Starting phenix.real_space_refine (version: dev) on Thu Apr 7 20:27:53 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld1_23279/04_2022/7ld1_23279.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld1_23279/04_2022/7ld1_23279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld1_23279/04_2022/7ld1_23279.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld1_23279/04_2022/7ld1_23279.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld1_23279/04_2022/7ld1_23279.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld1_23279/04_2022/7ld1_23279.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.044 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 29456 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 7046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 7046 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 47, 'TRANS': 925} Chain breaks: 12 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 742 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 13, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 9, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 382 Chain: "B" Number of atoms: 7046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 7046 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 47, 'TRANS': 925} Chain breaks: 12 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 742 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 13, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 9, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 382 Chain: "C" Number of atoms: 7026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7026 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 46, 'TRANS': 902} Chain breaks: 13 Unresolved non-hydrogen bonds: 405 Unresolved non-hydrogen angles: 518 Unresolved non-hydrogen dihedrals: 336 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 9, 'ASN:plan1': 12, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 5, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 264 Chain: "M" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1248 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 160} Link IDs: {'PTRANS': 12, 'TRANS': 219} Unresolved non-hydrogen bonds: 526 Unresolved non-hydrogen angles: 687 Unresolved non-hydrogen dihedrals: 438 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 6, 'TYR:plan': 9, 'ASN:plan1': 7, 'TRP:plan': 4, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 282 Chain: "N" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1251 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 485 Unresolved non-hydrogen angles: 620 Unresolved non-hydrogen dihedrals: 406 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 2, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 7, 'GLU:plan': 12, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 290 Chain: "P" Number of atoms: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1235 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 12, 'TRANS': 219} Unresolved non-hydrogen bonds: 539 Unresolved non-hydrogen angles: 704 Unresolved non-hydrogen dihedrals: 447 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 9, 'TYR:plan': 9, 'ASN:plan1': 7, 'TRP:plan': 4, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 291 Chain: "O" Number of atoms: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1235 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 143} Link IDs: {'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 501 Unresolved non-hydrogen angles: 640 Unresolved non-hydrogen dihedrals: 418 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 7, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 299 Chain: "H" Number of atoms: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1235 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 12, 'TRANS': 219} Unresolved non-hydrogen bonds: 539 Unresolved non-hydrogen angles: 704 Unresolved non-hydrogen dihedrals: 447 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 9, 'TYR:plan': 9, 'ASN:plan1': 7, 'TRP:plan': 4, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 291 Chain: "L" Number of atoms: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1235 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 143} Link IDs: {'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 501 Unresolved non-hydrogen angles: 640 Unresolved non-hydrogen dihedrals: 418 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 7, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 299 Chain: "D" 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: 1 Unresolved non-hydrogen chiralities: 3 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 chiralities: 2 Chain: "F" 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "G" 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "I" 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "J" 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "S" 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "T" 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "U" 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "V" 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "W" 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "X" 