Starting phenix.real_space_refine on Tue Feb 20 08:53:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7akd_11812/02_2024/7akd_11812.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7akd_11812/02_2024/7akd_11812.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7akd_11812/02_2024/7akd_11812.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7akd_11812/02_2024/7akd_11812.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7akd_11812/02_2024/7akd_11812.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7akd_11812/02_2024/7akd_11812.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 17403 2.51 5 N 4439 2.21 5 O 5404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 191": "OE1" <-> "OE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B ARG 1019": "NH1" <-> "NH2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C ARG 1107": "NH1" <-> "NH2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 6": "OE1" <-> "OE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D ARG 66": "NH1" <-> "NH2" Residue "D ARG 97": "NH1" <-> "NH2" Residue "E GLU 81": "OE1" <-> "OE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "H ARG 97": "NH1" <-> "NH2" Residue "L GLU 81": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27358 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 7517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 970, 7517 Classifications: {'peptide': 970} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 48, 'TRANS': 921} Chain breaks: 9 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 45 Chain: "B" Number of atoms: 7666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7666 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 49, 'TRANS': 940} Chain breaks: 7 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 7685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7685 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 49, 'TRANS': 942} Chain breaks: 8 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "E" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "H" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "L" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 9 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: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "U" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'MAN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 136 Unusual residues: {'FUC': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 178 Unusual residues: {'FUC': 1, 'NAG': 12} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 108 Unusual residues: {'FUC': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 15.56, per 1000 atoms: 0.57 Number of scatterers: 27358 At special positions: 0 Unit cell: (156.6, 143.64, 191.16, 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 112 16.00 O 5404 8.00 N 4439 7.00 C 17403 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, 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=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " 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=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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=1, symmetry=0 Links applied ALPHA1-3 " BMA O 3 " - " MAN O 4 " " MAN T 4 " - " MAN T 5 " ALPHA1-6 " BMA T 3 " - " MAN T 4 " " MAN U 1 " - " MAN U 2 " BETA1-4 " NAG F 1 " - " NAG F 2 " " 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 K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " BETA1-6 " NAG S 1 " - " FUC S 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG T 1 " - " FUC T 6 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 717 " " NAG A1309 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1304 " - " ASN B 234 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1310 " - " ASN B 717 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 616 " " NAG C1307 " - " ASN C 801 " " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN A 282 " " NAG I 1 " - " ASN A 331 " " NAG J 1 " - " ASN A 343 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN B 282 " " NAG O 1 " - " ASN B 343 " " NAG Q 1 " - " ASN B1098 " " NAG S 1 " - " ASN C 282 " " NAG T 1 " - " ASN C 343 " " NAG W 1 " - " ASN C1074 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.70 Conformation dependent library (CDL) restraints added in 5.2 seconds 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6352 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 57 sheets defined 24.6% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.64 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.421A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.003A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.087A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 782 removed outlier: 4.614A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.513A pdb=" N ASP A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.570A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.899A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.521A pdb=" N GLN A 901 " --> pdb=" O PRO A 897 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 941 removed outlier: 3.873A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 945 Processing helix chain 'A' and resid 946 through 965 removed outlier: 3.593A pdb=" N ASP A 950 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.564A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.973A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE A1018 " --> pdb=" O ARG A1014 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.330A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 344 removed outlier: 3.880A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.882A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.913A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.775A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.966A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.107A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.811A 