Starting phenix.real_space_refine on Thu Sep 18 18:06:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ays_43998/09_2025/9ays_43998.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ays_43998/09_2025/9ays_43998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ays_43998/09_2025/9ays_43998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ays_43998/09_2025/9ays_43998.map" model { file = "/net/cci-nas-00/data/ceres_data/9ays_43998/09_2025/9ays_43998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ays_43998/09_2025/9ays_43998.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 11576 2.51 5 N 3229 2.21 5 O 3800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18710 Number of models: 1 Model: "" Number of chains: 40 Chain: "H" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 605 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 121} Link IDs: {'TRANS': 120} Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 121 Planarities with less than four sites: {'UNK:plan-1': 121} Unresolved non-hydrogen planarities: 121 Chain: "L" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 505 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'TRANS': 100} Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 303 Unresolved non-hydrogen dihedrals: 101 Planarities with less than four sites: {'UNK:plan-1': 101} Unresolved non-hydrogen planarities: 101 Chain: "A" Number of atoms: 3591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3591 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 20, 'TRANS': 434} Chain breaks: 2 Chain: "B" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1139 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "C" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3564 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 20, 'TRANS': 430} Chain breaks: 2 Chain: "D" Number of atoms: 1147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1147 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Chain: "E" Number of atoms: 3586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3586 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 20, 'TRANS': 434} Chain breaks: 2 Chain: "F" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1145 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "G" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 510 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'TRANS': 101} Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 306 Unresolved non-hydrogen dihedrals: 102 Planarities with less than four sites: {'UNK:plan-1': 102} Unresolved non-hydrogen planarities: 102 Chain: "I" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 575 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'TRANS': 114} Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 345 Unresolved non-hydrogen dihedrals: 115 Planarities with less than four sites: {'UNK:plan-1': 115} Unresolved non-hydrogen planarities: 115 Chain: "J" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 520 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'TRANS': 103} Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 312 Unresolved non-hydrogen dihedrals: 104 Planarities with less than four sites: {'UNK:plan-1': 104} Unresolved non-hydrogen planarities: 104 Chain: "K" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 470 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'TRANS': 93} Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 282 Unresolved non-hydrogen dihedrals: 94 Planarities with less than four sites: {'UNK:plan-1': 94} Unresolved non-hydrogen planarities: 94 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.89, per 1000 atoms: 0.26 Number of scatterers: 18710 At special positions: 0 Unit cell: (150.48, 155.705, 142.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 3800 8.00 N 3229 7.00 C 11576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 330 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 444 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 330 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 444 " distance=2.03 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 330 " distance=2.03 Simple disulfide: pdb=" SG CYS E 377 " - pdb=" SG CYS E 444 " distance=2.03 Simple disulfide: pdb=" SG CYS E 384 " - pdb=" SG CYS E 417 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " " BMA W 3 " - " MAN W 4 " " BMA c 3 " - " MAN c 4 " ALPHA1-4 " BMA Q 3 " - " MAN Q 5 " ALPHA1-6 " BMA Q 3 " - " MAN Q 6 " " BMA W 3 " - " MAN W 5 " " BMA c 3 " - " MAN c 5 " BETA1-3 " NAG f 2 " - " NAG f 3 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " BETA1-6 " NAG O 1 " - " NAG O 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 234 " " NAG A 604 " - " ASN A 276 " " NAG A 605 " - " ASN A 301 " " NAG A 606 " - " ASN A 338 " " NAG A 607 " - " ASN A 354 " " NAG A 608 " - " ASN A 362 " " NAG A 609 " - " ASN A 391 " " NAG A 610 " - " ASN A 447 " " NAG A 611 " - " ASN A 289 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 137 " " NAG C 604 " - " ASN C 152 " " NAG C 605 " - " ASN C 276 " " NAG C 606 " - " ASN C 295 " " NAG C 607 " - " ASN C 301 " " NAG C 608 " - " ASN C 338 " " NAG C 609 " - " ASN C 354 " " NAG C 610 " - " ASN C 385 " " NAG C 611 " - " ASN C 391 " " NAG C 612 " - " ASN C 289 " " NAG C 613 " - " ASN C 234 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 618 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 152 " " NAG E 603 " - " ASN E 197 " " NAG E 604 " - " ASN E 234 " " NAG E 605 " - " ASN E 289 " " NAG E 606 " - " ASN E 295 " " NAG E 607 " - " ASN E 301 " " NAG E 608 " - " ASN E 354 " " NAG E 609 " - " ASN E 385 " " NAG E 610 " - " ASN E 447 " " NAG E 611 " - " ASN E 461 " " NAG E 612 " - " ASN E 241 " " NAG E 613 " - " ASN E 338 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG M 1 " - " ASN A 148 " " NAG N 1 " - " ASN A 152 " " NAG O 1 " - " ASN A 197 " " NAG P 1 " - " ASN A 241 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 295 " " NAG S 1 " - " ASN A 385 " " NAG T 1 " - " ASN A 331 " " NAG U 1 " - " ASN C 148 " " NAG V 1 " - " ASN C 197 " " NAG W 1 " - " ASN C 262 " " NAG X 1 " - " ASN C 331 " " NAG Y 1 " - " ASN C 362 " " NAG Z 1 " - " ASN C 447 " " NAG a 1 " - " ASN C 241 " " NAG b 1 " - " ASN D 611 " " NAG c 1 " - " ASN E 262 " " NAG d 1 " - " ASN E 276 " " NAG e 1 " - " ASN E 331 " " NAG f 1 " - " ASN E 362 " " NAG g 1 " - " ASN E 148 " " NAG h 1 " - " ASN E 391 " Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 714.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4632 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 35 sheets defined 30.7% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.773A pdb=" N UNK H 90 " --> pdb=" O UNK H 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.767A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 353 removed outlier: 3.785A pdb=" N HIS A 351 " --> pdb=" O GLN A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 424 through 428 Processing helix chain 'A' and resid 473 through 482 removed outlier: 3.651A pdb=" N ASN A 477 " --> pdb=" O ASP A 473 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLU A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 543 through 545 No H-bonds generated for 'chain 'B' and resid 543 through 545' Processing helix chain 'B' and resid 546 through 554 removed outlier: 4.413A pdb=" N GLN B 552 " --> pdb=" O ILE B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 568 removed outlier: 3.640A pdb=" N GLN B 562 " --> pdb=" O ALA B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 596 removed outlier: 3.518A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 663 Processing helix chain 'C' and resid 67 through 72 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.024A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 334 through 350 removed outlier: 3.731A pdb=" N LYS C 350 " --> pdb=" O LYS C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'C' and resid 474 through 483 removed outlier: 3.887A pdb=" N TRP C 478 " --> pdb=" O MET C 474 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLU C 481 " --> pdb=" O ASN C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 552 removed outlier: 3.720A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE D 548 " --> pdb=" O LEU D 544 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL D 549 " --> pdb=" O LEU D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 595 Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 663 Processing helix chain 'E' and resid 57 through 64 Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 98 through 116 removed outlier: 