_start: 0.9079 (ttp-170) cc_final: 0.8489 (tpt90) REVERT: D 591 GLN cc_start: 0.9148 (tm-30) cc_final: 0.8768 (tp-100) REVERT: D 622 ILE cc_start: 0.7672 (tp) cc_final: 0.7353 (tp) REVERT: D 634 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8887 (tm-30) REVERT: D 638 TYR cc_start: 0.7963 (m-80) cc_final: 0.7651 (m-80) REVERT: F 575 GLN cc_start: 0.8898 (mm110) cc_final: 0.8685 (mm110) REVERT: F 584 GLU cc_start: 0.8883 (tp30) cc_final: 0.8555 (tp30) REVERT: F 610 TRP cc_start: 0.8503 (t-100) cc_final: 0.8287 (t-100) REVERT: F 622 ILE cc_start: 0.8669 (pt) cc_final: 0.8462 (pt) REVERT: F 650 GLN cc_start: 0.9177 (tm-30) cc_final: 0.8514 (tm-30) REVERT: A 106 GLU cc_start: 0.8319 (pp20) cc_final: 0.7923 (pp20) REVERT: A 109 ILE cc_start: 0.9730 (tt) cc_final: 0.9530 (tp) REVERT: A 171 ASP cc_start: 0.8246 (m-30) cc_final: 0.8034 (m-30) REVERT: A 176 ASP cc_start: 0.8399 (m-30) cc_final: 0.8109 (m-30) REVERT: A 216 ILE cc_start: 0.9378 (mm) cc_final: 0.9086 (mm) REVERT: A 293 LYS cc_start: 0.8387 (mtmt) cc_final: 0.8175 (mtpt) REVERT: A 309 TYR cc_start: 0.8757 (m-80) cc_final: 0.7211 (m-80) REVERT: A 322 ASN cc_start: 0.8279 (m-40) cc_final: 0.7939 (p0) REVERT: A 417 TRP cc_start: 0.8284 (m-90) cc_final: 0.7387 (m-90) REVERT: A 472 TYR cc_start: 0.9076 (p90) cc_final: 0.8631 (p90) REVERT: C 95 MET cc_start: 0.9334 (ptm) cc_final: 0.8795 (ppp) REVERT: C 171 ASP cc_start: 0.8738 (m-30) cc_final: 0.8489 (m-30) REVERT: C 281 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8329 (mm-30) REVERT: C 322 ASN cc_start: 0.9065 (t0) cc_final: 0.8398 (p0) REVERT: C 467 TRP cc_start: 0.8882 (m-90) cc_final: 0.8661 (m-90) REVERT: C 492 ARG cc_start: 0.8678 (tpt-90) cc_final: 0.8346 (tpp-160) REVERT: N 171 ASP cc_start: 0.8734 (m-30) cc_final: 0.8459 (m-30) REVERT: N 175 LEU cc_start: 0.8757 (tp) cc_final: 0.8432 (tp) REVERT: N 208 TYR cc_start: 0.8250 (m-80) cc_final: 0.7556 (m-80) REVERT: N 358 ASP cc_start: 0.9169 (p0) cc_final: 0.8923 (p0) REVERT: N 416 MET cc_start: 0.8203 (ttp) cc_final: 0.6977 (ttp) REVERT: N 424 MET cc_start: 0.8085 (ttp) cc_final: 0.7404 (ttp) REVERT: N 469 SER cc_start: 0.9223 (t) cc_final: 0.8991 (p) REVERT: N 480 GLU cc_start: 0.8551 (mm-30) cc_final: 0.7643 (mp0) outliers start: 2 outliers final: 0 residues processed: 313 average time/residue: 0.1226 time to fit residues: 59.2887 Evaluate side-chains 250 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 169 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 28 optimal weight: 0.0570 chunk 210 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 161 optimal weight: 0.0980 chunk 77 optimal weight: 8.9990 overall best weight: 1.6304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN D 585 HIS ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 HIS C 278 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.097960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.083717 restraints weight = 58330.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.085779 restraints weight = 34441.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.087186 restraints weight = 23578.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.088178 restraints weight = 17940.