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 782 removed outlier: 3.673A pdb=" N VAL B 772 " --> pdb=" O THR B 768 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.913A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.774A pdb=" N SER B 875 " --> pdb=" O ALA B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 906 removed outlier: 3.878A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 907 through 910 removed outlier: 3.616A pdb=" N GLY B 910 " --> pdb=" O ASN B 907 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 907 through 910' Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.556A pdb=" N ILE B 923 " --> pdb=" O ASN B 919 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.752A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.827A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B1013 " --> pdb=" O THR B1009 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.477A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.811A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.731A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 removed outlier: 4.005A pdb=" N SER C 371 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.352A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.146A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.671A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 removed outlier: 3.540A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.313A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.657A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.713A pdb=" N ASP C 820 " --> pdb=" O SER C 816 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 4.040A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.753A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.685A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.767A 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: 3.533A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.114A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN C1010 " --> pdb=" O THR C1006 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE C1013 " --> pdb=" O THR C1009 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.657A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.828A pdb=" N THR D 90 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.827A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.643A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 226 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER A 205 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.854A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.866A pdb=" N ARG A 237 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.575A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.455A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 6.652A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.696A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.216A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 715 Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.513A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.067A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.594A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 29 removed outlier: 3.899A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.704A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.108A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.701A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE B 133 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR B 114 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N CYS B 131 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N SER B 116 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LYS B 129 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU B 118 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL B 127 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.637A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.944A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.606A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 718 removed outlier: 6.477A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 721 through 728 removed outlier: 3.606A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.618A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.702A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.990A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.573A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.521A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C 610 " --> pdb=" O ILE C 651 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.825A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.670A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.839A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.470A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 713 Processing sheet with id=AE6, first strand: chain 'C' and resid 719 through 728 removed outlier: 3.681A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 719 through 728 removed outlier: 3.681A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.640A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF1, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.537A pdb=" N GLN D 77 " --> pdb=" O ASP D 72 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.672A pdb=" N TRP D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TYR D 50 " --> pdb=" O TRP D 34 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.920A pdb=" N CYS D 95 " --> pdb=" O TRP D 111 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N TRP D 111 " --> pdb=" O CYS D 95 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ARG D 97 " --> pdb=" O GLU D 109 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.878A pdb=" N SER E 22 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.515A pdb=" N ALA E 84 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE E 48 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.515A pdb=" N ALA E 84 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN E 90 " --> pdb=" O THR E 97 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.537A pdb=" N GLN H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.672A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.919A pdb=" N CYS H 95 " --> pdb=" O TRP H 111 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N TRP H 111 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ARG H 97 " --> pdb=" O GLU H 109 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.879A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.514A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.514A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 1056 hydrogen bonds defined for protein. 