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 18.04, per 1000 atoms: 0.61 Number of scatterers: 29456 At special positions: 0 Unit cell: (160.816, 168.222, 211.6, 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 115 16.00 O 5837 8.00 N 5020 7.00 C 18484 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.05 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.05 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.05 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.01 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.01 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS N 42 " - pdb=" SG CYS N 113 " distance=2.04 Simple disulfide: pdb=" SG CYS O 42 " - pdb=" SG CYS O 113 " distance=2.03 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 113 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG A1201 " - " ASN A 709 " " NAG A1202 " - " ASN A1074 " " NAG A1203 " - " ASN A 61 " " NAG A1204 " - " ASN A 234 " " NAG A1205 " - " ASN A 603 " " NAG A1206 " - " ASN A 616 " " NAG A1207 " - " ASN A 657 " " NAG A1208 " - " ASN A 165 " " NAG B1201 " - " ASN B 616 " " NAG B1202 " - " ASN B 709 " " NAG B1203 " - " ASN B1074 " " NAG B1204 " - " ASN B 61 " " NAG B1205 " - " ASN B 122 " " NAG B1206 " - " ASN B 234 " " NAG B1207 " - " ASN B 603 " " NAG B1208 " - " ASN B 657 " " NAG B1209 " - " ASN B 165 " " NAG C1202 " - " ASN C 657 " " NAG C1203 " - " ASN C 122 " " NAG C1204 " - " ASN C 61 " " NAG C1205 " - " ASN C 616 " " NAG C1206 " - " ASN C 709 " " NAG C1207 " - " ASN C1074 " " NAG D 1 " - " ASN A1098 " " NAG E 1 " - " ASN A 282 " " NAG F 1 " - " ASN A 331 " " NAG G 1 " - " ASN A 343 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN B1134 " " NAG Q 1 " - " ASN B 282 " " NAG R 1 " - " ASN B 331 " " NAG S 1 " - " ASN B 343 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN C 331 " " NAG W 1 " - " ASN C 343 " " NAG X 1 " - " ASN C 717 " Time building additional restraints: 11.65 Conformation dependent library (CDL) restraints added in 5.0 seconds 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7938 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 66 sheets defined 21.4% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.55 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.637A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.014A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 426 through 430 removed outlier: 4.012A pdb=" N THR A 430 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 441 Processing helix chain 'A' and resid 446 through 451 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.730A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 756 removed outlier: 3.512A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.645A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.617A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.685A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.590A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.593A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 968 removed outlier: 3.681A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 968 " --> pdb=" O LYS A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.589A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.597A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.741A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 405 through 409 Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.658A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.798A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.434A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.763A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.738A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 Processing helix chain 'B' and resid 908 through 910 No H-bonds generated for 'chain 'B' and resid 908 through 910' Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 968 removed outlier: 3.745A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.667A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.585A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 4.268A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 446 through 450 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 756 removed outlier: 3.776A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.710A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.528A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.744A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.801A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.798A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.800A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.183A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.770A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.831A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 84 Processing helix chain 'M' and resid 92 through 96 Processing helix chain 'M' and resid 106 through 110 Processing helix chain 'M' and resid 224 through 228 Processing helix chain 'M' and resid 237 through 241 Processing helix chain 'N' and resid 165 through 169 removed outlier: 4.000A pdb=" N GLU N 168 " --> pdb=" O TYR N 165 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA N 169 " --> pdb=" O PRO N 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 165 through 169' Processing helix chain 'N' and resid 209 through 214 Processing helix chain 'P' and resid 45 through 50 Processing helix chain 'P' and resid 92 through 95 Processing helix chain 'P' and resid 128 through 132 removed outlier: 4.443A pdb=" N LEU P 131 " --> pdb=" O TYR P 128 " (cutoff:3.500A) Processing helix chain 'P' and resid 237 through 241 Processing helix chain 'O' and resid 74 through 77 Processing helix chain 'O' and resid 84 through 87 Processing helix chain 'O' and resid 146 through 156 removed outlier: 4.409A pdb=" N LEU O 150 " --> pdb=" O ASP O 147 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLY O 153 " --> pdb=" O LEU O 150 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR O 154 " --> pdb=" O LYS O 151 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER O 156 " --> pdb=" O GLY O 153 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 178 Processing helix chain 'O' and resid 209 through 214 Processing helix chain 'H' and resid 80 through 85 removed outlier: 4.317A pdb=" N GLY H 85 " --> pdb=" O GLN H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 95 removed outlier: 4.223A pdb=" N SER H 94 " --> pdb=" O ARG H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 226 Processing helix chain 'L' and resid 84 through 87 Processing helix chain 'L' and resid 146 through 153 Processing helix chain 'L' and resid 175 through 178 Processing helix chain 'L' and resid 209 through 214 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.263A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 removed outlier: 4.024A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.925A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.942A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.699A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.868A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.080A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.006A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.865A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.865A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB4, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.670A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.128A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.691A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.315A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 325 through 327 removed outlier: 5.088A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 354 through 355 Processing sheet with id=AC3, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.840A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.942A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 702 through 704 removed outlier: 6.597A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.675A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AC8, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AC9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD1, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.534A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.783A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.247A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.615A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AD7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.128A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.567A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE1, first strand: chain 'C' and resid 1120 through 1123 Processing sheet with id=AE2, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE3, first strand: chain 'M' and resid 28 through 31 removed outlier: 7.041A pdb=" N GLU M 29 " --> pdb=" O THR M 147 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 37 through 38 Processing sheet with id=AE5, first strand: chain 'M' and resid 69 through 70 Processing sheet with id=AE6, first strand: chain 'M' and resid 158 through 159 Processing sheet with id=AE7, first strand: chain 'M' and resid 174 through 175 removed outlier: 3.575A pdb=" N VAL M 218 " --> pdb=" O HIS M 201 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 24 through 25 Processing sheet with id=AE9, first strand: chain 'N' and resid 29 through 30 Processing sheet with id=AF1, first strand: chain 'N' and resid 78 through 79 removed outlier: 6.535A pdb=" N TRP N 60 " --> pdb=" O LEU N 72 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TYR N 74 " --> pdb=" O LEU N 58 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU N 58 " --> pdb=" O TYR N 74 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 159 through 164 removed outlier: 4.827A pdb=" N TYR N 198 " --> pdb=" O ASN N 163 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 170 through 171 Processing sheet with id=AF4, first strand: chain 'N' and resid 216 through 218 Processing sheet with id=AF5, first strand: chain 'P' and resid 24 through 26 removed outlier: 3.734A pdb=" N VAL P 24 " --> pdb=" O GLN P 42 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU P 100 " --> pdb=" O VAL P 39 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'P' and resid 29 