4.034A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.525A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 143 removed outlier: 3.700A pdb=" N ARG E 143 " --> pdb=" O ASP E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 349 Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 367 through 372 Processing helix chain 'E' and resid 376 through 380 removed outlier: 3.824A pdb=" N GLY E 379 " --> pdb=" O ASN E 376 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU E 380 " --> pdb=" O CYS E 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 376 through 380' Processing helix chain 'E' and resid 386 through 389 Processing helix chain 'E' and resid 424 through 428 Processing helix chain 'E' and resid 473 through 482 removed outlier: 4.337A pdb=" N GLU E 481 " --> pdb=" O ASN E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 537 through 557 removed outlier: 4.032A pdb=" N LEU F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE F 548 " --> pdb=" O LEU F 544 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG F 557 " --> pdb=" O SER F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 561 through 566 Processing helix chain 'F' and resid 568 through 595 removed outlier: 3.539A pdb=" N GLY F 572 " --> pdb=" O LEU F 568 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 661 removed outlier: 3.631A pdb=" N GLN F 652 " --> pdb=" O GLU F 648 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN F 653 " --> pdb=" O SER F 649 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 81 removed outlier: 4.239A pdb=" N UNK G 81 " --> pdb=" O UNK G 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 96 No H-bonds generated for 'chain 'I' and resid 93 through 96' Processing helix chain 'K' and resid 41 through 46 removed outlier: 3.785A pdb=" N UNK K 45 " --> pdb=" O UNK K 41 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.837A pdb=" N UNK H 46 " --> pdb=" O UNK H 37 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N UNK H 37 " --> pdb=" O UNK H 46 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N UNK H 48 " --> pdb=" O UNK H 35 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N UNK H 33 " --> pdb=" O UNK H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AA4, first strand: chain 'L' and resid 12 through 13 Processing sheet with id=AA5, first strand: chain 'L' and resid 43 through 44 Processing sheet with id=AA6, first strand: chain 'A' and resid 493 through 498 removed outlier: 5.040A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA8, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.689A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.841A pdb=" N THR A 202 " --> pdb=" O TYR A 434 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 310 removed outlier: 3.831A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASP A 320 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LYS A 305 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N THR A 318 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE A 307 " --> pdb=" O TYR A 316 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N TYR A 316 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE A 309 " --> pdb=" O TRP A 314 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N TRP A 314 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 313 through 322 current: chain 'A' and resid 380 through 384 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 380 through 384 current: chain 'A' and resid 464 through 469 Processing sheet with id=AB4, first strand: chain 'C' and resid 494 through 498 removed outlier: 5.526A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.878A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB7, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB8, first strand: chain 'C' and resid 161 through 169 removed outlier: 4.043A pdb=" N GLU C 190 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.613A pdb=" N THR C 202 " --> pdb=" O TYR C 434 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 302 removed outlier: 6.089A pdb=" N GLN C 293 " --> pdb=" O SER C 333 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 328 through 333 current: chain 'C' and resid 380 through 384 removed outlier: 3.876A pdb=" N PHE C 381 " --> pdb=" O LYS C 420 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 412 through 420 current: chain 'C' and resid 465 through 469 Processing sheet with id=AC2, first strand: chain 'C' and resid 304 through 310 removed outlier: 6.612A pdb=" N GLN C 313 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 493 through 498 removed outlier: 5.596A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC5, first strand: chain 'E' and resid 75 through 76 removed outlier: 4.242A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.649A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 161 through 169 Processing sheet with id=AC8, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.446A pdb=" N ALA E 200 " --> pdb=" O ALA E 432 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N TYR E 434 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR E 202 " --> pdb=" O TYR E 434 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 310 removed outlier: 6.876A pdb=" N ASN E 301 " --> pdb=" O ILE E 321 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ILE E 321 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR E 303 " --> pdb=" O GLY E 319 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLN E 313 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 313 through 322 current: chain 'E' and resid 381 through 384 removed outlier: 3.892A pdb=" N PHE E 381 " --> pdb=" O LYS E 420 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 412 through 420 current: chain 'E' and resid 467 through 469 Processing sheet with id=AD1, first strand: chain 'E' and resid 358 through 360 Processing sheet with id=AD2, first strand: chain 'G' and resid 21 through 22 removed outlier: 3.812A pdb=" N UNK G 62 " --> pdb=" O UNK G 72 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 44 through 46 Processing sheet with id=AD4, first strand: chain 'G' and resid 48 through 49 Processing sheet with id=AD5, first strand: chain 'I' and resid 3 through 4 removed outlier: 4.054A pdb=" N UNK I 20 " --> pdb=" O UNK I 4 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 30 through 34 Processing sheet with id=AD7, first strand: chain 'K' and resid 17 through 21 Processing sheet with id=AD8, first strand: chain 'K' and resid 79 through 81 562 hydrogen bonds defined for protein. 1524 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.41 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6052 1.34 - 1.46: 4219 1.46 - 1.58: 8575 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 18984 Sorted by residual: bond pdb=" C1 NAG f 2 " pdb=" O5 NAG f 2 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" N VAL C 242 " pdb=" CA VAL C 242 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.14e-02 7.69e+03 1.11e+01 bond pdb=" N ILE C 138 " pdb=" CA ILE C 138 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.15e-02 7.56e+03 1.08e+01 bond pdb=" C1 BMA M 3 " pdb=" C2 BMA M 3 " ideal model delta sigma weight residual 1.519 1.581 -0.062 2.00e-02 2.50e+03 9.72e+00 bond pdb=" C1 NAG W 2 " pdb=" O5 NAG W 2 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 9.05e+00 ... (remaining 18979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 24223 1.88 - 3.75: 1457 3.75 - 5.63: 159 5.63 - 7.50: 46 7.50 - 9.38: 9 Bond angle restraints: 25894 Sorted by residual: angle pdb=" C ALA C 48 " pdb=" N GLU C 49 " pdb=" CA GLU C 49 " ideal model delta sigma weight residual 121.94 129.69 -7.75 1.76e+00 3.23e-01 1.94e+01 angle pdb=" N GLY A 41 " pdb=" CA GLY A 41 " pdb=" C GLY A 41 " ideal model delta sigma weight residual 115.67 108.73 6.94 1.59e+00 3.96e-01 1.91e+01 angle pdb=" N SER D 553 " pdb=" CA SER D 553 " pdb=" CB SER D 553 " ideal model delta sigma weight residual 114.17 110.23 3.94 1.14e+00 7.69e-01 1.20e+01 angle pdb=" C LEU B 556 " pdb=" N ARG B 557 " pdb=" CA ARG B 557 " ideal model delta sigma weight residual 121.54 128.14 -6.60 1.91e+00 2.74e-01 1.19e+01 angle pdb=" C PHE C 233 " pdb=" N ASN C 234 " pdb=" CA ASN C 234 " ideal model delta sigma weight residual 126.45 132.48 -6.03 1.77e+00 3.19e-01 1.16e+01 ... (remaining 25889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.85: 12062 21.85 - 43.71: 516 43.71 - 65.56: 86 65.56 - 87.42: 38 87.42 - 109.27: 21 Dihedral angle restraints: 12723 sinusoidal: 5636 harmonic: 7087 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 152.65 -59.65 1 1.00e+01 1.00e-02 4.75e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -134.91 48.91 1 1.00e+01 