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.088833 restraints weight = 14634.068| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17462 Z= 0.150 Angle : 0.707 8.785 23955 Z= 0.338 Chirality : 0.045 0.284 3005 Planarity : 0.004 0.059 2940 Dihedral : 7.064 56.020 4107 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.06 % Allowed : 0.77 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.20), residues: 1727 helix: 1.70 (0.25), residues: 419 sheet: 0.49 (0.26), residues: 376 loop : -0.86 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 264 TYR 0.037 0.002 TYR A 182 PHE 0.012 0.001 PHE C 306 TRP 0.037 0.002 TRP A 112 HIS 0.006 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00334 (17342) covalent geometry : angle 0.67188 (23626) SS BOND : bond 0.00333 ( 31) SS BOND : angle 1.23210 ( 62) hydrogen bonds : bond 0.04239 ( 528) hydrogen bonds : angle 5.16658 ( 1422) link_ALPHA1-3 : bond 0.01740 ( 2) link_ALPHA1-3 : angle 1.50115 ( 6) link_ALPHA1-6 : bond 0.00955 ( 3) link_ALPHA1-6 : angle 1.29668 ( 9) link_BETA1-4 : bond 0.00811 ( 26) link_BETA1-4 : angle 2.52291 ( 78) link_NAG-ASN : bond 0.00321 ( 58) link_NAG-ASN : angle 1.99737 ( 174) *********************** 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 311 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 310 time to evaluate : 0.593 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 634 GLU cc_start: 0.8866 (mp0) cc_final: 0.8557 (mp0) REVERT: B 638 TYR cc_start: 0.8330 (m-80) cc_final: 0.7728 (m-80) REVERT: B 647 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8802 (mt-10) REVERT: D 535 MET cc_start: 0.9398 (mpp) cc_final: 0.9032 (mpp) REVERT: D 542 ARG cc_start: 0.6722 (tpt-90) cc_final: 0.6276 (tpt-90) REVERT: D 588 ARG cc_start: 0.9130 (ttp-170) cc_final: 0.8481 (tpt90) REVERT: D 622 ILE cc_start: 0.7842 (tp) cc_final: 0.7517 (tp) REVERT: D 634 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8916 (tm-30) REVERT: D 638 TYR cc_start: 0.8047 (m-80) cc_final: 0.7741 (m-80) REVERT: D 654 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8067 (mt-10) REVERT: D 661 LEU cc_start: 0.8837 (tp) cc_final: 0.8616 (tt) REVERT: F 584 GLU cc_start: 0.8944 (tp30) cc_final: 0.8517 (tp30) REVERT: F 610 TRP cc_start: 0.8522 (t-100) cc_final: 0.8305 (t-100) REVERT: F 614 TRP cc_start: 0.6114 (m100) cc_final: 0.5724 (m100) REVERT: F 648 GLU cc_start: 0.8343 (tp30) cc_final: 0.8092 (tp30) REVERT: F 650 GLN cc_start: 0.9074 (tm-30) cc_final: 0.8454 (tm-30) REVERT: A 106 GLU cc_start: 0.8300 (pp20) cc_final: 0.7852 (pp20) REVERT: A 107 ASP cc_start: 0.8646 (m-30) cc_final: 0.8148 (m-30) REVERT: A 176 ASP cc_start: 0.8374 (m-30) cc_final: 0.8021 (m-30) REVERT: A 185 ILE cc_start: 0.9248 (tp) cc_final: 0.8938 (mm) REVERT: A 216 ILE cc_start: 0.9370 (mm) cc_final: 0.9120 (mm) REVERT: A 309 TYR cc_start: 0.8743 (m-80) cc_final: 0.7123 (m-80) REVERT: A 322 ASN cc_start: 0.8314 (m-40) cc_final: 0.7970 (p0) REVERT: A 417 TRP cc_start: 0.8369 (m-90) cc_final: 0.7550 (m-90) REVERT: A 472 TYR cc_start: 0.9092 (p90) cc_final: 0.8751 (p90) REVERT: C 95 MET cc_start: 0.9259 (ptm) cc_final: 0.8804 (ppp) REVERT: C 171 ASP cc_start: 0.8704 (m-30) cc_final: 0.8436 (m-30) REVERT: C 281 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8307 (mm-30) REVERT: C 286 GLU cc_start: 0.7823 (tt0) cc_final: 0.7445 (tt0) REVERT: C 322 ASN cc_start: 0.9085 (t0) cc_final: 0.8496 (p0) REVERT: C 358 ASP cc_start: 0.8573 (t70) cc_final: 0.8038 (t70) REVERT: C 467 TRP cc_start: 0.8808 (m-90) cc_final: 0.8488 (m-90) REVERT: C 492 ARG cc_start: 0.8678 (tpt-90) cc_final: 0.8322 (tpp-160) REVERT: N 171 ASP cc_start: 0.8703 (m-30) cc_final: 0.8451 (m-30) REVERT: N 175 LEU cc_start: 0.8742 (tp) cc_final: 0.8393 (tp) REVERT: N 208 TYR cc_start: 0.8212 (m-80) cc_final: 0.7577 (m-80) REVERT: N 358 ASP cc_start: 0.9171 (p0) cc_final: 0.8940 (p0) REVERT: N 469 SER cc_start: 0.9209 (t) cc_final: 0.9007 (p) REVERT: N 480 GLU cc_start: 0.8461 (mm-30) cc_final: 0.7751 (mp0) outliers start: 1 outliers final: 0 residues processed: 311 average time/residue: 0.1295 time to fit residues: 61.9011 Evaluate side-chains 249 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 205 optimal weight: 10.0000 chunk 188 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 183 optimal weight: 20.0000 chunk 164 optimal weight: 7.9990 chunk 209 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 122 optimal weight: 0.0980 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN D 564 HIS ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 637 ASN A 82 GLN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.095053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.080927 restraints weight = 58033.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.082918 restraints weight = 34158.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.084297 restraints weight = 23414.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.085241 restraints weight = 17786.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.085940 restraints weight = 14547.861| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 17462 Z= 0.300 Angle : 0.879 9.148 23955 Z= 0.416 Chirality : 0.049 0.281 3005 Planarity : 0.004 0.062 2940 Dihedral : 7.878 56.015 4107 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.19 % Allowed : 0.32 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.20), residues: 1727 helix: 1.10 (0.25), residues: 431 sheet: 0.17 (0.25), residues: 391 loop : -1.20 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 617 TYR 0.030 0.003 TYR C 208 PHE 0.023 0.002 PHE C 201 TRP 0.043 0.003 TRP B 631 HIS 0.013 0.002 HIS D 585 Details of bonding type rmsd covalent geometry : bond 0.00660 (17342) covalent geometry : angle 0.84233 (23626) SS BOND : bond 0.00594 ( 31) SS BOND : angle 1.60610 ( 62) hydrogen bonds : bond 0.04907 ( 528) hydrogen bonds : angle 5.64604 ( 1422) link_ALPHA1-3 : bond 0.01747 ( 2) link_ALPHA1-3 : angle 1.29664 ( 6) link_ALPHA1-6 : bond 0.00884 ( 3) link_ALPHA1-6 : angle 1.39827 ( 9) link_BETA1-4 : bond 0.00892 ( 26) link_BETA1-4 : angle 2.78633 ( 78) link_NAG-ASN : bond 0.00617 ( 58) link_NAG-ASN : angle 2.33312 ( 174) ********************** 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 284 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 281 time to evaluate : 0.510 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 638 TYR cc_start: 0.8476 (m-80) cc_final: 0.7828 (m-80) REVERT: B 647 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8588 (mp0) REVERT: B 657 GLU cc_start: 0.8950 (tp30) cc_final: 0.8731 (tp30) REVERT: D 535 MET cc_start: 0.9384 (mpp) cc_final: 0.9176 (mpp) REVERT: D 540 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8433 (tm-30) REVERT: D 591 GLN cc_start: 0.9192 (tm-30) cc_final: 0.8691 (tp-100) REVERT: D 622 ILE cc_start: 0.7958 (tp) cc_final: 0.7633 (tp) REVERT: D 634 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8954 (tm-30) REVERT: D 638 TYR cc_start: 0.8205 (m-80) cc_final: 0.7881 (m-80) REVERT: D 654 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8111 (mt-10) REVERT: F 530 MET cc_start: 0.8477 (mmp) cc_final: 0.6806 (mtt) REVERT: F 584 GLU cc_start: 0.8994 (tp30) cc_final: 0.8531 (tp30) REVERT: F 610 TRP cc_start: 0.8518 (t-100) cc_final: 0.8220 (t-100) REVERT: F 648 GLU cc_start: 0.8527 (tp30) cc_final: 0.8272 (tp30) REVERT: F 650 GLN cc_start: 0.9142 (tm-30) cc_final: 