through 31 Processing sheet with id=AF7, first strand: chain 'P' and resid 76 through 79 removed outlier: 6.756A pdb=" N TRP P 55 " --> pdb=" O MET P 67 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE P 69 " --> pdb=" O ILE P 53 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE P 53 " --> pdb=" O ILE P 69 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR P 139 " --> pdb=" O ARG P 117 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'P' and resid 157 through 159 removed outlier: 3.847A pdb=" N SER P 157 " --> pdb=" O LYS P 180 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS P 180 " --> pdb=" O LEU P 215 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU P 215 " --> pdb=" O LYS P 180 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU P 212 " --> pdb=" O GLN P 208 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'P' and resid 174 through 176 Processing sheet with id=AG1, first strand: chain 'P' and resid 231 through 232 Processing sheet with id=AG2, first strand: chain 'O' and resid 24 through 25 Processing sheet with id=AG3, first strand: chain 'O' and resid 71 through 73 removed outlier: 6.781A pdb=" N TRP O 60 " --> pdb=" O LEU O 72 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 159 through 161 removed outlier: 7.520A pdb=" N THR O 197 " --> pdb=" O GLN O 191 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLN O 191 " --> pdb=" O THR O 197 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER O 199 " --> pdb=" O THR O 189 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 169 through 172 removed outlier: 4.413A pdb=" N GLU O 220 " --> pdb=" O GLN O 172 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 38 through 42 Processing sheet with id=AG7, first strand: chain 'H' and resid 76 through 79 removed outlier: 6.407A pdb=" N TRP H 55 " --> pdb=" O MET H 67 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ILE H 69 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE H 53 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL H 56 " --> pdb=" O TYR H 114 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 157 through 160 Processing sheet with id=AG9, first strand: chain 'L' and resid 23 through 25 Processing sheet with id=AH1, first strand: chain 'L' and resid 78 through 79 removed outlier: 6.505A pdb=" N TRP L 60 " --> pdb=" O LEU L 72 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N TYR L 74 " --> pdb=" O LEU L 58 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU L 58 " --> pdb=" O TYR L 74 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 157 through 160 Processing sheet with id=AH3, first strand: chain 'L' and resid 180 through 181 1182 hydrogen bonds defined for protein. 3075 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: 23.68 Time building geometry restraints manager: 12.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 4994 1.27 - 1.41: 7291 1.41 - 1.55: 17399 1.55 - 1.69: 144 1.69 - 1.82: 148 Bond restraints: 29976 Sorted by residual: bond pdb=" C4 NAG T 2 " pdb=" O4 NAG T 2 " ideal model delta sigma weight residual 1.423 1.500 -0.077 1.00e-02 1.00e+04 5.95e+01 bond pdb=" C4 NAG R 2 " pdb=" O4 NAG R 2 " ideal model delta sigma weight residual 1.423 1.494 -0.071 1.00e-02 1.00e+04 4.99e+01 bond pdb=" C4 NAG K 2 " pdb=" O4 NAG K 2 " ideal model delta sigma weight residual 1.423 1.491 -0.068 1.00e-02 1.00e+04 4.61e+01 bond pdb=" C4 NAG D 2 " pdb=" O4 NAG D 2 " ideal model delta sigma weight residual 1.423 1.491 -0.068 1.00e-02 1.00e+04 4.56e+01 bond pdb=" C4 NAG W 2 " pdb=" O4 NAG W 2 " ideal model delta sigma weight residual 1.423 1.488 -0.065 1.00e-02 1.00e+04 4.20e+01 ... (remaining 29971 not shown) Histogram of bond angle deviations from ideal: 96.29 - 104.07: 404 104.07 - 111.85: 12404 111.85 - 119.62: 12479 119.62 - 127.40: 15605 127.40 - 135.18: 211 Bond angle restraints: 41103 Sorted by residual: angle pdb=" C2 NAG R 1 " pdb=" C1 NAG R 1 " pdb=" O5 NAG R 1 " ideal model delta sigma weight residual 109.64 120.71 -11.07 5.38e-01 3.45e+00 4.23e+02 angle pdb=" C2 NAG B1202 " pdb=" C1 NAG B1202 " pdb=" O5 NAG B1202 " ideal model delta sigma weight residual 109.64 119.89 -10.25 5.38e-01 3.45e+00 3.63e+02 angle pdb=" C2 NAG A1201 " pdb=" C1 NAG A1201 " pdb=" O5 NAG A1201 " ideal model delta sigma weight residual 109.64 119.54 -9.90 5.38e-01 3.45e+00 3.39e+02 angle pdb=" CA PHE B 559 " pdb=" CB PHE B 559 " pdb=" CG PHE B 559 " ideal model delta sigma weight residual 113.80 120.98 -7.18 1.00e+00 1.00e+00 5.16e+01 angle pdb=" N VAL A 289 " pdb=" CA VAL A 289 " pdb=" C VAL A 289 " ideal model delta sigma weight residual 111.90 117.33 -5.43 8.10e-01 1.52e+00 4.50e+01 ... (remaining 41098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 16541 17.40 - 34.80: 935 34.80 - 52.20: 148 52.20 - 69.60: 55 69.60 - 87.00: 22 Dihedral angle restraints: 17701 sinusoidal: 5443 harmonic: 12258 Sorted by residual: dihedral pdb=" C LYS B 300 " pdb=" N LYS B 300 " pdb=" CA LYS B 300 " pdb=" CB LYS B 300 " ideal model delta harmonic sigma weight residual -122.60 -137.63 15.03 0 2.50e+00 1.60e-01 3.61e+01 dihedral pdb=" CA PHE M 183 " pdb=" C PHE M 183 " pdb=" N PRO M 184 " pdb=" CA PRO M 184 " ideal model delta