1.00e-02 3.29e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -132.13 46.13 1 1.00e+01 1.00e-02 2.95e+01 ... (remaining 12720 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.199: 3335 0.199 - 0.398: 17 0.398 - 0.597: 1 0.597 - 0.795: 0 0.795 - 0.994: 1 Chirality restraints: 3354 Sorted by residual: chirality pdb=" C1 NAG h 2 " pdb=" O4 NAG h 1 " pdb=" C2 NAG h 2 " pdb=" O5 NAG h 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.48e+01 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN C 241 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-01 2.50e+01 2.47e+01 chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.23e+01 ... (remaining 3351 not shown) Planarity restraints: 3299 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 613 " -0.345 2.00e-02 2.50e+03 2.99e-01 1.11e+03 pdb=" C7 NAG E 613 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG E 613 " -0.106 2.00e-02 2.50e+03 pdb=" N2 NAG E 613 " 0.532 2.00e-02 2.50e+03 pdb=" O7 NAG E 613 " -0.161 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 612 " 0.291 2.00e-02 2.50e+03 2.49e-01 7.74e+02 pdb=" C7 NAG E 612 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG E 612 " -0.016 2.00e-02 2.50e+03 pdb=" N2 NAG E 612 " -0.420 2.00e-02 2.50e+03 pdb=" O7 NAG E 612 " 0.209 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG h 2 " 0.235 2.00e-02 2.50e+03 1.96e-01 4.78e+02 pdb=" C7 NAG h 2 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG h 2 " 0.166 2.00e-02 2.50e+03 pdb=" N2 NAG h 2 " -0.322 2.00e-02 2.50e+03 pdb=" O7 NAG h 2 " -0.014 2.00e-02 2.50e+03 ... (remaining 3296 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1686 2.74 - 3.28: 20082 3.28 - 3.82: 30470 3.82 - 4.36: 35959 4.36 - 4.90: 58748 Nonbonded interactions: 146945 Sorted by model distance: nonbonded pdb=" OE2 GLU A 269 " pdb=" NE2 GLN A 347 " model vdw 2.199 3.120 nonbonded pdb=" OG1 THR E 297 " pdb=" O ILE E 442 " model vdw 2.224 3.040 nonbonded pdb=" NE2 GLN A 203 " pdb=" O ALA A 204 " model vdw 2.242 3.120 nonbonded pdb=" O VAL A 68 " pdb=" OG1 THR A 71 " model vdw 2.242 3.040 nonbonded pdb=" O3 NAG M 2 " pdb=" O5 BMA M 3 " model vdw 2.279 3.040 ... (remaining 146940 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 178 or resid 189 through 398 or resid 410 throu \ gh 611)) selection = (chain 'C' and (resid 33 through 178 or resid 189 through 611)) selection = (chain 'E' and (resid 33 through 398 or resid 410 through 611)) } ncs_group { reference = (chain 'B' and (resid 521 through 661 or resid 701 through 702)) selection = (chain 'D' and (resid 521 through 661 or resid 701 through 702)) selection = (chain 'F' and resid 521 through 702) } ncs_group { reference = (chain 'G' and resid 9 through 102) selection = (chain 'I' and resid 21 through 114) selection = (chain 'J' and resid 11 through 104) selection = chain 'K' selection = (chain 'L' and resid 8 through 101) } ncs_group { reference = (chain 'M' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' } ncs_group { reference = chain 'W' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 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: 0.310 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 18.030 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 19113 Z= 0.341 Angle : 1.088 20.476 26251 Z= 0.538 Chirality : 0.057 0.994 3354 Planarity : 0.010 0.299 3234 Dihedral : 13.517 109.274 8001 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.77 (0.19), residues: 1767 helix: 0.09 (0.24), residues: 435 sheet: -0.79 (0.27), residues: 372 loop : -0.59 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 557 TYR 0.047 0.003 TYR A 61 PHE 0.044 0.003 PHE A 467 TRP 0.042 0.003 TRP D 571 HIS 0.012 0.002 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00671 (18984) covalent geometry : angle 0.99312 (25894) SS BOND : bond 0.00447 ( 30) SS BOND : angle 1.29759 ( 60) hydrogen bonds : bond 0.15482 ( 562) hydrogen bonds : angle 7.46235 ( 1524) link_ALPHA1-3 : bond 0.00483 ( 3) link_ALPHA1-3 : angle 2.87534 ( 9) link_ALPHA1-4 : bond 0.00556 ( 1) link_ALPHA1-4 : angle 2.05965 ( 3) link_ALPHA1-6 : bond 0.00900 ( 3) link_ALPHA1-6 : angle 1.58024 ( 9) link_BETA1-3 : bond 0.03534 ( 1) link_BETA1-3 : angle 12.61569 ( 3) link_BETA1-4 : bond 0.01731 ( 24) link_BETA1-4 : angle 6.15966 ( 72) link_BETA1-6 : bond 0.01761 ( 2) link_BETA1-6 : angle 4.12368 ( 6) link_NAG-ASN : bond 0.00751 ( 65) link_NAG-ASN : angle 3.20680 ( 195) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.7550 (m-80) cc_final: 0.7284 (m-80) REVERT: A 151 PHE cc_start: 0.6825 (t80) cc_final: 0.6187 (t80) REVERT: A 167 LEU cc_start: 0.9150 (mm) cc_final: 0.8899 (mm) REVERT: A 217 TYR cc_start: 0.8900 (m-80) cc_final: 0.8602 (m-10) REVERT: A 322 ILE cc_start: 0.7922 (mm) cc_final: 0.7639 (mm) REVERT: A 360 PHE cc_start: 0.8410 (m-80) cc_final: 0.7917 (m-80) REVERT: A 367 ASP cc_start: 0.8994 (p0) cc_final: 0.8762 (p0) REVERT: A 369 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8102 (mm-30) REVERT: A 383 TYR cc_start: 0.8258 (m-80) cc_final: 0.7769 (m-80) REVERT: A 426 TRP cc_start: 0.8166 (m100) cc_final: 0.7947 (m100) REVERT: B 537 LEU cc_start: 0.8725 (mt) cc_final: 0.8403 (mt) REVERT: B 543 ASN cc_start: 0.9286 (m110) cc_final: 0.8774 (m110) REVERT: B 571 TRP cc_start: 0.8201 (m-90) cc_final: 0.7927 (m-10) REVERT: B 584 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8212 (mt-10) REVERT: B 596 TRP cc_start: 0.9010 (m-10) cc_final: 0.8671 (m-90) REVERT: C 45 TRP cc_start: 0.8880 (p90) cc_final: 0.8330 (p90) REVERT: C 100 MET cc_start: 0.8584 (ptp) cc_final: 0.8248 (ppp) REVERT: C 104 MET cc_start: 0.8935 (ttt) cc_final: 0.8613 (ttm) REVERT: C 125 LEU cc_start: 0.9074 (tt) cc_final: 0.8731 (tt) REVERT: C 321 ILE cc_start: 0.7956 (mm) cc_final: 0.7420 (tp) REVERT: C 389 LEU cc_start: 0.9627 (mt) cc_final: 0.9405 (mt) REVERT: C 419 ILE cc_start: 0.9612 (mm) cc_final: 0.9409 (mm) REVERT: C 473 ASP cc_start: 0.9278 (t0) cc_final: 0.9007 (t0) REVERT: D 522 PHE cc_start: 0.9036 (t80) cc_final: 0.8824 (t80) REVERT: D 543 ASN cc_start: 0.9059 (m-40) cc_final: 0.8837 (m-40) REVERT: D 545 LEU cc_start: 0.9280 (tp) cc_final: 0.8773 (mt) REVERT: D 549 VAL cc_start: 0.7586 (t) cc_final: 0.7190 (t) REVERT: D 560 GLU cc_start: 0.8737 (pm20) cc_final: 0.8489 (pm20) REVERT: E 49 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8022 (mt-10) REVERT: E 84 ILE cc_start: 0.9350 (mm) cc_final: 0.9135 (mp) REVERT: E 107 ASP cc_start: 0.9354 (m-30) cc_final: 0.9082 (m-30) REVERT: E 108 ILE cc_start: 0.9358 (tt) cc_final: 0.9116 (mm) REVERT: E 375 PHE cc_start: 0.7935 (p90) cc_final: 0.7309 (p90) REVERT: F 549 VAL cc_start: 0.8521 (t) cc_final: 0.8033 (t) REVERT: F 588 ARG cc_start: 0.8944 (ttp80) cc_final: 0.8392 (ptt90) REVERT: F 626 MET cc_start: 0.6558 (mtt) cc_final: 0.5987 (mtt) REVERT: F 628 TRP cc_start: 0.9039 (m100) cc_final: 0.8726 (m100) REVERT: F 635 ILE cc_start: 0.8588 (pt) cc_final: 0.7842 (tt) REVERT: F 647 GLU cc_start: 0.9402 (pt0) cc_final: 0.8969 (pp20) REVERT: F 650 GLN cc_start: 0.9319 (tp40) cc_final: 0.8802 (tp40) REVERT: F 651 ASN cc_start: 0.9293 (m-40) cc_final: 0.8813 (m-40) outliers start: 0 outliers final: 0 residues processed: 402 average time/residue: 0.1484 time to fit residues: 90.3413 Evaluate side-chains 278 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 216 optimal weight: 30.0000 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 50.0000 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 235 optimal weight: 30.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 HIS ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 431 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 GLN E 424 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.087290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.074718 restraints weight = 81219.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.076740 restraints weight = 48849.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.078160 restraints weight = 33511.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.079151 restraints weight = 24967.