2808 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: 13.58 Time building geometry restraints manager: 12.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8594 1.35 - 1.47: 7398 1.47 - 1.60: 11826 1.60 - 1.72: 1 1.72 - 1.85: 140 Bond restraints: 27959 Sorted by residual: bond pdb=" C1 FUC T 6 " pdb=" C2 FUC T 6 " ideal model delta sigma weight residual 1.528 1.622 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C1 FUC T 6 " pdb=" O5 FUC T 6 " ideal model delta sigma weight residual 1.400 1.481 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C1 MAN U 2 " pdb=" O5 MAN U 2 " ideal model delta sigma weight residual 1.399 1.450 -0.051 2.00e-02 2.50e+03 6.42e+00 bond pdb=" C1 BMA O 3 " pdb=" C2 BMA O 3 " ideal model delta sigma weight residual 1.519 1.569 -0.050 2.00e-02 2.50e+03 6.27e+00 bond pdb=" C1 MAN U 2 " pdb=" C2 MAN U 2 " ideal model delta sigma weight residual 1.526 1.576 -0.050 2.00e-02 2.50e+03 6.24e+00 ... (remaining 27954 not shown) Histogram of bond angle deviations from ideal: 100.48 - 107.20: 913 107.20 - 113.91: 15902 113.91 - 120.62: 10510 120.62 - 127.34: 10509 127.34 - 134.05: 240 Bond angle restraints: 38074 Sorted by residual: angle pdb=" N VAL A 608 " pdb=" CA VAL A 608 " pdb=" CB VAL A 608 " ideal model delta sigma weight residual 112.32 104.67 7.65 1.15e+00 7.56e-01 4.42e+01 angle pdb=" N ASN A 606 " pdb=" CA ASN A 606 " pdb=" C ASN A 606 " ideal model delta sigma weight residual 110.06 117.00 -6.94 1.43e+00 4.89e-01 2.36e+01 angle pdb=" C ASN A 606 " pdb=" CA ASN A 606 " pdb=" CB ASN A 606 " ideal model delta sigma weight residual 111.97 102.93 9.04 1.99e+00 2.53e-01 2.06e+01 angle pdb=" N VAL C 608 " pdb=" CA VAL C 608 " pdb=" CB VAL C 608 " ideal model delta sigma weight residual 112.32 107.50 4.82 1.15e+00 7.56e-01 1.76e+01 angle pdb=" N ILE H 110 " pdb=" CA ILE H 110 " pdb=" CB ILE H 110 " ideal model delta sigma weight residual 111.41 116.96 -5.55 1.38e+00 5.25e-01 1.62e+01 ... (remaining 38069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.34: 16765 24.34 - 48.69: 578 48.69 - 73.03: 143 73.03 - 97.37: 67 97.37 - 121.72: 46 Dihedral angle restraints: 17599 sinusoidal: 7725 harmonic: 9874 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -149.74 63.74 1 1.00e+01 1.00e-02 5.35e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 152.90 -59.90 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 147.14 -54.14 1 1.00e+01 1.00e-02 3.98e+01 ... (remaining 17596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 4511 0.144 - 0.287: 46 0.287 - 0.431: 8 0.431 - 0.575: 1 0.575 - 0.719: 1 Chirality restraints: 4567 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.81e+00 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.55e+00 ... (remaining 4564 not shown) Planarity restraints: 4816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 714 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO C 715 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO C 715 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 715 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 760 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.37e+00 pdb=" C CYS A 760 " 0.053 2.00e-02 2.50e+03 pdb=" O CYS A 760 " -0.020 2.00e-02 2.50e+03 pdb=" N THR A 761 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C1059 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.09e+00 pdb=" C GLY C1059 " -0.049 2.00e-02 2.50e+03 pdb=" O GLY C1059 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL C1060 " 0.016 2.00e-02 2.50e+03 ... (remaining 4813 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 440 2.68 - 3.24: 25814 3.24 - 3.79: 37203 3.79 - 4.35: 49724 4.35 - 4.90: 85238 Nonbonded interactions: 198419 Sorted by model distance: nonbonded pdb=" OD1 ASN B 360 " pdb=" OG1 THR B 523 " model vdw 2.126 2.440 nonbonded pdb=" O GLU A 661 " pdb=" OH TYR A 695 " model vdw 2.138 2.440 nonbonded pdb=" OG SER C 708 " pdb=" OG SER C 711 " model vdw 2.141 2.440 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.201 2.440 nonbonded pdb=" OD1 ASN B 343 " pdb=" N2 NAG O 1 " model vdw 2.221 2.520 ... (remaining 198414 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 66 or resid 82 through 96 or (resid 97 and (nam \ e N or name CA or name C or name O or name CB )) or resid 98 through 109 or (res \ id 110 through 111 and (name N or name CA or name C or name O or name CB )) or r \ esid 112 through 113 or resid 116 through 128 or (resid 129 and (name N or name \ CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 thro \ ugh 138 and (name N or name CA or name C or name O or name CB )) or resid 139 th \ rough 140 or resid 166 through 172 or resid 187 through 241 or (resid 242 throug \ h 263 and (name N or name CA or name C or name O or name CB )) or resid 265 thro \ ugh 613 or (resid 614 and (name N or name CA or name C or name O or name CB )) o \ r resid 615 through 618 or (resid 619 and (name N or name CA or name C or name O \ or name CB )) or resid 620 through 676 or resid 690 through 827 or resid 856 th \ rough 920 or (resid 921 and (name N or name CA or name