harmonic sigma weight residual 180.00 151.60 28.40 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA ASN P 76 " pdb=" C ASN P 76 " pdb=" N THR P 77 " pdb=" CA THR P 77 " ideal model delta harmonic sigma weight residual -180.00 -151.70 -28.30 0 5.00e+00 4.00e-02 3.20e+01 ... (remaining 17698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.214: 4978 0.214 - 0.428: 145 0.428 - 0.643: 5 0.643 - 0.857: 1 0.857 - 1.071: 4 Chirality restraints: 5133 Sorted by residual: chirality pdb=" C1 BMA T 3 " pdb=" O4 NAG T 2 " pdb=" C2 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-02 2.50e+03 1.49e+03 chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.09e+02 chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.01e+02 ... (remaining 5130 not shown) Planarity restraints: 5423 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 904 " 0.261 2.00e-02 2.50e+03 1.44e-01 4.13e+02 pdb=" CG TYR A 904 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR A 904 " -0.116 2.00e-02 2.50e+03 pdb=" CD2 TYR A 904 " -0.135 2.00e-02 2.50e+03 pdb=" CE1 TYR A 904 " -0.094 2.00e-02 2.50e+03 pdb=" CE2 TYR A 904 " -0.073 2.00e-02 2.50e+03 pdb=" CZ TYR A 904 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 904 " 0.217 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 904 " 0.218 2.00e-02 2.50e+03 1.20e-01 2.88e+02 pdb=" CG TYR B 904 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR B 904 " -0.099 2.00e-02 2.50e+03 pdb=" CD2 TYR B 904 " -0.112 2.00e-02 2.50e+03 pdb=" CE1 TYR B 904 " -0.079 2.00e-02 2.50e+03 pdb=" CE2 TYR B 904 " -0.058 2.00e-02 2.50e+03 pdb=" CZ TYR B 904 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 904 " 0.181 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 886 " -0.197 2.00e-02 2.50e+03 1.02e-01 2.62e+02 pdb=" CG TRP A 886 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP A 886 " 0.080 2.00e-02 2.50e+03 pdb=" CD2 TRP A 886 " 0.074 2.00e-02 2.50e+03 pdb=" NE1 TRP A 886 " 0.074 2.00e-02 2.50e+03 pdb=" CE2 TRP A 886 " -0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP A 886 " 0.125 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 886 " -0.138 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 886 " 0.068 2.00e-02 2.50e+03 pdb=" CH2 TRP A 886 " -0.094 2.00e-02 2.50e+03 ... (remaining 5420 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 14974 2.99 - 3.47: 30297 3.47 - 3.95: 46820 3.95 - 4.42: 52329 4.42 - 4.90: 86521 Nonbonded interactions: 230941 Sorted by model distance: nonbonded pdb=" OE2 GLU C 819 " pdb=" OG SER C1055 " model vdw 2.514 2.440 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.535 2.440 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.542 2.440 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.543 2.440 nonbonded pdb=" O5 NAG D 1 " pdb=" O6 NAG D 1 " model vdw 2.546 2.432 ... (remaining 230936 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 466 or resid 491 through 1147 or resid 1201 thr \ ough 1207)) selection = (chain 'B' and (resid 27 through 466 or resid 491 through 1147 or resid 1201 thr \ ough 1207)) selection = (chain 'C' and (resid 27 through 352 or (resid 353 through 360 and (name N or na \ me CA or name C or name O or name CB )) or resid 361 or (resid 362 through 378 a \ nd (name N or name CA or name C or name O or name CB )) or resid 379 through 395 \ or (resid 396 through 403 and (name N or name CA or name C or name O or name CB \ )) or resid 404 or (resid 405 through 411 and (name N or name CA or name C or n \ ame O or name CB )) or resid 412 through 413 or (resid 414 through 415 and (name \ N or name CA or name C or name O or name CB )) or resid 416 through 436 or (res \ id 437 through 445 and (name N or name CA or name C or name O or name CB )) or r \ esid 446 through 499 or (resid 500 through 501 and (name N or name CA or name C \ or name O or name CB )) or resid 502 or (resid 503 and (name N or name CA or nam \ e C or name O or name CB )) or resid 504 or (resid 505 through 506 and (name N o \ r name CA or name C or name O or name CB )) or resid 507 through 508 or (resid 5 \ 09 through 524 and (name N or name CA or name C or name O or name CB )) or resid \ 525 through 1147 or resid 1201 through 1207)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'E' selection = chain 'Q' } ncs_group { reference = chain 'H' selection = (chain 'M' and (resid 20 through 121 or (resid 122 through 124 and (name N or na \ me CA or name C or name O or name CB )) or resid 125 through 128 or (resid 129 t \ hrough 130 and (name N or name CA or name C or name O or name CB )) or resid 131 \ through 251)) selection = chain 'P' } ncs_group { reference = chain 'L' selection = (chain 'N' and (resid 20 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 101 or (resid 102 through 112 and \ (name N or name CA or name C or name O or name CB )) or resid 113 through 239)) selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 115 5.16 5 C 18484 2.51 5 N 5020 2.21 5 O 5837 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 individual isotropic 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.240 Check model and map are aligned: 0.450 Convert atoms to be neutral: 0.260 Process input model: 89.720 Find NCS