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.079837 restraints weight = 19817.332| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 19113 Z= 0.173 Angle : 0.789 20.186 26251 Z= 0.363 Chirality : 0.046 0.480 3354 Planarity : 0.004 0.057 3234 Dihedral : 9.185 78.363 4593 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.25 % Allowed : 3.88 % Favored : 95.86 % 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: -0.45 (0.20), residues: 1767 helix: 0.51 (0.24), residues: 443 sheet: -0.54 (0.25), residues: 413 loop : -0.49 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 542 TYR 0.019 0.002 TYR A 61 PHE 0.021 0.002 PHE F 522 TRP 0.037 0.002 TRP B 610 HIS 0.008 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00365 (18984) covalent geometry : angle 0.70274 (25894) SS BOND : bond 0.00363 ( 30) SS BOND : angle 1.19556 ( 60) hydrogen bonds : bond 0.05132 ( 562) hydrogen bonds : angle 5.88149 ( 1524) link_ALPHA1-3 : bond 0.00958 ( 3) link_ALPHA1-3 : angle 2.98762 ( 9) link_ALPHA1-4 : bond 0.01312 ( 1) link_ALPHA1-4 : angle 1.35138 ( 3) link_ALPHA1-6 : bond 0.00825 ( 3) link_ALPHA1-6 : angle 2.08988 ( 9) link_BETA1-3 : bond 0.03059 ( 1) link_BETA1-3 : angle 9.66783 ( 3) link_BETA1-4 : bond 0.01453 ( 24) link_BETA1-4 : angle 4.55570 ( 72) link_BETA1-6 : bond 0.01091 ( 2) link_BETA1-6 : angle 2.27166 ( 6) link_NAG-ASN : bond 0.00563 ( 65) link_NAG-ASN : angle 2.82204 ( 195) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 350 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.7604 (m-80) cc_final: 0.7139 (m-80) REVERT: A 66 HIS cc_start: 0.7138 (m-70) cc_final: 0.6881 (m-70) REVERT: A 83 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7843 (tm-30) REVERT: A 116 LEU cc_start: 0.9316 (mt) cc_final: 0.9072 (mt) REVERT: A 142 MET cc_start: 0.8454 (mmt) cc_final: 0.8002 (tpp) REVERT: A 151 PHE cc_start: 0.6887 (t80) cc_final: 0.6260 (t80) REVERT: A 172 ASP cc_start: 0.8521 (m-30) cc_final: 0.8124 (m-30) REVERT: A 367 ASP cc_start: 0.8927 (p0) cc_final: 0.8665 (p0) REVERT: A 383 TYR cc_start: 0.8378 (m-80) cc_final: 0.7994 (m-80) REVERT: A 433 MET cc_start: 0.8681 (ttp) cc_final: 0.8457 (ttp) REVERT: A 474 MET cc_start: 0.7929 (ttt) cc_final: 0.7658 (ttm) REVERT: B 537 LEU cc_start: 0.8774 (mt) cc_final: 0.8479 (mt) REVERT: B 543 ASN cc_start: 0.9335 (m110) cc_final: 0.8919 (m110) REVERT: B 584 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8167 (mt-10) REVERT: B 596 TRP cc_start: 0.9084 (m-10) cc_final: 0.8770 (m-90) REVERT: C 45 TRP cc_start: 0.8796 (p90) cc_final: 0.8385 (p90) REVERT: C 104 MET cc_start: 0.8856 (ttt) cc_final: 0.8618 (ttm) REVERT: C 419 ILE cc_start: 0.9589 (mm) cc_final: 0.9374 (mm) REVERT: C 434 TYR cc_start: 0.7880 (t80) cc_final: 0.7657 (t80) REVERT: D 545 LEU cc_start: 0.9375 (tp) cc_final: 0.9030 (mt) REVERT: D 587 LEU cc_start: 0.9741 (mm) cc_final: 0.9412 (mm) REVERT: D 656 ASN cc_start: 0.9254 (m-40) cc_final: 0.8128 (m-40) REVERT: E 99 ASN cc_start: 0.8850 (t0) cc_final: 0.8005 (t0) REVERT: E 108 ILE cc_start: 0.9422 (tt) cc_final: 0.9099 (mm) REVERT: E 143 ARG cc_start: 0.8047 (mmt90) cc_final: 0.7281 (mtp-110) REVERT: E 355 ASN cc_start: 0.9031 (p0) cc_final: 0.8792 (p0) REVERT: F 530 MET cc_start: 0.7491 (ttt) cc_final: 0.7204 (ttt) REVERT: F 628 TRP cc_start: 0.9022 (m100) cc_final: 0.8562 (m100) REVERT: F 643 TYR cc_start: 0.9150 (m-10) cc_final: 0.8925 (m-10) REVERT: F 647 GLU cc_start: 0.9285 (pt0) cc_final: 0.8921 (pp20) REVERT: F 650 GLN cc_start: 0.9172 (tp40) cc_final: 0.8935 (tp40) REVERT: F 656 ASN cc_start: 0.9223 (t0) cc_final: 0.8917 (m-40) outliers start: 4 outliers final: 0 residues processed: 353 average time/residue: 0.1466 time to fit residues: 78.9791 Evaluate side-chains 260 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 231 optimal weight: 30.0000 chunk 86 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 203 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 199 optimal weight: 10.0000 chunk 201 optimal weight: 20.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 HIS ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN B 552 GLN ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 249 HIS D 543 ASN ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 GLN E 477 ASN F 564 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.078152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.066549 restraints weight = 89018.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.068341 restraints weight = 53520.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.069583 restraints weight = 36822.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.070481 restraints weight = 27794.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.071067 restraints weight = 22303.132| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.114 19113 Z= 0.440 Angle : 1.292 19.012 26251 Z= 0.596 Chirality : 0.060 0.452 3354 Planarity : 0.007 0.068 3234 Dihedral : 10.546 73.123 4593 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 20.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.34 % Favored : 93.60 % Rotamer: Outliers : 0.56 % Allowed : 6.64 % Favored : 92.79 % 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: -1.63 (0.18), residues: 1767 helix: -0.55 (0.23), residues: 444 sheet: -0.98 (0.25), residues: 387 loop : -1.35 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 428 TYR 0.025 0.003 TYR C 61 PHE 0.036 0.004 PHE A 151 TRP 0.049 0.005 TRP F 571 HIS 0.013 0.003 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00931 (18984) covalent geometry : angle 1.21788 (25894) SS BOND : bond 0.01092 ( 30) SS BOND : angle 1.77512 ( 60) hydrogen bonds : bond 0.06485 ( 562) hydrogen bonds : angle 7.03312 ( 1524) link_ALPHA1-3 : bond 0.00633 ( 3) link_ALPHA1-3 : angle 4.03249 ( 9) link_ALPHA1-4 : bond 0.02382 ( 1) link_ALPHA1-4 : angle 2.00875 ( 3) link_ALPHA1-6 : bond 0.00860 ( 3) link_ALPHA1-6 : angle 2.32881 ( 9) link_BETA1-3 : bond 0.01740 ( 1) link_BETA1-3 : angle 8.81299 ( 3) link_BETA1-4 : bond 0.01336 ( 24) link_BETA1-4 : angle 4.87304 ( 72) link_BETA1-6 : bond 0.00686 ( 2) link_BETA1-6 : angle 2.39069 ( 6) link_NAG-ASN : bond 0.01104 ( 65) link_NAG-ASN : angle 3.93808 ( 195) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 291 time to evaluate : 0.538 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: A 39 TYR cc_start: 0.7674 (m-80) cc_final: 0.6976 (m-80) REVERT: A 52 LEU cc_start: 0.8778 (tp) cc_final: 0.8491 (tp) REVERT: A 66 HIS cc_start: 0.7405 (m-70) cc_final: 0.7017 (m-70) REVERT: A 93 PHE cc_start: 0.8055 (m-10) cc_final: 0.7628 (m-10) REVERT: A 104 MET cc_start: 0.9248 (ttp) cc_final: 0.8934 (ptm) REVERT: A 116 LEU cc_start: 0.9220 (mt) cc_final: 0.8858 (mt) REVERT: A 142 MET cc_start: 0.8503 (mmt) cc_final: 0.8236 (tpp) REVERT: A 151 PHE cc_start: 0.7848 (t80) cc_final: 0.6738 (t80) REVERT: A 153 MET cc_start: 0.8194 (mtt) cc_final: 0.7885 (mtt) REVERT: A 172 ASP cc_start: 0.8467 (m-30) cc_final: 0.8111 (m-30) REVERT: A 217 TYR cc_start: 0.9142 (m-80) cc_final: 0.8646 (m-80) REVERT: A 260 LEU cc_start: 0.9167 (mt) cc_final: 0.8804 (mt) REVERT: A 448 ILE cc_start: 0.9577 (mp) cc_final: 0.9308 (tt) REVERT: B 537 LEU cc_start: 0.8924 (mt) cc_final: 0.8663 (mt) REVERT: B 543 ASN cc_start: 0.9317 (m110) cc_final: 0.8773 (t0) REVERT: B 584 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8037 (mt-10) REVERT: B 601 LYS cc_start: 0.8788 (mptt) cc_final: 0.8380 (mtmt) REVERT: B 606 THR cc_start: 0.8943 (p) cc_final: 0.8659 (p) REVERT: C 104 MET cc_start: 0.9084 (ttt) cc_final: 0.8814 (ttm) REVERT: C 249 HIS cc_start: 0.9279 (p-80) cc_final: 0.9070 (p90) REVERT: C 285 LEU cc_start: 0.9438 (mp) cc_final: 0.9105 (tp) REVERT: C 425 MET cc_start: 0.8087 (ptm) cc_final: 0.7744 (ptm) REVERT: C 478 TRP cc_start: 0.8950 (m-10) cc_final: 0.8194 (m-10) REVERT: D 536 THR cc_start: 0.8975 (p) cc_final: 0.8529 (t) REVERT: D 548 ILE cc_start: 0.8291 (pt) cc_final: 0.8055 (pt) REVERT: D 560 GLU cc_start: 0.8748 (pm20) cc_final: 0.7605 (pm20) REVERT: D 643 TYR cc_start: 0.9050 (m-10) cc_final: 0.8343 (m-80) REVERT: E 113 ASP cc_start: 0.8776 (p0) cc_final: 0.8567 (t0) REVERT: E 316 TYR cc_start: 0.7629 (m-80) cc_final: 0.7136 (m-80) REVERT: E 355 ASN cc_start: 0.9192 (p0) cc_final: 0.8991 (p0) REVERT: F 643 TYR cc_start: 0.9275 (m-10) cc_final: 0.8881 (m-10) REVERT: F 647 GLU cc_start: 0.9306 (pt0) cc_final: 0.8926 (pp20) REVERT: F 648 GLU cc_start: 0.9009 (tm-30) cc_final: 0.8708 (tp30) REVERT: F 650 GLN cc_start: 0.9425 (tp40) cc_final: 0.8569 (tm-30) REVERT: F 651 ASN cc_start: 0.9360 (m110) cc_final: 0.8841 (m110) REVERT: F 654 GLU cc_start: 0.8498 (pp20) cc_final: 0.8129 (pp20) outliers start: 9 outliers final: 2 residues processed: 297 average time/residue: 0.1550 time to fit residues: 68.6614 Evaluate side-chains 217 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 215 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 77 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 133 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 181 optimal weight: 3.9990 chunk 192 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN C 105 HIS ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN C 302 ASN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN E 72 HIS F 564 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.083574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.071565 restraints weight = 84212.