C or name O or name CB )) \ or resid 922 through 1143 or (resid 1144 through 1146 and (name N or name CA or \ name C or name O or name CB )) or resid 1147 or resid 1301 through 1305 or resi \ d 1307)) selection = (chain 'B' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 through 110 or (resid 111 and (name N or name CA or name C or name O or nam \ e CB )) or resid 112 or (resid 113 and (name N or name CA or name C or name O or \ name CB )) or resid 116 through 134 or (resid 135 through 138 and (name N or na \ me CA or name C or name O or name CB )) or resid 139 through 140 or resid 166 th \ rough 196 or resid 200 through 385 or (resid 386 and (name N or name CA or name \ C or name O or name CB )) or resid 387 through 470 or resid 491 through 613 or ( \ resid 614 and (name N or name CA or name C or name O or name CB )) or resid 615 \ through 618 or (resid 619 and (name N or name CA or name C or name O or name CB \ )) or resid 620 through 920 or (resid 921 and (name N or name CA or name C or na \ me O or name CB )) or resid 922 through 1141 or (resid 1142 and (name N or name \ CA or name C or name O or name CB )) or resid 1143 or (resid 1144 through 1146 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1147 or resid 1 \ 301 through 1305 or resid 1307)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 through 109 or (resid 110 through 111 and (name N or name CA or name C or n \ ame O or name CB )) or resid 112 or (resid 113 and (name N or name CA or name C \ or name O or name CB )) or resid 116 through 123 or (resid 124 through 125 and ( \ name N or name CA or name C or name O or name CB )) or resid 126 through 131 or \ (resid 132 and (name N or name CA or name C or name O or name CB )) or resid 133 \ or (resid 134 through 138 and (name N or name CA or name C or name O or name CB \ )) or resid 139 through 140 or resid 166 through 171 or (resid 172 and (name N \ or name CA or name C or name O or name CB )) or resid 187 through 196 or resid 2 \ 00 through 263 or resid 265 through 385 or (resid 386 and (name N or name CA or \ name C or name O or name CB )) or resid 387 through 470 or resid 491 through 827 \ or resid 856 through 1141 or (resid 1142 and (name N or name CA or name C or na \ me O or name CB )) or resid 1143 through 1144 or (resid 1145 through 1146 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1147 or resid 1301 t \ hrough 1305 or resid 1307)) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.690 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: 14.370 Check model and map are aligned: 0.490 Set scattering table: 0.270 Process input model: 78.070 Find NCS groups from input model: 2.080 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 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 : 0.004 0.094 27959 Z= 0.242 Angle : 0.717 10.532 38074 Z= 0.375 Chirality : 0.053 0.719 4567 Planarity : 0.005 0.103 4789 Dihedral : 15.682 121.719 11130 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.21 % Allowed : 4.26 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -1.66 (0.13), residues: 3342 helix: -1.82 (0.17), residues: 631 sheet: 0.17 (0.17), residues: 809 loop : -1.43 (0.12), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 104 HIS 0.003 0.000 HIS B1048 PHE 0.020 0.001 PHE B 377 TYR 0.017 0.001 TYR B1067 ARG 0.033 0.003 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 479 time to evaluate : 2.765 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: A 582 LEU cc_start: 0.7589 (mt) cc_final: 0.7073 (pp) REVERT: A 754 LEU cc_start: 0.9044 (pp) cc_final: 0.8808 (tp) REVERT: A 948 LEU cc_start: 0.7921 (pp) cc_final: 0.7595 (pp) REVERT: A 974 SER cc_start: 0.9351 (t) cc_final: 0.8899 (m) REVERT: A 1002 GLN cc_start: 0.7684 (pt0) cc_final: 0.7139 (pt0) REVERT: B 338 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7306 (t80) REVERT: B 347 PHE cc_start: 0.5450 (t80) cc_final: 0.4992 (m-80) REVERT: B 753 LEU cc_start: 0.8700 (tt) cc_final: 0.8447 (tt) REVERT: C 338 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.7801 (t80) REVERT: C 456 PHE cc_start: 0.8018 (m-80) cc_final: 0.7753 (m-80) REVERT: C 533 LEU cc_start: 0.8640 (mt) cc_final: 0.8193 (tt) REVERT: C 663 ASP cc_start: 0.7824 (t0) cc_final: 0.7513 (m-30) REVERT: C 973 ILE cc_start: 0.8580 (mp) cc_final: 0.8370 (tt) REVERT: E 35 TRP cc_start: 0.7788 (m100) cc_final: 0.7497 (m100) REVERT: H 58 ASN cc_start: 0.6211 (m-40) cc_final: 0.5895 (m-40) REVERT: L 58 ILE cc_start: 0.8140 (mm) cc_final: 0.7862 (mm) outliers start: 6 outliers final: 2 residues processed: 485 average time/residue: 0.3743 time to fit residues: 287.5029 Evaluate side-chains 244 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 240 time to evaluate : 2.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain C residue 338 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 286 optimal weight: 2.9990 chunk 256 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 265 optimal weight: 0.6980 chunk 102 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 307 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B 271 GLN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 314 GLN C 709 ASN C 914 ASN L 6 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27959 Z= 0.237 Angle : 0.685 13.110 38074 Z= 0.346 Chirality : 0.049 0.414 4567 Planarity : 0.004 0.051 4789 Dihedral : 11.654 116.585 5252 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.06 % Allowed : 8.96 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.72 (0.13), residues: 3342 helix: 0.04 (0.20), residues: 658 sheet: 0.50 (0.17), residues: 809 loop : -1.13 (0.13), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 436 HIS 0.004 0.001 HIS A 655 PHE 0.028 0.002 PHE H 78 TYR 0.021 0.002 TYR B 91 ARG 0.004 0.000 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 269 time to evaluate : 3.370 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: A 582 LEU cc_start: 0.7553 (mt) cc_final: 0.7023 (pp) REVERT: A 974 SER cc_start: 0.9185 (t) cc_final: 0.8923 (m) REVERT: B 87 ASN cc_start: 0.7718 (m-40) cc_final: 0.7513 (m-40) REVERT: B 201 PHE cc_start: 0.8071 (t80) cc_final: 0.7799 (t80) REVERT: B 338 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.7413 (t80) REVERT: B 347 PHE cc_start: 0.5775 (t80) cc_final: 0.5281 (m-80) REVERT: B 394 ASN cc_start: 0.8230 (m-40) cc_final: 0.7966 (m-40) REVERT: C 338 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.7663 (t80) REVERT: C 429 PHE cc_start: 0.9412 (t80) cc_final: 0.9135 (t80) REVERT: C 453 TYR cc_start: 0.8268 (p90) cc_final: 0.8039 (p90) REVERT: C 533 LEU cc_start: 0.8628 (mt) cc_final: 0.8195 (tt) REVERT: C 663 ASP cc_start: 0.8005 (t0) cc_final: 0.7624 (m-30) REVERT: E 35 TRP cc_start: 0.7754 (m100) cc_final: 0.7400 (m100) REVERT: L 58 ILE cc_start: 0.8100 (mm) cc_final: 0.7864 (mm) outliers start: 60 outliers final: 38 residues processed: 313 average time/residue: 0.3609 time to fit residues: 185.9483 Evaluate side-chains 264 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 224 time to evaluate : 3.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 171 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 256 optimal weight: 0.9980 chunk 209 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 308 optimal weight: 8.9990 chunk 333 optimal weight: 0.0980 chunk 274 optimal weight: 4.9990 chunk 305 optimal weight: 7.9990 chunk 105 optimal weight: 0.6980 chunk 247 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN H 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27959 Z= 0.165 Angle : 0.598 11.918 38074 Z= 0.296 Chirality : 0.046 0.393 4567 Planarity : 0.004 0.040 4789 Dihedral : 9.848 114.541 5252 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.13 % Allowed : 10.10 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.35 (0.14), residues: 3342 helix: 0.78 (0.21), residues: 662 sheet: 0.76 (0.18), residues: 798 loop : -1.07 (0.13), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.004 0.001 HIS B 207 PHE 0.025 0.001 PHE C 429 TYR 0.021 0.001 TYR C 423 ARG 0.005 0.000 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 252 time to evaluate : 3.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.7469 (mt) cc_final: 0.6980 (pp) REVERT: A 675 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7215 (tm-30) REVERT: A 754 LEU cc_start: 0.8995 (pp) cc_final: 0.8664 (tp) REVERT: A 974 SER cc_start: 0.9136 (t) cc_final: 0.8902 (m) REVERT: A 1002 GLN cc_start: 0.7658 (pt0) cc_final: 0.7308 (pt0) REVERT: B 338 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.7361 (t80) REVERT: B 347 PHE cc_start: 0.5802 (OUTLIER) cc_final: 0.5307 (m-80) REVERT: C 140 PHE cc_start: 0.6935 (p90) cc_final: 0.6721 (p90) REVERT: C 403 ARG cc_start: 0.7510 (ttm170) cc_final: 0.7161 (ttm-80) REVERT: C 406 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7364 (mt-10) REVERT: C 429 PHE cc_start: 0.9142 (t80) cc_final: 0.8761 (t80) REVERT: C 453 TYR cc_start: 0.8299 (p90) cc_final: 0.8059 (p90) REVERT: C 533 LEU cc_start: 0.8614 (mt) cc_final: 0.8160 (tt) REVERT: C 663 ASP cc_start: 0.7872 (t0) cc_final: 0.7578 (m-30) REVERT: H 116 MET cc_start: 0.6838 (tpp) cc_final: 0.6421 (tpp) REVERT: L 46 LEU cc_start: 0.8447 (tp) cc_final: 0.8227 (tt) REVERT: L 47 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6679 (mt) REVERT: L 58 ILE cc_start: 0.8082 (mm) cc_final: 0.7815 (mm) REVERT: L 94 TRP cc_start: 0.6992 (t-100) cc_final: 0.6021 (t60) outliers start: 62 outliers final: 38 residues processed: 297 average time/residue: 0.4020 time to fit residues: 201.0180 Evaluate side-chains 268 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 226 time to evaluate : 3.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 304 optimal weight: 10.0000 chunk 231 optimal weight: 7.9990 chunk 160 optimal weight: 0.8980 chunk 34 optimal weight: 20.0000 chunk 147 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 309 optimal weight: 1.9990 chunk 327 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 293 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 487 ASN B 655 HIS ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B1002 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN D 32 HIS E 92 ASN L 6 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 27959 Z= 0.324 Angle : 0.704 12.089 38074 Z= 0.358 Chirality : 0.049 0.411 4567 Planarity : 0.005 0.066 4789 Dihedral : 9.181 105.936 5250 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.37 % Allowed : 10.99 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.65 (0.14), residues: 3342 helix: 0.49 (0.21), residues: 665 sheet: 0.58 (0.17), residues: 828 loop : -1.30 (0.13), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 436 HIS 0.007 0.001 HIS B1064 PHE 0.027 0.003 PHE C1089 TYR 0.023 0.002 TYR C 204 ARG 0.004 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 233 time to evaluate : 2.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.7677 (mt) cc_final: 0.7052 (pp) REVERT: A 900 MET cc_start: 0.8124 (mtt) cc_final: 0.7744 (mtt) REVERT: B 338 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.7621 (t80) REVERT: B 347 PHE cc_start: 0.6256 (t80) cc_final: 0.5343 (m-80) REVERT: B 1135 ASN cc_start: 0.7975 (t0) cc_final: 0.7584 (t0) REVERT: C 403 ARG cc_start: 0.7861 (ttm170) cc_final: 0.6901 (ttm-80) REVERT: C 429 PHE cc_start: 0.9339 (t80) cc_final: 0.9102 (t80) REVERT: C 533 LEU cc_start: 0.8715 (mt) cc_final: 0.8198 (tt) REVERT: D 78 PHE cc_start: 0.4866 (p90) cc_final: 0.4630 (p90) REVERT: D 95 CYS cc_start: 0.5209 (p) cc_final: 0.4728 (p) REVERT: L 46 LEU cc_start: 0.8570 (tp) cc_final: 0.8303 (tt) REVERT: L 47 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6756 (mt) REVERT: L 58 ILE cc_start: 0.8121 (mm) cc_final: 0.7863 (mm) outliers start: 98 outliers final: 65 residues processed: 310 average time/residue: 0.3650 time to fit residues: 188.3290 Evaluate