groups from input model: 3.080 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 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 : 0.012 0.095 29976 Z= 0.838 Angle : 1.916 11.075 41103 Z= 1.287 Chirality : 0.099 1.071 5133 Planarity : 0.013 0.147 5386 Dihedral : 12.733 87.002 9661 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 0.15 Ramachandran Plot: Outliers : 1.61 % Allowed : 9.23 % Favored : 89.16 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.12), residues: 4159 helix: -1.16 (0.16), residues: 726 sheet: -0.87 (0.21), residues: 547 loop : -1.78 (0.11), residues: 2886 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 150 time to evaluate : 3.225 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 outliers start: 56 outliers final: 10 residues processed: 200 average time/residue: 0.3855 time to fit residues: 129.3450 Evaluate side-chains 96 residues out of total 3707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 3.326 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3291 time to fit residues: 9.9390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 357 optimal weight: 1.9990 chunk 320 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 216 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 331 optimal weight: 40.0000 chunk 128 optimal weight: 40.0000 chunk 201 optimal weight: 6.9990 chunk 246 optimal weight: 4.9990 chunk 384 optimal weight: 9.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B 764 ASN B 907 ASN B 919 ASN C 314 GLN C 317 ASN C 321 GLN C 919 ASN C 957 GLN ** P 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.093 29976 Z= 0.244 Angle : 0.709 13.791 41103 Z= 0.388 Chirality : 0.048 0.355 5133 Planarity : 0.005 0.054 5386 Dihedral : 6.565 29.643 4843 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.33 % Favored : 92.52 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.13), residues: 4159 helix: 0.66 (0.19), residues: 726 sheet: -1.40 (0.16), residues: 954 loop : -1.35 (0.12), residues: 2479 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 3707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 99 time to evaluate : 3.164 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 outliers start: 23 outliers final: 10 residues processed: 117 average time/residue: 0.3674 time to fit residues: 76.5016 Evaluate side-chains 88 residues out of total 3707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 3.676 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2784 time to fit residues: 9.5236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 213 optimal weight: 0.3980 chunk 119 optimal weight: 4.9990 chunk 319 optimal weight: 50.0000 chunk 261 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 384 optimal weight: 20.0000 chunk 415 optimal weight: 50.0000 chunk 342 optimal weight: 7.9990 chunk 381 optimal weight: 7.9990 chunk 131 optimal weight: 50.0000 chunk 308 optimal weight: 0.0470 overall best weight: 2.6884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A1088 HIS B 755 GLN B 907 ASN C 606 ASN C 901 GLN ** P 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 29976 Z= 0.263 Angle : 0.632 10.192 41103 Z= 0.339 Chirality : 0.047 0.347 5133 Planarity : 0.004 0.053 5386 Dihedral : 5.718 23.979 4843 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.49 % Favored : 91.44 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.13), residues: 4159 helix: 1.16 (0.20), residues: 722 sheet: -1.27 (0.16), residues: 972 loop : -1.24 (0.13), residues: 2465 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 3707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 3.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 102 average time/residue: 0.3847 time to fit residues: 68.6802 Evaluate side-chains 81 residues out of total 3707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 3.469 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2669 time to fit residues: 8.9368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 380 optimal weight: 0.0770 chunk 289 optimal weight: 8.9990 chunk 199 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 258 optimal weight: 2.9990 chunk 386 optimal weight: 50.0000 chunk 408 optimal weight: 7.9990 chunk 201 optimal weight: 0.7980 chunk 366 optimal weight: 50.0000 chunk 110 optimal weight: 2.9990 overall best weight: 2.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN B 907 ASN C 955 ASN ** N 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 29976 Z= 0.263 Angle : 0.601 10.933 41103 Z= 0.319 Chirality : 0.046 0.333 5133 Planarity : 0.004 0.062 5386 Dihedral : 5.481 24.329 4843 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.36 % Favored : 92.57 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.13), residues: 4159 helix: 1.35 (0.20), residues: 720 sheet: -1.31 (0.16), residues: 1003 loop : -1.19 (0.13), residues: 2436 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 3707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 79 time to evaluate : 3.