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.073447 restraints weight = 50668.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.074770 restraints weight = 34857.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.075708 restraints weight = 26221.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.076356 restraints weight = 20996.842| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19113 Z= 0.153 Angle : 0.829 16.765 26251 Z= 0.379 Chirality : 0.048 0.427 3354 Planarity : 0.004 0.052 3234 Dihedral : 8.530 62.925 4593 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.06 % Allowed : 2.44 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.92 (0.19), residues: 1767 helix: 0.51 (0.24), residues: 434 sheet: -0.88 (0.26), residues: 384 loop : -0.99 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 418 TYR 0.021 0.002 TYR B 643 PHE 0.019 0.002 PHE C 210 TRP 0.031 0.002 TRP E 478 HIS 0.007 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00330 (18984) covalent geometry : angle 0.74753 (25894) SS BOND : bond 0.00363 ( 30) SS BOND : angle 1.42922 ( 60) hydrogen bonds : bond 0.04547 ( 562) hydrogen bonds : angle 5.86223 ( 1524) link_ALPHA1-3 : bond 0.01049 ( 3) link_ALPHA1-3 : angle 2.89131 ( 9) link_ALPHA1-4 : bond 0.01596 ( 1) link_ALPHA1-4 : angle 1.25117 ( 3) link_ALPHA1-6 : bond 0.00856 ( 3) link_ALPHA1-6 : angle 1.55410 ( 9) link_BETA1-3 : bond 0.02406 ( 1) link_BETA1-3 : angle 9.97577 ( 3) link_BETA1-4 : bond 0.01189 ( 24) link_BETA1-4 : angle 4.16079 ( 72) link_BETA1-6 : bond 0.01122 ( 2) link_BETA1-6 : angle 2.05603 ( 6) link_NAG-ASN : bond 0.00634 ( 65) link_NAG-ASN : angle 3.02393 ( 195) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 351 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.7423 (m-80) cc_final: 0.6986 (m-80) REVERT: A 52 LEU cc_start: 0.8773 (tp) cc_final: 0.8319 (tp) REVERT: A 66 HIS cc_start: 0.7105 (m-70) cc_final: 0.6735 (m-70) REVERT: A 151 PHE cc_start: 0.7263 (t80) cc_final: 0.6045 (t80) REVERT: A 167 LEU cc_start: 0.9241 (mm) cc_final: 0.9036 (mm) REVERT: A 433 MET cc_start: 0.8359 (ttm) cc_final: 0.7868 (ttp) REVERT: B 537 LEU cc_start: 0.9003 (mt) cc_final: 0.8730 (mt) REVERT: B 543 ASN cc_start: 0.9218 (m110) cc_final: 0.8626 (t0) REVERT: B 579 ARG cc_start: 0.8091 (mtp180) cc_final: 0.7618 (mtp180) REVERT: B 584 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8118 (mt-10) REVERT: B 603 ILE cc_start: 0.8411 (mm) cc_final: 0.8110 (mm) REVERT: B 652 GLN cc_start: 0.8982 (tt0) cc_final: 0.8571 (tm-30) REVERT: B 654 GLU cc_start: 0.8989 (tt0) cc_final: 0.8777 (tt0) REVERT: B 656 ASN cc_start: 0.9027 (m110) cc_final: 0.8606 (m110) REVERT: C 39 TYR cc_start: 0.8925 (m-80) cc_final: 0.8499 (m-10) REVERT: C 104 MET cc_start: 0.8961 (ttt) cc_final: 0.8716 (ttm) REVERT: C 434 TYR cc_start: 0.8085 (t80) cc_final: 0.7873 (t80) REVERT: D 536 THR cc_start: 0.8753 (p) cc_final: 0.8242 (t) REVERT: D 542 ARG cc_start: 0.9059 (ttp80) cc_final: 0.8429 (tmm-80) REVERT: D 588 ARG cc_start: 0.9232 (mmm-85) cc_final: 0.8901 (mmm-85) REVERT: D 643 TYR cc_start: 0.8988 (m-10) cc_final: 0.8348 (m-80) REVERT: D 646 LEU cc_start: 0.8866 (mt) cc_final: 0.8599 (tp) REVERT: E 100 MET cc_start: 0.8988 (tpp) cc_final: 0.8712 (tpp) REVERT: E 143 ARG cc_start: 0.8137 (mmt90) cc_final: 0.7343 (mtp-110) REVERT: E 153 MET cc_start: 0.8120 (tpt) cc_final: 0.7711 (tmm) REVERT: E 217 TYR cc_start: 0.8279 (m-80) cc_final: 0.7173 (m-10) REVERT: E 316 TYR cc_start: 0.7490 (m-80) cc_final: 0.6631 (m-80) REVERT: E 355 ASN cc_start: 0.9132 (p0) cc_final: 0.8886 (p0) REVERT: E 359 ARG cc_start: 0.9065 (ptm-80) cc_final: 0.8350 (ptm160) REVERT: F 522 PHE cc_start: 0.8587 (t80) cc_final: 0.8371 (t80) REVERT: F 643 TYR cc_start: 0.9203 (m-10) cc_final: 0.8957 (m-10) REVERT: F 647 GLU cc_start: 0.9240 (pt0) cc_final: 0.8835 (pp20) REVERT: F 648 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8453 (tp30) REVERT: F 650 GLN cc_start: 0.9131 (tp40) cc_final: 0.8722 (tm-30) REVERT: F 651 ASN cc_start: 0.9213 (m110) cc_final: 0.8522 (m110) outliers start: 1 outliers final: 0 residues processed: 351 average time/residue: 0.1562 time to fit residues: 82.0170 Evaluate side-chains 257 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 36 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 193 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 178 optimal weight: 0.2980 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 249 HIS C 347 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.081091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.069185 restraints weight = 86392.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.071016 restraints weight = 52042.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.072311 restraints weight = 35884.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.073188 restraints weight = 27059.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.073882 restraints weight = 21774.399| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 19113 Z= 0.225 Angle : 0.850 16.377 26251 Z= 0.391 Chirality : 0.048 0.445 3354 Planarity : 0.004 0.057 3234 Dihedral : 8.317 60.104 4593 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.06 % Allowed : 3.32 % Favored : 96.62 % 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: -0.95 (0.19), residues: 1767 helix: 0.65 (0.25), residues: 434 sheet: -0.93 (0.26), residues: 381 loop : -1.08 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 585 TYR 0.019 0.002 TYR A 61 PHE 0.018 0.002 PHE A 53 TRP 0.039 0.003 TRP F 571 HIS 0.007 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00482 (18984) covalent geometry : angle 0.76923 (25894) SS BOND : bond 0.00414 ( 30) SS BOND : angle 1.25440 ( 60) hydrogen bonds : bond 0.04545 ( 562) hydrogen bonds : angle 5.86328 ( 1524) link_ALPHA1-3 : bond 0.00745 ( 3) link_ALPHA1-3 : angle 3.26243 ( 9) link_ALPHA1-4 : bond 0.01734 ( 1) link_ALPHA1-4 : angle 0.95729 ( 3) link_ALPHA1-6 : bond 0.00710 ( 3) link_ALPHA1-6 : angle 1.47914 ( 9) link_BETA1-3 : bond 0.01837 ( 1) link_BETA1-3 : angle 9.23763 ( 3) link_BETA1-4 : bond 0.01126 ( 24) link_BETA1-4 : angle 4.00866 ( 72) link_BETA1-6 : bond 0.00942 ( 2) link_BETA1-6 : angle 2.11922 ( 6) link_NAG-ASN : bond 0.00631 ( 65) link_NAG-ASN : angle 3.17970 ( 195) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 304 time to evaluate : 0.674 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: A 39 TYR cc_start: 0.7442 (m-80) cc_final: 0.7107 (m-80) REVERT: A 52 LEU cc_start: 0.8961 (tp) cc_final: 0.8678 (tt) REVERT: A 66 HIS cc_start: 0.7225 (m-70) cc_final: 0.6764 (m-70) REVERT: A 142 MET cc_start: 0.8472 (tpp) cc_final: 0.8182 (tpp) REVERT: A 151 PHE cc_start: 0.7687 (t80) cc_final: 0.6445 (t80) REVERT: A 172 ASP cc_start: 0.8655 (m-30) cc_final: 0.8304 (m-30) REVERT: B 543 ASN cc_start: 0.9218 (m110) cc_final: 0.8728 (t0) REVERT: B 584 GLU cc_start: 0.8591 (mt-10) cc_final: 0.7960 (mp0) REVERT: B 603 ILE cc_start: 0.8233 (mm) cc_final: 0.8019 (mm) REVERT: B 652 GLN cc_start: 0.9098 (tt0) cc_final: 0.8577 (tm-30) REVERT: B 656 ASN cc_start: 0.8988 (m110) cc_final: 0.8568 (m110) REVERT: C 39 TYR cc_start: 0.8985 (m-80) cc_final: 0.8664 (m-10) REVERT: C 67 ASN cc_start: 0.8944 (OUTLIER) cc_final: 0.8164 (t0) REVERT: C 104 MET cc_start: 0.9014 (ttt) cc_final: 0.8803 (ttm) REVERT: C 478 TRP cc_start: 0.8991 (m-10) cc_final: 0.8174 (m-10) REVERT: D 536 THR cc_start: 0.8890 (p) cc_final: 0.8376 (t) REVERT: D 588 ARG cc_start: 0.9300 (mmm-85) cc_final: 0.8784 (mmm-85) REVERT: D 643 TYR cc_start: 0.8998 (m-10) cc_final: 0.8393 (m-80) REVERT: D 646 LEU cc_start: 0.9013 (mt) cc_final: 0.8714 (tp) REVERT: E 95 MET cc_start: 0.9490 (ppp) cc_final: 0.9131 (ppp) REVERT: E 104 MET cc_start: 0.8378 (tpt) cc_final: 0.7958 (tpp) REVERT: E 143 ARG cc_start: 0.8027 (mmt90) cc_final: 0.7253 (mtp-110) REVERT: E 153 MET cc_start: 0.8115 (tpt) cc_final: 0.7758 (tmm) REVERT: E 316 TYR cc_start: 0.7592 (m-80) cc_final: 0.6839 (m-80) REVERT: F 530 MET cc_start: 0.7732 (ttt) cc_final: 0.7208 (ppp) REVERT: F 624 ASP cc_start: 0.8024 (m-30) cc_final: 0.7740 (m-30) REVERT: F 643 TYR cc_start: 0.9280 (m-10) cc_final: 0.8959 (m-10) REVERT: F 648 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8233 (tp30) REVERT: F 650 GLN cc_start: 0.9238 (tp40) cc_final: 0.8751 (tm-30) REVERT: F 651 ASN cc_start: 0.9268 (m110) cc_final: 0.8868 (m110) outliers start: 1 outliers final: 0 residues processed: 305 average time/residue: 0.1471 time to fit residues: 68.7596 Evaluate side-chains 237 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 236 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 210 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 chunk 212 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 221 optimal weight: 30.0000 chunk 44 optimal weight: 6.9990 chunk 230 optimal weight: 20.0000 chunk 194 optimal weight: 0.8980 chunk 123 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 164 optimal weight: 9.