side-chains 275 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 208 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 272 optimal weight: 0.1980 chunk 186 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 243 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 279 optimal weight: 3.9990 chunk 226 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 167 optimal weight: 0.9990 chunk 294 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN B 801 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN C1002 GLN H 77 GLN L 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 27959 Z= 0.206 Angle : 0.615 12.890 38074 Z= 0.306 Chirality : 0.046 0.420 4567 Planarity : 0.004 0.062 4789 Dihedral : 8.646 101.442 5250 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.93 % Favored : 97.04 % Rotamer: Outliers : 2.61 % Allowed : 13.02 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.47 (0.14), residues: 3342 helix: 0.88 (0.21), residues: 659 sheet: 0.70 (0.17), residues: 819 loop : -1.27 (0.13), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 94 HIS 0.003 0.001 HIS B1064 PHE 0.020 0.002 PHE B 201 TYR 0.017 0.001 TYR C 200 ARG 0.004 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 217 time to evaluate : 3.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.7678 (mt) cc_final: 0.7112 (pp) REVERT: A 900 MET cc_start: 0.8092 (mtt) cc_final: 0.7699 (mtt) REVERT: B 338 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.7689 (t80) REVERT: B 347 PHE cc_start: 0.6268 (t80) cc_final: 0.5327 (m-80) REVERT: B 913 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7344 (pm20) REVERT: C 403 ARG cc_start: 0.7793 (ttm170) cc_final: 0.6882 (ttm-80) REVERT: C 453 TYR cc_start: 0.8107 (p90) cc_final: 0.7876 (p90) REVERT: C 533 LEU cc_start: 0.8724 (mt) cc_final: 0.8187 (tt) REVERT: D 95 CYS cc_start: 0.5146 (p) cc_final: 0.4644 (p) REVERT: H 58 ASN cc_start: 0.7109 (t0) cc_final: 0.6529 (t0) REVERT: H 116 MET cc_start: 0.7036 (tpp) cc_final: 0.6701 (tpp) REVERT: L 47 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6861 (mt) REVERT: L 58 ILE cc_start: 0.8069 (mm) cc_final: 0.7816 (mm) REVERT: L 94 TRP cc_start: 0.6704 (t-100) cc_final: 0.5815 (t60) outliers start: 76 outliers final: 54 residues processed: 278 average time/residue: 0.3754 time to fit residues: 176.7220 Evaluate side-chains 263 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 206 time to evaluate : 3.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 110 optimal weight: 4.9990 chunk 295 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 192 optimal weight: 0.8980 chunk 80 optimal weight: 8.9990 chunk 327 optimal weight: 7.9990 chunk 272 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN B 422 ASN B 501 ASN B 762 GLN C 234 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN C1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27959 Z= 0.258 Angle : 0.634 12.974 38074 Z= 0.318 Chirality : 0.047 0.422 4567 Planarity : 0.004 0.060 4789 Dihedral : 8.314 92.686 5248 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.09 % Allowed : 13.29 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.56 (0.14), residues: 3342 helix: 0.84 (0.21), residues: 659 sheet: 0.55 (0.17), residues: 828 loop : -1.30 (0.13), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 436 HIS 0.005 0.001 HIS B1064 PHE 0.022 0.002 PHE A1121 TYR 0.019 0.001 TYR C1067 ARG 0.005 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 211 time to evaluate : 3.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.7729 (mt) cc_final: 0.7127 (pp) REVERT: A 900 MET cc_start: 0.8132 (mtt) cc_final: 0.7759 (mtt) REVERT: B 338 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.7754 (t80) REVERT: B 347 PHE cc_start: 0.6327 (t80) cc_final: 0.5314 (m-80) REVERT: B 913 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7401 (pm20) REVERT: B 1135 ASN cc_start: 0.7983 (t0) cc_final: 0.7558 (t0) REVERT: C 403 ARG cc_start: 0.7876 (ttm170) cc_final: 0.6917 (ttm-80) REVERT: C 453 TYR cc_start: 0.8149 (p90) cc_final: 0.7908 (p90) REVERT: C 533 LEU cc_start: 0.8762 (mt) cc_final: 0.8241 (tt) REVERT: D 95 CYS cc_start: 0.5169 (p) cc_final: 0.4660 (p) REVERT: E 35 TRP cc_start: 0.7575 (m100) cc_final: 0.7293 (m100) REVERT: H 58 ASN cc_start: 0.7232 (t0) cc_final: 0.6706 (t0) REVERT: H 116 MET cc_start: 0.7158 (tpp) cc_final: 0.6787 (tpp) REVERT: L 47 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6906 (mt) REVERT: L 58 ILE cc_start: 0.8110 (mm) cc_final: 0.7874 (mm) REVERT: L 94 TRP cc_start: 0.6611 (t-100) cc_final: 0.5836 (t60) outliers start: 90 outliers final: 68 residues processed: 285 average time/residue: 0.3576 time to fit residues: 170.5063 Evaluate side-chains 277 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 206 time to evaluate : 3.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 316 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 186 optimal weight: 0.9980 chunk 239 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 chunk 276 optimal weight: 0.6980 chunk 183 optimal weight: 3.9990 chunk 326 optimal weight: 2.9990 chunk 204 optimal weight: 8.9990 chunk 199 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 914 ASN C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 27959 Z= 0.250 Angle : 0.634 13.257 38074 Z= 0.317 Chirality : 0.049 0.901 4567 Planarity : 0.004 0.056 4789 Dihedral : 8.220 84.792 5248 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.43 % Allowed : 13.53 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.62 (0.14), residues: 3342 helix: 0.92 (0.21), residues: 652 sheet: 0.50 (0.18), residues: 827 loop : -1.38 (0.13), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 64 HIS 0.004 0.001 HIS B1064 PHE 0.023 0.002 PHE B 201 TYR 0.018 0.001 TYR A1067 ARG 0.005 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 204 time to evaluate : 3.