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 96 average time/residue: 0.3774 time to fit residues: 64.3989 Evaluate side-chains 78 residues out of total 3707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 3.474 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3116 time to fit residues: 9.5896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 340 optimal weight: 5.9990 chunk 232 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 304 optimal weight: 5.9990 chunk 168 optimal weight: 0.6980 chunk 348 optimal weight: 50.0000 chunk 282 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 208 optimal weight: 7.9990 chunk 366 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 690 GLN B 804 GLN B 907 ASN B 935 GLN N 67 GLN ** P 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.082 29976 Z= 0.331 Angle : 0.614 10.089 41103 Z= 0.325 Chirality : 0.046 0.342 5133 Planarity : 0.004 0.069 5386 Dihedral : 5.374 32.669 4843 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.20 % Favored : 91.73 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.13), residues: 4159 helix: 1.38 (0.20), residues: 717 sheet: -1.35 (0.16), residues: 1009 loop : -1.17 (0.13), residues: 2433 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 3707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 76 time to evaluate : 3.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 9 residues processed: 103 average time/residue: 0.3869 time to fit residues: 70.8253 Evaluate side-chains 79 residues out of total 3707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 3.406 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2930 time to fit residues: 9.1312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 137 optimal weight: 50.0000 chunk 368 optimal weight: 30.0000 chunk 80 optimal weight: 7.9990 chunk 240 optimal weight: 0.1980 chunk 100 optimal weight: 7.9990 chunk 409 optimal weight: 50.0000 chunk 339 optimal weight: 8.9990 chunk 189 optimal weight: 0.6980 chunk 34 optimal weight: 50.0000 chunk 135 optimal weight: 8.9990 chunk 214 optimal weight: 6.9990 overall best weight: 4.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 690 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.092 29976 Z= 0.402 Angle : 0.650 9.984 41103 Z= 0.343 Chirality : 0.047 0.372 5133 Planarity : 0.005 0.064 5386 Dihedral : 5.457 42.256 4843 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.25 % Favored : 91.70 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.13), residues: 4159 helix: 1.28 (0.20), residues: 719 sheet: -1.40 (0.16), residues: 998 loop : -1.22 (0.13), residues: 2442 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 3707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 73 time to evaluate : 3.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 91 average time/residue: 0.3924 time to fit residues: 64.1643 Evaluate side-chains 81 residues out of total 3707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 3.283 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2715 time to fit residues: 9.3218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 394 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 233 optimal weight: 3.9990 chunk 298 optimal weight: 9.9990 chunk 231 optimal weight: 0.9980 chunk 344 optimal weight: 6.9990 chunk 228 optimal weight: 20.0000 chunk 407 optimal weight: 40.0000 chunk 255 optimal weight: 0.7980 chunk 248 optimal weight: 0.6980 chunk 188 optimal weight: 0.8980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1058 HIS B 907 ASN C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.083 29976 Z= 0.202 Angle : 0.564 12.975 41103 Z= 0.298 Chirality : 0.045 0.354 5133 Planarity : 0.004 0.067 5386 Dihedral : 5.159 46.333 4843 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.50 % Favored : 92.40 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.13), residues: 4159 helix: 1.55 (0.20), residues: 717 sheet: -1.30 (0.16), residues: 1021 loop : -1.09 (0.13), residues: 2421 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 3707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 3.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 89 average time/residue: 0.4322 time to fit residues: 68.0346 Evaluate side-chains 74 residues out of total 3707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 3.314 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2986 time to fit residues: 6.8705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 252 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 243 optimal weight: 4.9990 chunk 122 optimal weight: 50.0000 chunk 80 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 259 optimal weight: 7.9990 chunk 277 optimal weight: 1.9990 chunk 201 optimal weight: 10.0000 chunk 37 optimal weight: 0.4980 chunk 320 optimal weight: 40.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 907 ASN C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 29976 Z= 0.217 Angle : 0.554 9.453 41103 Z= 0.292 Chirality : 0.044 0.344 5133 Planarity : 0.004 0.067 5386 Dihedral : 5.036 50.745 4843 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.43 % Favored : 92.50 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.13), residues: 4159 helix: 1.61 (0.20), residues: 709 sheet: -1.25 (0.16), residues: 1016 loop : -1.05 (0.13), residues: 2434 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 3707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 3.