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 HIS ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 ASN F 564 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.079349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.067645 restraints weight = 86383.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.069438 restraints weight = 52214.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.070682 restraints weight = 35971.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.071583 restraints weight = 27143.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.072181 restraints weight = 21848.510| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 19113 Z= 0.293 Angle : 0.931 16.453 26251 Z= 0.431 Chirality : 0.050 0.439 3354 Planarity : 0.005 0.045 3234 Dihedral : 8.700 59.860 4593 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.13 % Allowed : 3.07 % Favored : 96.80 % 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: -1.05 (0.19), residues: 1767 helix: 0.44 (0.25), residues: 440 sheet: -0.86 (0.27), residues: 360 loop : -1.16 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 588 TYR 0.014 0.002 TYR E 383 PHE 0.036 0.003 PHE E 210 TRP 0.034 0.003 TRP F 614 HIS 0.007 0.002 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00621 (18984) covalent geometry : angle 0.85931 (25894) SS BOND : bond 0.00628 ( 30) SS BOND : angle 1.43508 ( 60) hydrogen bonds : bond 0.04832 ( 562) hydrogen bonds : angle 6.15538 ( 1524) link_ALPHA1-3 : bond 0.00677 ( 3) link_ALPHA1-3 : angle 3.58708 ( 9) link_ALPHA1-4 : bond 0.02480 ( 1) link_ALPHA1-4 : angle 1.21135 ( 3) link_ALPHA1-6 : bond 0.00689 ( 3) link_ALPHA1-6 : angle 1.57084 ( 9) link_BETA1-3 : bond 0.01372 ( 1) link_BETA1-3 : angle 8.79008 ( 3) link_BETA1-4 : bond 0.01073 ( 24) link_BETA1-4 : angle 3.99012 ( 72) link_BETA1-6 : bond 0.00849 ( 2) link_BETA1-6 : angle 2.36935 ( 6) link_NAG-ASN : bond 0.00694 ( 65) link_NAG-ASN : angle 3.17095 ( 195) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 290 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.7494 (m-80) cc_final: 0.6890 (m-80) REVERT: A 52 LEU cc_start: 0.8835 (tp) cc_final: 0.8536 (tt) REVERT: A 66 HIS cc_start: 0.7234 (m-70) cc_final: 0.7031 (m-70) REVERT: A 172 ASP cc_start: 0.8589 (m-30) cc_final: 0.8326 (m-30) REVERT: B 537 LEU cc_start: 0.8986 (mt) cc_final: 0.8725 (mt) REVERT: B 543 ASN cc_start: 0.9209 (m110) cc_final: 0.8787 (t0) REVERT: B 584 GLU cc_start: 0.8614 (mt-10) cc_final: 0.7992 (mp0) REVERT: B 603 ILE cc_start: 0.8223 (mm) cc_final: 0.7989 (mm) REVERT: B 626 MET cc_start: 0.6809 (tpt) cc_final: 0.6608 (tpt) REVERT: B 652 GLN cc_start: 0.9163 (tt0) cc_final: 0.8870 (tt0) REVERT: C 39 TYR cc_start: 0.9049 (m-80) cc_final: 0.8793 (m-10) REVERT: C 45 TRP cc_start: 0.9421 (p90) cc_final: 0.9090 (p90) REVERT: C 104 MET cc_start: 0.9104 (ttt) cc_final: 0.8676 (ttm) REVERT: C 142 MET cc_start: 0.9059 (mmm) cc_final: 0.8765 (mtp) REVERT: C 249 HIS cc_start: 0.9212 (p-80) cc_final: 0.8986 (p90) REVERT: C 478 TRP cc_start: 0.8975 (m-10) cc_final: 0.8051 (m-10) REVERT: D 536 THR cc_start: 0.8966 (p) cc_final: 0.8547 (t) REVERT: D 548 ILE cc_start: 0.8301 (pt) cc_final: 0.7325 (pt) REVERT: D 584 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8851 (mt-10) REVERT: D 643 TYR cc_start: 0.9031 (m-10) cc_final: 0.8379 (m-80) REVERT: E 95 MET cc_start: 0.9468 (ppp) cc_final: 0.8760 (ppp) REVERT: E 143 ARG cc_start: 0.8239 (mmt90) cc_final: 0.7324 (mtp-110) REVERT: E 316 TYR cc_start: 0.7725 (m-80) cc_final: 0.6987 (m-80) REVERT: E 478 TRP cc_start: 0.8641 (m100) cc_final: 0.8349 (m100) REVERT: F 530 MET cc_start: 0.7690 (ttt) cc_final: 0.6910 (ppp) REVERT: F 564 HIS cc_start: 0.7574 (OUTLIER) cc_final: 0.7007 (t-90) REVERT: F 628 TRP cc_start: 0.9343 (m100) cc_final: 0.8577 (m100) REVERT: F 648 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8276 (tp30) REVERT: F 650 GLN cc_start: 0.9242 (tp40) cc_final: 0.8764 (tm-30) REVERT: F 651 ASN cc_start: 0.9287 (m110) cc_final: 0.8908 (m110) REVERT: F 656 ASN cc_start: 0.9106 (t0) cc_final: 0.8870 (m-40) outliers start: 2 outliers final: 0 residues processed: 292 average time/residue: 0.1401 time to fit residues: 63.3864 Evaluate side-chains 227 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 190 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 181 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 chunk 204 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 38 optimal weight: 0.1980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.081091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.069272 restraints weight = 85495.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.071062 restraints weight = 51783.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.072361 restraints weight = 35880.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.073277 restraints weight = 27080.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.073920 restraints weight = 21782.726| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19113 Z= 0.177 Angle : 0.808 16.479 26251 Z= 0.374 Chirality : 0.047 0.428 3354 Planarity : 0.004 0.046 3234 Dihedral : 8.184 57.925 4593 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.06 % Allowed : 1.63 % Favored : 98.31 % 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: -1.06 (0.19), residues: 1767 helix: 0.45 (0.24), residues: 449 sheet: -0.90 (0.27), residues: 366 loop : -1.16 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 585 TYR 0.016 0.002 TYR E 383 PHE 0.020 0.002 PHE F 522 TRP 0.033 0.002 TRP A 112 HIS 0.008 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00381 (18984) covalent geometry : angle 0.73258 (25894) SS BOND : bond 0.00443 ( 30) SS BOND : angle 1.40056 ( 60) hydrogen bonds : bond 0.04266 ( 562) hydrogen bonds : angle 5.81473 ( 1524) link_ALPHA1-3 : bond 0.00849 ( 3) link_ALPHA1-3 : angle 3.18297 ( 9) link_ALPHA1-4 : bond 0.01758 ( 1) link_ALPHA1-4 : angle 0.88564 ( 3) link_ALPHA1-6 : bond 0.00709 ( 3) link_ALPHA1-6 : angle 1.31780 ( 9) link_BETA1-3 : bond 0.01324 ( 1) link_BETA1-3 : angle 8.93919 ( 3) link_BETA1-4 : bond 0.01111 ( 24) link_BETA1-4 : angle 3.76132 ( 72) link_BETA1-6 : bond 0.00882 ( 2) link_BETA1-6 : angle 2.04696 ( 6) link_NAG-ASN : bond 0.00604 ( 65) link_NAG-ASN : angle 2.96341 ( 195) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 311 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.7417 (m-80) cc_final: 0.7120 (m-80) REVERT: A 66 HIS cc_start: 0.7143 (m-70) cc_final: 0.6943 (m-70) REVERT: A 112 TRP cc_start: 0.8943 (t-100) cc_final: 0.8362 (t-100) REVERT: A 142 MET cc_start: 0.8628 (tpp) cc_final: 0.8254 (tpp) REVERT: A 172 ASP cc_start: 0.8541 (m-30) cc_final: 0.8259 (m-30) REVERT: B 543 ASN cc_start: 0.9187 (m110) cc_final: 0.8807 (t0) REVERT: B 544 LEU cc_start: 0.8433 (tp) cc_final: 0.8228 (tp) REVERT: B 584 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8041 (mp0) REVERT: B 603 ILE cc_start: 0.8225 (mm) cc_final: 0.8003 (mm) REVERT: C 39 TYR cc_start: 0.8967 (m-80) cc_final: 0.8734 (m-10) REVERT: C 80 ASN cc_start: 0.9151 (m-40) cc_final: 0.8780 (p0) REVERT: C 104 MET cc_start: 0.9031 (ttt) cc_final: 0.8649 (ttm) REVERT: C 142 MET cc_start: 0.9102 (mmm) cc_final: 0.8777 (mtp) REVERT: C 249 HIS cc_start: 0.9180 (p-80) cc_final: 0.8964 (p90) REVERT: C 478 TRP cc_start: 0.8958 (m-10) cc_final: 0.8022 (m-10) REVERT: C 503 ARG cc_start: 0.6050 (mtt180) cc_final: 0.5819 (mtt90) REVERT: D 536 THR cc_start: 0.8989 (p) cc_final: 0.8586 (t) REVERT: D 584 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8841 (mt-10) REVERT: D 588 ARG cc_start: 0.9194 (mmm-85) cc_final: 0.8941 (mmm-85) REVERT: D 643 TYR cc_start: 0.9008 (m-10) cc_final: 0.8343 (m-80) REVERT: D 646 LEU cc_start: 0.8994 (mt) cc_final: 0.8750 (tp) REVERT: E 95 MET cc_start: 0.9370 (ppp) cc_final: 0.8939 (ppp) REVERT: E 104 MET cc_start: 0.8556 (tpt) cc_final: 0.7888 (tpp) REVERT: E 153 MET cc_start: 0.7728 (tpt) cc_final: 0.7407 (tmm) REVERT: E 215 ILE cc_start: 0.9270 (mm) cc_final: 0.9037 (mm) REVERT: E 316 TYR cc_start: 0.7657 (m-80) cc_final: 0.6818 (m-80) REVERT: E 425 MET cc_start: 0.8735 (mmm) cc_final: 0.8467 (mmm) REVERT: E 478 TRP cc_start: 0.8617 (m100) cc_final: 0.7293 (m100) REVERT: E 489 LYS cc_start: 0.8687 (tptm) cc_final: 0.8348 (tptp) REVERT: F 530 MET cc_start: 0.7449 (ttt) cc_final: 0.6696 (ppp) REVERT: F 535 MET cc_start: 0.8009 (mmm) cc_final: 0.7782 (mmm) REVERT: F 628 TRP cc_start: 0.9317 (m100) cc_final: 0.8643 (m100) REVERT: F 648 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8216 (tp30) REVERT: F 650 GLN cc_start: 0.9099 (tp40) cc_final: 0.8756 (tm-30) REVERT: F 651 ASN cc_start: 0.9237 (m110) cc_final: 0.8838 (m110) REVERT: F 656 ASN cc_start: 0.9080 (t0) cc_final: 0.8839 (m-40) outliers start: 1 outliers final: 0 residues processed: 312 average time/residue: 0.1422 time to fit residues: 68.5937 Evaluate side-chains 240 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 183 optimal weight: 6.9990 chunk 217 optimal weight: 20.0000 chunk 160 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 208 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 219 optimal weight: 9.9990 chunk 222 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 170 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN E 477 ASN ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.079827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.068270 restraints weight = 87520.