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.7730 (mt) cc_final: 0.7176 (pp) REVERT: A 900 MET cc_start: 0.8136 (mtt) cc_final: 0.7746 (mtt) REVERT: B 338 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.7805 (t80) REVERT: B 347 PHE cc_start: 0.6378 (t80) cc_final: 0.5350 (m-80) REVERT: B 644 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.5822 (tm-30) REVERT: B 913 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7427 (pm20) REVERT: B 1135 ASN cc_start: 0.8010 (t0) cc_final: 0.7572 (t0) REVERT: C 403 ARG cc_start: 0.7975 (ttm170) cc_final: 0.6967 (ttm-80) REVERT: C 453 TYR cc_start: 0.8148 (p90) cc_final: 0.7868 (p90) REVERT: C 533 LEU cc_start: 0.8772 (mt) cc_final: 0.8242 (tt) REVERT: C 584 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8569 (pt) REVERT: C 985 ASP cc_start: 0.6472 (OUTLIER) cc_final: 0.6043 (m-30) REVERT: D 95 CYS cc_start: 0.5223 (p) cc_final: 0.4660 (p) REVERT: D 99 VAL cc_start: 0.9516 (p) cc_final: 0.9283 (m) REVERT: E 35 TRP cc_start: 0.7577 (m100) cc_final: 0.7317 (m100) REVERT: H 58 ASN cc_start: 0.7182 (t0) cc_final: 0.6680 (t0) REVERT: H 116 MET cc_start: 0.7116 (tpp) cc_final: 0.6830 (tpp) REVERT: L 35 TRP cc_start: 0.8160 (m100) cc_final: 0.7920 (m100) REVERT: L 47 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6852 (mt) REVERT: L 58 ILE cc_start: 0.8103 (mm) cc_final: 0.7897 (mm) REVERT: L 94 TRP cc_start: 0.6579 (t-100) cc_final: 0.5822 (t60) outliers start: 100 outliers final: 75 residues processed: 285 average time/residue: 0.3550 time to fit residues: 168.6763 Evaluate side-chains 279 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 198 time to evaluate : 2.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 202 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 195 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 222 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 256 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN C1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 27959 Z= 0.190 Angle : 0.607 13.116 38074 Z= 0.301 Chirality : 0.047 0.756 4567 Planarity : 0.004 0.047 4789 Dihedral : 7.941 76.880 5248 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.99 % Allowed : 13.87 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.51 (0.14), residues: 3342 helix: 1.09 (0.22), residues: 652 sheet: 0.54 (0.18), residues: 830 loop : -1.33 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 436 HIS 0.003 0.001 HIS B1064 PHE 0.024 0.001 PHE B 201 TYR 0.020 0.001 TYR A1138 ARG 0.007 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 212 time to evaluate : 3.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.7704 (mt) cc_final: 0.7174 (pp) REVERT: A 900 MET cc_start: 0.7985 (mtt) cc_final: 0.7603 (mtt) REVERT: A 1031 GLU cc_start: 0.8050 (tt0) cc_final: 0.7770 (mt-10) REVERT: B 338 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.7785 (t80) REVERT: B 347 PHE cc_start: 0.6381 (OUTLIER) cc_final: 0.5300 (m-80) REVERT: B 644 GLN cc_start: 0.7260 (OUTLIER) cc_final: 0.5847 (tm-30) REVERT: B 697 MET cc_start: 0.7775 (mtp) cc_final: 0.7309 (ttm) REVERT: B 913 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7421 (pm20) REVERT: B 1135 ASN cc_start: 0.8001 (t0) cc_final: 0.7578 (t0) REVERT: C 403 ARG cc_start: 0.7923 (ttm170) cc_final: 0.6927 (ttm-80) REVERT: C 453 TYR cc_start: 0.8122 (p90) cc_final: 0.7836 (p90) REVERT: C 533 LEU cc_start: 0.8760 (mt) cc_final: 0.8232 (tt) REVERT: C 568 ASP cc_start: 0.6465 (m-30) cc_final: 0.5892 (p0) REVERT: C 584 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8563 (pt) REVERT: C 914 ASN cc_start: 0.9028 (OUTLIER) cc_final: 0.8732 (p0) REVERT: C 985 ASP cc_start: 0.6462 (OUTLIER) cc_final: 0.6082 (m-30) REVERT: D 95 CYS cc_start: 0.5289 (p) cc_final: 0.4733 (p) REVERT: D 99 VAL cc_start: 0.9489 (p) cc_final: 0.9265 (m) REVERT: E 35 TRP cc_start: 0.7567 (m100) cc_final: 0.7295 (m100) REVERT: H 58 ASN cc_start: 0.7187 (t0) cc_final: 0.6692 (t0) REVERT: H 60 ASN cc_start: 0.8004 (t0) cc_final: 0.7730 (t0) REVERT: L 35 TRP cc_start: 0.8152 (m100) cc_final: 0.7938 (m100) REVERT: L 47 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6724 (mt) REVERT: L 94 TRP cc_start: 0.6501 (t-100) cc_final: 0.5712 (t60) outliers start: 87 outliers final: 69 residues processed: 280 average time/residue: 0.3411 time to fit residues: 160.6940 Evaluate side-chains 281 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 204 time to evaluate : 3.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 297 optimal weight: 6.9990 chunk 313 optimal weight: 7.9990 chunk 285 optimal weight: 0.9990 chunk 304 optimal weight: 5.9990 chunk 312 optimal weight: 0.0000 chunk 183 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 275 optimal weight: 2.9990 chunk 287 optimal weight: 1.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN C1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 27959 Z= 0.226 Angle : 0.623 13.031 38074 Z= 0.309 Chirality : 0.047 0.668 4567 Planarity : 0.004 0.044 4789 Dihedral : 7.826 67.251 5248 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.02 % Allowed : 14.05 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.58 (0.14), residues: 3342 helix: 1.04 (0.21), residues: 652 sheet: 0.46 (0.18), residues: 817 loop : -1.35 (0.13), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 64 HIS 0.004 0.001 HIS B1064 PHE 0.024 0.002 PHE B 201 TYR 0.017 0.001 TYR A1067 ARG 0.007 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 204 time to evaluate : 3.