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 84 average time/residue: 0.3812 time to fit residues: 58.6096 Evaluate side-chains 75 residues out of total 3707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 3.512 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3070 time to fit residues: 6.5589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 370 optimal weight: 0.0670 chunk 390 optimal weight: 7.9990 chunk 356 optimal weight: 0.9990 chunk 379 optimal weight: 20.0000 chunk 228 optimal weight: 0.0770 chunk 165 optimal weight: 9.9990 chunk 298 optimal weight: 20.0000 chunk 116 optimal weight: 0.3980 chunk 343 optimal weight: 50.0000 chunk 359 optimal weight: 7.9990 chunk 378 optimal weight: 8.9990 overall best weight: 1.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN A1011 GLN B 901 GLN B 907 ASN C 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 29976 Z= 0.209 Angle : 0.543 9.196 41103 Z= 0.285 Chirality : 0.044 0.359 5133 Planarity : 0.004 0.066 5386 Dihedral : 4.919 56.603 4843 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.38 % Favored : 92.52 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.13), residues: 4159 helix: 1.69 (0.20), residues: 699 sheet: -1.20 (0.16), residues: 1037 loop : -1.01 (0.13), residues: 2423 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 3707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 3.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 80 average time/residue: 0.3558 time to fit residues: 52.1637 Evaluate side-chains 72 residues out of total 3707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 70 time to evaluate : 3.205 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2723 time to fit residues: 5.1885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 249 optimal weight: 5.9990 chunk 401 optimal weight: 9.9990 chunk 245 optimal weight: 0.7980 chunk 190 optimal weight: 2.9990 chunk 279 optimal weight: 0.5980 chunk 421 optimal weight: 50.0000 chunk 387 optimal weight: 30.0000 chunk 335 optimal weight: 20.0000 chunk 34 optimal weight: 50.0000 chunk 259 optimal weight: 1.9990 chunk 205 optimal weight: 10.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN B 907 ASN C 895 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 29976 Z= 0.245 Angle : 0.558 12.295 41103 Z= 0.292 Chirality : 0.045 0.357 5133 Planarity : 0.004 0.069 5386 Dihedral : 4.911 57.157 4843 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.43 % Favored : 92.47 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.13), residues: 4159 helix: 1.63 (0.20), residues: 706 sheet: -1.21 (0.16), residues: 1048 loop : -1.01 (0.13), residues: 2405 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8318 Ramachandran restraints generated. 4159 Oldfield, 0 Emsley, 4159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 3707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 3.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 77 average time/residue: 0.3924 time to fit residues: 54.4656 Evaluate side-chains 72 residues out of total 3707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 70 time to evaluate : 3.570 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3394 time to fit residues: 5.7705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 266 optimal weight: 2.9990 chunk 357 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 309 optimal weight: 40.0000 chunk 49 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 336 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 345 optimal weight: 40.0000 chunk 42 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 907 ASN ** C 207 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 = 0.4064 r_free = 0.4064 target = 0.083771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.055231 restraints weight = 147252.962| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 4.37 r_work: 0.3298 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work: 0.3278 rms_B_bonded: 4.14 restraints_weight: 0.1250 r_work: 0.3268 rms_B_bonded: 4.17 restraints_weight: 0.0625 r_work: 0.3258 rms_B_bonded: 4.22 restraints_weight: 0.0312 r_work: 0.3247 rms_B_bonded: 4.30 restraints_weight: 0.0156 r_work: 0.3236 rms_B_bonded: 4.39 restraints_weight: 0.0078 r_work: 0.3224 rms_B_bonded: 4.50 restraints_weight: 0.0039 r_work: 0.3212 rms_B_bonded: 4.63 restraints_weight: 0.0020 r_work: 0.3199 rms_B_bonded: 4.79 restraints_weight: 0.0010 r_work: 0.3185 rms_B_bonded: 4.97 restraints_weight: 0.0005 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.086 29976 Z= 0.402 Angle : 0.626 11.013 41103 Z= 0.326 Chirality : 0.046 0.395 5133 Planarity : 0.004 0.068 5386 Dihedral : 5.077 49.804 4843 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.46 % Favored : 91.49 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.13), residues: 4159 helix: 1.46 (0.20), residues: 707 sheet: -1.30 (0.16), residues: 1040 loop : -1.09 (0.13), residues: 2412 =============================================================================== Job complete usr+sys time: 4104.96 seconds wall clock time: 77 minutes 8.92 seconds (4628.92 seconds total)