0.8527 (tm-30) REVERT: A 104 MET cc_start: 0.9478 (ptm) cc_final: 0.9109 (ttp) REVERT: A 106 GLU cc_start: 0.8300 (pp20) cc_final: 0.7898 (pp20) REVERT: A 107 ASP cc_start: 0.8758 (m-30) cc_final: 0.8265 (m-30) REVERT: A 176 ASP cc_start: 0.8429 (m-30) cc_final: 0.8086 (m-30) REVERT: A 216 ILE cc_start: 0.9349 (mm) cc_final: 0.9105 (mm) REVERT: A 309 TYR cc_start: 0.8568 (m-80) cc_final: 0.7326 (m-80) REVERT: A 322 ASN cc_start: 0.8356 (m-40) cc_final: 0.8007 (p0) REVERT: A 472 TYR cc_start: 0.9167 (p90) cc_final: 0.8789 (p90) REVERT: C 51 THR cc_start: 0.8937 (m) cc_final: 0.8613 (t) REVERT: C 95 MET cc_start: 0.9324 (ptm) cc_final: 0.9070 (tmm) REVERT: C 122 LEU cc_start: 0.9677 (mt) cc_final: 0.9469 (mm) REVERT: C 171 ASP cc_start: 0.8826 (m-30) cc_final: 0.8567 (m-30) REVERT: C 358 ASP cc_start: 0.8604 (t70) cc_final: 0.8341 (t70) REVERT: C 467 TRP cc_start: 0.9038 (m-90) cc_final: 0.8602 (m-90) REVERT: C 492 ARG cc_start: 0.8699 (tpt-90) cc_final: 0.8303 (tpp-160) REVERT: N 171 ASP cc_start: 0.8718 (m-30) cc_final: 0.8435 (m-30) REVERT: N 208 TYR cc_start: 0.8341 (m-80) cc_final: 0.7688 (m-80) REVERT: N 358 ASP cc_start: 0.9144 (p0) cc_final: 0.8859 (p0) REVERT: N 469 SER cc_start: 0.9360 (t) cc_final: 0.9061 (p) REVERT: N 480 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7997 (mm-30) outliers start: 3 outliers final: 0 residues processed: 284 average time/residue: 0.1223 time to fit residues: 53.5820 Evaluate side-chains 224 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 38 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 201 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 198 optimal weight: 20.0000 chunk 59 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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** D 585 HIS D 658 GLN F 552 GLN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.096429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.082186 restraints weight = 57814.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.084236 restraints weight = 33865.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.085669 restraints weight = 23059.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.086663 restraints weight = 17499.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.087321 restraints weight = 14202.205| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17462 Z= 0.171 Angle : 0.759 13.788 23955 Z= 0.358 Chirality : 0.046 0.290 3005 Planarity : 0.004 0.038 2940 Dihedral : 7.403 53.714 4107 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.06 % Allowed : 0.51 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.20), residues: 1727 helix: 1.32 (0.25), residues: 433 sheet: 0.28 (0.26), residues: 385 loop : -1.03 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 617 TYR 0.026 0.002 TYR C 208 PHE 0.028 0.002 PHE A 53 TRP 0.051 0.002 TRP N 96 HIS 0.006 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00383 (17342) covalent geometry : angle 0.71939 (23626) SS BOND : bond 0.00314 ( 31) SS BOND : angle 1.11072 ( 62) hydrogen bonds : bond 0.04394 ( 528) hydrogen bonds : angle 5.30436 ( 1422) link_ALPHA1-3 : bond 0.01726 ( 2) link_ALPHA1-3 : angle 1.55180 ( 6) link_ALPHA1-6 : bond 0.00934 ( 3) link_ALPHA1-6 : angle 1.32592 ( 9) link_BETA1-4 : bond 0.00828 ( 26) link_BETA1-4 : angle 2.56332 ( 78) link_NAG-ASN : bond 0.00318 ( 58) link_NAG-ASN : angle 2.35076 ( 174) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2570.01 seconds wall clock time: 45 minutes 33.47 seconds (2733.47 seconds total)