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.7736 (mt) cc_final: 0.7183 (pp) REVERT: A 900 MET cc_start: 0.8094 (mtt) cc_final: 0.7714 (mtt) REVERT: A 1031 GLU cc_start: 0.8073 (tt0) cc_final: 0.7785 (mt-10) REVERT: B 338 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.7839 (t80) REVERT: B 347 PHE cc_start: 0.6400 (t80) cc_final: 0.5314 (m-80) REVERT: B 644 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.5878 (tm-30) REVERT: B 697 MET cc_start: 0.7788 (mtp) cc_final: 0.7340 (ttm) REVERT: B 913 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7417 (pm20) REVERT: B 1135 ASN cc_start: 0.8056 (t0) cc_final: 0.7756 (t0) REVERT: C 403 ARG cc_start: 0.7948 (ttm170) cc_final: 0.6946 (ttm-80) REVERT: C 453 TYR cc_start: 0.8135 (p90) cc_final: 0.7881 (p90) REVERT: C 533 LEU cc_start: 0.8778 (mt) cc_final: 0.8228 (tt) REVERT: C 568 ASP cc_start: 0.6554 (m-30) cc_final: 0.6021 (p0) REVERT: C 584 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8564 (pt) REVERT: C 914 ASN cc_start: 0.9060 (OUTLIER) cc_final: 0.8714 (p0) REVERT: C 985 ASP cc_start: 0.6609 (OUTLIER) cc_final: 0.6184 (m-30) REVERT: D 95 CYS cc_start: 0.5441 (p) cc_final: 0.4977 (p) REVERT: D 99 VAL cc_start: 0.9506 (p) cc_final: 0.9278 (m) REVERT: D 109 GLU cc_start: 0.7198 (tm-30) cc_final: 0.6970 (tm-30) REVERT: E 35 TRP cc_start: 0.7555 (m100) cc_final: 0.7285 (m100) REVERT: H 58 ASN cc_start: 0.7243 (t0) cc_final: 0.6676 (t0) REVERT: L 35 TRP cc_start: 0.8169 (m100) cc_final: 0.7937 (m100) REVERT: L 47 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6855 (mt) REVERT: L 94 TRP cc_start: 0.6555 (t-100) cc_final: 0.5748 (t60) outliers start: 88 outliers final: 74 residues processed: 274 average time/residue: 0.3395 time to fit residues: 156.5145 Evaluate side-chains 282 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 201 time to evaluate : 2.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 303 optimal weight: 8.9990 chunk 199 optimal weight: 4.9990 chunk 321 optimal weight: 0.0470 chunk 196 optimal weight: 0.5980 chunk 152 optimal weight: 0.7980 chunk 223 optimal weight: 7.9990 chunk 337 optimal weight: 0.9990 chunk 310 optimal weight: 2.9990 chunk 268 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN C1002 GLN H 77 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 27959 Z= 0.168 Angle : 0.597 12.366 38074 Z= 0.294 Chirality : 0.046 0.611 4567 Planarity : 0.004 0.040 4789 Dihedral : 7.545 59.211 5248 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.75 % Allowed : 14.46 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.44 (0.14), residues: 3342 helix: 1.20 (0.22), residues: 659 sheet: 0.57 (0.18), residues: 822 loop : -1.30 (0.13), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 104 HIS 0.002 0.000 HIS B1048 PHE 0.025 0.001 PHE B 201 TYR 0.020 0.001 TYR A1138 ARG 0.008 0.000 ARG C 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 213 time to evaluate : 3.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.7707 (mt) cc_final: 0.7178 (pp) REVERT: A 1031 GLU cc_start: 0.8030 (tt0) cc_final: 0.7729 (mt-10) REVERT: B 338 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.7823 (t80) REVERT: B 347 PHE cc_start: 0.6183 (OUTLIER) cc_final: 0.5090 (m-80) REVERT: B 377 PHE cc_start: 0.7532 (t80) cc_final: 0.7312 (t80) REVERT: B 644 GLN cc_start: 0.7249 (OUTLIER) cc_final: 0.5850 (tm-30) REVERT: B 697 MET cc_start: 0.7775 (mtp) cc_final: 0.7321 (ttm) REVERT: B 913 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7383 (pm20) REVERT: B 1135 ASN cc_start: 0.8051 (t0) cc_final: 0.7745 (t0) REVERT: C 403 ARG cc_start: 0.7915 (ttm170) cc_final: 0.6908 (ttm-80) REVERT: C 453 TYR cc_start: 0.8084 (p90) cc_final: 0.7823 (p90) REVERT: C 533 LEU cc_start: 0.8744 (mt) cc_final: 0.8184 (tt) REVERT: C 568 ASP cc_start: 0.6607 (m-30) cc_final: 0.6106 (p0) REVERT: C 584 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8547 (pt) REVERT: C 914 ASN cc_start: 0.8936 (OUTLIER) cc_final: 0.8650 (p0) REVERT: C 918 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8212 (mm-30) REVERT: C 985 ASP cc_start: 0.6536 (OUTLIER) cc_final: 0.6125 (m-30) REVERT: D 95 CYS cc_start: 0.5465 (p) cc_final: 0.4989 (p) REVERT: D 99 VAL cc_start: 0.9487 (p) cc_final: 0.9249 (m) REVERT: D 109 GLU cc_start: 0.7120 (tm-30) cc_final: 0.6899 (tm-30) REVERT: E 35 TRP cc_start: 0.7540 (m100) cc_final: 0.7270 (m100) REVERT: H 58 ASN cc_start: 0.7211 (t0) cc_final: 0.6812 (t0) REVERT: L 5 THR cc_start: 0.8081 (OUTLIER) cc_final: 0.7816 (p) REVERT: L 35 TRP cc_start: 0.8165 (m100) cc_final: 0.7950 (m100) REVERT: L 47 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6703 (mt) REVERT: L 94 TRP cc_start: 0.6525 (t-100) cc_final: 0.5747 (t60) outliers start: 80 outliers final: 68 residues processed: 276 average time/residue: 0.3548 time to fit residues: 163.6825 Evaluate side-chains 281 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 203 time to evaluate : 3.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 164 optimal weight: 0.9980 chunk 213 optimal weight: 0.8980 chunk 286 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 247 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 74 optimal weight: 0.8980 chunk 269 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 276 optimal weight: 1.9990 chunk 34 optimal weight: 0.0040 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN C1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.154010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.118994 restraints weight = 41025.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.121232 restraints weight = 100041.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.121295 restraints weight = 48917.110| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 27959 Z= 0.201 Angle : 0.607 12.507 38074 Z= 0.298 Chirality : 0.046 0.576 4567 Planarity : 0.004 0.042 4789 Dihedral : 7.426 59.892 5248 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.92 % Allowed : 14.46 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.49 (0.14), residues: 3342 helix: 1.15 (0.21), residues: 658 sheet: 0.55 (0.18), residues: 819 loop : -1.33 (0.13), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 64 HIS 0.004 0.001 HIS B1064 PHE 0.025 0.001 PHE B 201 TYR 0.022 0.001 TYR C 421 ARG 0.008 0.000 ARG C 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4785.41 seconds wall clock time: 88 minutes 50.27 seconds (5330.27 seconds total)