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.070057 restraints weight = 52986.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.071287 restraints weight = 36642.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.072199 restraints weight = 27713.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.072809 restraints weight = 22234.135| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 19113 Z= 0.245 Angle : 0.871 16.467 26251 Z= 0.405 Chirality : 0.048 0.432 3354 Planarity : 0.004 0.047 3234 Dihedral : 8.306 59.795 4593 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.06 % Allowed : 1.25 % Favored : 98.68 % 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: -1.20 (0.19), residues: 1767 helix: 0.35 (0.24), residues: 450 sheet: -0.90 (0.27), residues: 366 loop : -1.31 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 588 TYR 0.024 0.002 TYR E 383 PHE 0.042 0.003 PHE F 522 TRP 0.038 0.003 TRP B 614 HIS 0.012 0.002 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00524 (18984) covalent geometry : angle 0.79749 (25894) SS BOND : bond 0.00447 ( 30) SS BOND : angle 1.40023 ( 60) hydrogen bonds : bond 0.04511 ( 562) hydrogen bonds : angle 6.04193 ( 1524) link_ALPHA1-3 : bond 0.00683 ( 3) link_ALPHA1-3 : angle 3.52206 ( 9) link_ALPHA1-4 : bond 0.02175 ( 1) link_ALPHA1-4 : angle 1.12308 ( 3) link_ALPHA1-6 : bond 0.00657 ( 3) link_ALPHA1-6 : angle 1.52015 ( 9) link_BETA1-3 : bond 0.00908 ( 1) link_BETA1-3 : angle 8.08555 ( 3) link_BETA1-4 : bond 0.01015 ( 24) link_BETA1-4 : angle 3.81269 ( 72) link_BETA1-6 : bond 0.00881 ( 2) link_BETA1-6 : angle 2.13748 ( 6) link_NAG-ASN : bond 0.00654 ( 65) link_NAG-ASN : angle 3.12815 ( 195) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 292 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.7398 (m-80) cc_final: 0.7032 (m-80) REVERT: A 66 HIS cc_start: 0.7172 (m-70) cc_final: 0.6924 (m-70) REVERT: A 112 TRP cc_start: 0.8949 (t-100) cc_final: 0.8739 (t-100) REVERT: A 142 MET cc_start: 0.8530 (tpp) cc_final: 0.8160 (tpp) REVERT: A 172 ASP cc_start: 0.8631 (m-30) cc_final: 0.8336 (m-30) REVERT: B 543 ASN cc_start: 0.9193 (m110) cc_final: 0.8875 (t0) REVERT: B 603 ILE cc_start: 0.8274 (mm) cc_final: 0.8028 (mm) REVERT: C 45 TRP cc_start: 0.9417 (p90) cc_final: 0.9108 (p90) REVERT: C 80 ASN cc_start: 0.9127 (m-40) cc_final: 0.8765 (p0) REVERT: C 95 MET cc_start: 0.9188 (ppp) cc_final: 0.8969 (ppp) REVERT: C 104 MET cc_start: 0.9062 (ttt) cc_final: 0.8654 (ttm) REVERT: C 142 MET cc_start: 0.9092 (mmm) cc_final: 0.8795 (mtp) REVERT: C 249 HIS cc_start: 0.9242 (p-80) cc_final: 0.9033 (p90) REVERT: C 478 TRP cc_start: 0.8948 (m-10) cc_final: 0.8029 (m-10) REVERT: D 536 THR cc_start: 0.8971 (p) cc_final: 0.8584 (t) REVERT: D 584 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8800 (mt-10) REVERT: D 643 TYR cc_start: 0.9005 (m-10) cc_final: 0.8343 (m-80) REVERT: E 100 MET cc_start: 0.9163 (mmm) cc_final: 0.8931 (mmp) REVERT: E 104 MET cc_start: 0.8753 (tpt) cc_final: 0.8045 (tpp) REVERT: E 143 ARG cc_start: 0.8295 (mmt90) cc_final: 0.7297 (mtp-110) REVERT: E 153 MET cc_start: 0.7779 (tpt) cc_final: 0.7440 (tmm) REVERT: E 316 TYR cc_start: 0.7727 (m-80) cc_final: 0.6765 (m-80) REVERT: E 423 ILE cc_start: 0.9278 (mm) cc_final: 0.9061 (mm) REVERT: E 478 TRP cc_start: 0.8718 (m100) cc_final: 0.7470 (m100) REVERT: E 489 LYS cc_start: 0.8758 (tptm) cc_final: 0.8341 (tptm) REVERT: F 535 MET cc_start: 0.8039 (mmm) cc_final: 0.7821 (mmm) REVERT: F 628 TRP cc_start: 0.9313 (m100) cc_final: 0.9000 (m100) REVERT: F 647 GLU cc_start: 0.9244 (pt0) cc_final: 0.8819 (pp20) REVERT: F 648 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8494 (tp30) REVERT: F 650 GLN cc_start: 0.9064 (tp40) cc_final: 0.8716 (tm-30) REVERT: F 651 ASN cc_start: 0.9262 (m110) cc_final: 0.8623 (m110) REVERT: F 656 ASN cc_start: 0.9095 (t0) cc_final: 0.8870 (m-40) outliers start: 1 outliers final: 0 residues processed: 293 average time/residue: 0.1410 time to fit residues: 64.2606 Evaluate side-chains 227 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 137 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 155 optimal weight: 0.0070 chunk 21 optimal weight: 20.0000 chunk 150 optimal weight: 8.9990 chunk 135 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 211 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 chunk 202 optimal weight: 30.0000 chunk 116 optimal weight: 9.9990 overall best weight: 1.2802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.082751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.070849 restraints weight = 84465.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.072695 restraints weight = 51892.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.073949 restraints weight = 35977.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.074893 restraints weight = 27154.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.075556 restraints weight = 21766.287| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19113 Z= 0.141 Angle : 0.766 16.361 26251 Z= 0.357 Chirality : 0.046 0.426 3354 Planarity : 0.004 0.045 3234 Dihedral : 7.622 59.496 4593 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.91 (0.19), residues: 1767 helix: 0.51 (0.25), residues: 455 sheet: -0.88 (0.26), residues: 381 loop : -1.01 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 585 TYR 0.027 0.002 TYR E 217 PHE 0.033 0.002 PHE F 522 TRP 0.035 0.002 TRP B 614 HIS 0.008 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00302 (18984) covalent geometry : angle 0.69272 (25894) SS BOND : bond 0.00381 ( 30) SS BOND : angle 1.45494 ( 60) hydrogen bonds : bond 0.04032 ( 562) hydrogen bonds : angle 5.70142 ( 1524) link_ALPHA1-3 : bond 0.00975 ( 3) link_ALPHA1-3 : angle 2.98933 ( 9) link_ALPHA1-4 : bond 0.01696 ( 1) link_ALPHA1-4 : angle 0.92476 ( 3) link_ALPHA1-6 : bond 0.00752 ( 3) link_ALPHA1-6 : angle 1.26735 ( 9) link_BETA1-3 : bond 0.00939 ( 1) link_BETA1-3 : angle 8.35600 ( 3) link_BETA1-4 : bond 0.01096 ( 24) link_BETA1-4 : angle 3.58965 ( 72) link_BETA1-6 : bond 0.00982 ( 2) link_BETA1-6 : angle 1.97846 ( 6) link_NAG-ASN : bond 0.00585 ( 65) link_NAG-ASN : angle 2.86566 ( 195) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6940 (m-70) cc_final: 0.6676 (m-70) REVERT: A 100 MET cc_start: 0.9084 (ptp) cc_final: 0.8757 (ttp) REVERT: A 383 TYR cc_start: 0.8594 (m-10) cc_final: 0.8331 (m-10) REVERT: B 543 ASN cc_start: 0.9146 (m110) cc_final: 0.8759 (t0) REVERT: B 603 ILE cc_start: 0.8108 (mm) cc_final: 0.7891 (mm) REVERT: B 643 TYR cc_start: 0.8985 (m-80) cc_final: 0.8702 (m-80) REVERT: B 652 GLN cc_start: 0.9022 (tt0) cc_final: 0.8657 (tm-30) REVERT: B 656 ASN cc_start: 0.8915 (m110) cc_final: 0.8471 (m110) REVERT: C 39 TYR cc_start: 0.8921 (m-80) cc_final: 0.8711 (m-10) REVERT: C 80 ASN cc_start: 0.9111 (m-40) cc_final: 0.8510 (p0) REVERT: C 142 MET cc_start: 0.9043 (mmm) cc_final: 0.8819 (mtp) REVERT: C 249 HIS cc_start: 0.9245 (p-80) cc_final: 0.8955 (p90) REVERT: C 478 TRP cc_start: 0.8889 (m-10) cc_final: 0.7937 (m-10) REVERT: D 536 THR cc_start: 0.8928 (p) cc_final: 0.8472 (t) REVERT: D 548 ILE cc_start: 0.8334 (pt) cc_final: 0.7677 (pt) REVERT: D 549 VAL cc_start: 0.7769 (t) cc_final: 0.7362 (t) REVERT: D 581 LEU cc_start: 0.9192 (tt) cc_final: 0.8978 (mp) REVERT: D 584 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8704 (mt-10) REVERT: D 588 ARG cc_start: 0.9251 (mmm-85) cc_final: 0.8812 (mmm-85) REVERT: D 643 TYR cc_start: 0.8971 (m-10) cc_final: 0.8235 (m-80) REVERT: E 95 MET cc_start: 0.9302 (ppp) cc_final: 0.8755 (ppp) REVERT: E 100 MET cc_start: 0.9147 (mmm) cc_final: 0.8932 (mmp) REVERT: E 104 MET cc_start: 0.8622 (tpt) cc_final: 0.7610 (tpp) REVERT: E 143 ARG cc_start: 0.7741 (mmt90) cc_final: 0.7159 (mtp-110) REVERT: E 160 LYS cc_start: 0.8910 (mmtt) cc_final: 0.8404 (mtmt) REVERT: E 215 ILE cc_start: 0.9173 (mm) cc_final: 0.8880 (mm) REVERT: E 316 TYR cc_start: 0.7780 (m-80) cc_final: 0.6802 (m-80) REVERT: E 478 TRP cc_start: 0.8677 (m100) cc_final: 0.7483 (m100) REVERT: F 522 PHE cc_start: 0.8605 (t80) cc_final: 0.8281 (t80) REVERT: F 530 MET cc_start: 0.7436 (ttp) cc_final: 0.6674 (ppp) REVERT: F 568 LEU cc_start: 0.8005 (tp) cc_final: 0.7564 (tp) REVERT: F 628 TRP cc_start: 0.9090 (m100) cc_final: 0.8573 (m100) REVERT: F 647 GLU cc_start: 0.9185 (pt0) cc_final: 0.8780 (pp20) REVERT: F 648 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8461 (tp30) REVERT: F 650 GLN cc_start: 0.8960 (tp40) cc_final: 0.8621 (tm-30) REVERT: F 651 ASN cc_start: 0.9199 (m110) cc_final: 0.8556 (m110) REVERT: F 656 ASN cc_start: 0.9069 (t0) cc_final: 0.8838 (m-40) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.1464 time to fit residues: 71.9869 Evaluate side-chains 246 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 216 optimal weight: 30.0000 chunk 98 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 177 optimal weight: 2.9990 chunk 198 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 195 optimal weight: 5.9990 chunk 13 optimal weight: 20.0000 chunk 230 optimal weight: 30.0000 chunk 218 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 ASN ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.082189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.070354 restraints weight = 85158.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.072223 restraints weight = 51110.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.073520 restraints weight = 34832.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.074420 restraints weight = 26014.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.075118 restraints weight = 20774.293| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19113 Z= 0.152 Angle : 0.769 16.485 26251 Z= 0.360 Chirality : 0.046 0.421 3354 Planarity : 0.004 0.082 3234 Dihedral : 7.348 59.151 4593 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.06 % Allowed : 0.44 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.88 (0.19), residues: 1767 helix: 0.51 (0.25), residues: 453 sheet: -0.74 (0.26), residues: 374 loop : -1.03 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 418 TYR 0.020 0.002 TYR B 643 PHE 0.027 0.002 PHE F 522 TRP 0.036 0.002 TRP B 614 HIS 0.008 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00329 (18984) covalent geometry : angle 0.69864 (25894) SS BOND : bond 0.00295 ( 30) SS BOND : angle 1.33570 ( 60) hydrogen bonds : bond 0.04097 ( 562) hydrogen bonds : angle 5.61887 ( 1524) link_ALPHA1-3 : bond 0.00831 ( 3) link_ALPHA1-3 : angle 3.08479 ( 9) link_ALPHA1-4 : bond 0.01531 ( 1) link_ALPHA1-4 : angle 0.86051 ( 3) link_ALPHA1-6 : bond 0.00671 ( 3) link_ALPHA1-6 : angle 1.33138 ( 9) link_BETA1-3 : bond 0.00628 ( 1) link_BETA1-3 : angle 7.63584 ( 3) link_BETA1-4 : bond 0.01067 ( 24) link_BETA1-4 : angle 3.56999 ( 72) link_BETA1-6 : bond 0.00963 ( 2) link_BETA1-6 : angle 1.98972 ( 6) link_NAG-ASN : bond 0.00569 ( 65) link_NAG-ASN : angle 2.81800 ( 195) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3534 Ramachandran restraints generated. 1767 Oldfield, 0 Emsley, 1767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 309 time to evaluate : 0.688 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: A 66 HIS cc_start: 0.6885 (m-70) cc_final: 0.6610 (m-70) REVERT: A 383 TYR cc_start: 0.8494 (m-10) cc_final: 0.8273 (m-80) REVERT: B 543 ASN cc_start: 0.9171 (m110) cc_final: 0.8772 (t0) REVERT: B 652 GLN cc_start: 0.8956 (tt0) cc_final: 0.8646 (tm-30) REVERT: B 656 ASN cc_start: 0.8902 (m110) cc_final: 0.8460 (m110) REVERT: C 80 ASN cc_start: 0.9053 (m-40) cc_final: 0.8641 (p0) REVERT: C 95 MET cc_start: 0.9220 (ppp) cc_final: 0.8805 (ppp) REVERT: C 104 MET cc_start: 0.8929 (ttt) cc_final: 0.8577 (ttm) REVERT: C 249 HIS cc_start: 0.9267 (p-80) cc_final: 0.8924 (p90) REVERT: C 425 MET cc_start: 0.7776 (ppp) cc_final: 0.7495 (ppp) REVERT: C 478 TRP cc_start: 0.8890 (m-10) cc_final: 0.7922 (m-10) REVERT: D 536 THR cc_start: 0.8980 (p) cc_final: 0.8545 (t) REVERT: D 548 ILE cc_start: 0.8292 (pt) cc_final: 0.7638 (pt) REVERT: D 581 LEU cc_start: 0.9149 (tt) cc_final: 0.8942 (mp) REVERT: D 584 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8632 (mt-10) REVERT: D 641 ILE cc_start: 0.9379 (tt) cc_final: 0.9046 (pt) REVERT: D 643 TYR cc_start: 0.8969 (m-10) cc_final: 0.8266 (m-80) REVERT: D 646 LEU cc_start: 0.8967 (mt) cc_final: 0.8767 (tp) REVERT: E 49 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7556 (mt-10) REVERT: E 95 MET cc_start: 0.9318 (ppp) cc_final: 0.8772 (ppp) REVERT: E 99 ASN cc_start: 0.7955 (t0) cc_final: 0.7737 (t0) REVERT: E 104 MET cc_start: 0.8534 (tpt) cc_final: 0.7564 (tpp) REVERT: E 143 ARG cc_start: 0.7753 (mmt90) cc_final: 0.7168 (mtp-110) REVERT: E 160 LYS cc_start: 0.8934 (mmtt) cc_final: 0.8420 (mtmt) REVERT: E 210 PHE cc_start: 0.7696 (p90) cc_final: 0.7410 (p90) REVERT: E 215 ILE cc_start: 0.9152 (mm) cc_final: 0.8802 (mm) REVERT: E 316 TYR cc_start: 0.7621 (m-80) cc_final: 0.6609 (m-80) REVERT: E 433 MET cc_start: 0.8394 (ttm) cc_final: 0.8120 (ttm) REVERT: E 478 TRP cc_start: 0.8730 (m100) cc_final: 0.7576 (m100) REVERT: F 522 PHE cc_start: 0.8568 (t80) cc_final: 0.8136 (t80) REVERT: F 568 LEU cc_start: 0.7986 (tp) cc_final: 0.7483 (tp) REVERT: F 647 GLU cc_start: 0.9187 (pt0) cc_final: 0.8801 (pp20) REVERT: F 648 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8454 (tp30) REVERT: F 650 GLN cc_start: 0.8849 (tp40) cc_final: 0.8555 (tm-30) REVERT: F 651 ASN cc_start: 0.9194 (m110) cc_final: 0.8469 (m110) REVERT: F 656 ASN cc_start: 0.9067 (t0) cc_final: 0.8824 (m-40) outliers start: 1 outliers final: 0 residues processed: 310 average time/residue: 0.1453 time to fit residues: 69.4704 Evaluate side-chains 242 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 39 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 217 optimal weight: 20.0000 chunk 138 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 169 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 chunk 131 optimal weight: 9.9990 chunk 65 optimal weight: 0.2980 chunk 122 optimal weight: 5.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 ASN ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.081662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.070058 restraints weight = 86226.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.071868 restraints weight = 52259.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.073135 restraints weight = 36045.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.074062 restraints weight = 27148.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.074702 restraints weight = 21704.630| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.5534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19113 Z= 0.200 Angle : 0.811 16.525 26251 Z= 0.381 Chirality : 0.048 0.423 3354 Planarity : 0.004 0.054 3234 Dihedral : 7.519 57.957 4593 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.98 (0.19), residues: 1767 helix: 0.43 (0.25), residues: 455 sheet: -0.77 (0.27), residues: 372 loop : -1.12 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 418 TYR 0.022 0.002 TYR E 217 PHE 0.032 0.002 PHE F 522 TRP 0.036 0.003 TRP B 614 HIS 0.006 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00431 (18984) covalent geometry : angle 0.74483 (25894) SS BOND : bond 0.00361 ( 30) SS BOND : angle 1.26034 ( 60) hydrogen bonds : bond 0.04378 ( 562) hydrogen bonds : angle 5.79056 ( 1524) link_ALPHA1-3 : bond 0.00695 ( 3) link_ALPHA1-3 : angle 3.29920 ( 9) link_ALPHA1-4 : bond 0.01769 ( 1) link_ALPHA1-4 : angle 0.82916 ( 3) link_ALPHA1-6 : bond 0.00635 ( 3) link_ALPHA1-6 : angle 1.41173 ( 9) link_BETA1-3 : bond 0.00366 ( 1) link_BETA1-3 : angle 6.50026 ( 3) link_BETA1-4 : bond 0.01027 ( 24) link_BETA1-4 : angle 3.62644 ( 72) link_BETA1-6 : bond 0.00774 ( 2) link_BETA1-6 : angle 1.80134 ( 6) link_NAG-ASN : bond 0.00575 ( 65) link_NAG-ASN : angle 2.87177 ( 195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2752.50 seconds wall clock time: 49 minutes 2.78 seconds (2942.78 seconds total)