Starting phenix.real_space_refine on Thu Dec 14 08:50:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cs2_7582/12_2023/6cs2_7582.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cs2_7582/12_2023/6cs2_7582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cs2_7582/12_2023/6cs2_7582.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cs2_7582/12_2023/6cs2_7582.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cs2_7582/12_2023/6cs2_7582.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cs2_7582/12_2023/6cs2_7582.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 148 5.16 5 C 17677 2.51 5 N 4480 2.21 5 O 5553 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D ARG 518": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 27858 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 6914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 891, 6914 Classifications: {'peptide': 891} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 848} Chain breaks: 5 Chain: "B" Number of atoms: 8405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8405 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1020} Chain breaks: 6 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 6927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 893, 6927 Classifications: {'peptide': 893} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 850} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 4431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4431 Classifications: {'peptide': 544} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 520} Chain: "E" 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: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "L" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: 6 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "Q" 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: 6 Unresolved non-hydrogen chiralities: 3 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "b" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "e" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 14.47, per 1000 atoms: 0.52 Number of scatterers: 27858 At special positions: 0 Unit cell: (189.52, 149.35, 231.75, 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 148 16.00 O 5553 8.00 N 4480 7.00 C 17677 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 133 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.02 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.02 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.02 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.04 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.02 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.04 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.04 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.02 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.04 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 133 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.02 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.02 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.03 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.02 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " " BMA P 3 " - " MAN P 4 " " BMA S 3 " - " MAN S 4 " " BMA a 3 " - " MAN a 4 " " BMA b 3 " - " MAN b 4 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 4 " ALPHA1-6 " BMA U 3 " - " MAN U 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 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 K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " NAG-ASN " NAG A1301 " - " ASN A 65 " " NAG A1308 " - " ASN A 589 " " NAG B1310 " - " ASN B 589 " " NAG B1320 " - " ASN B1056 " " NAG C1309 " - " ASN C 589 " " NAG C1320 " - " ASN C1056 " " NAG E 1 " - " ASN A 269 " " NAG F 1 " - " ASN A 318 " " NAG G 1 " - " ASN A 691 " " NAG H 1 " - " ASN A 699 " " NAG I 1 " - " ASN A 783 " " NAG J 1 " - " ASN A1056 " " NAG K 1 " - " ASN A1080 " " NAG L 1 " - " ASN A1116 " " NAG M 1 " - " ASN A 602 " " NAG N 1 " - " ASN B 65 " " NAG O 1 " - " ASN B 269 " " NAG P 1 " - " ASN B 318 " " NAG Q 1 " - " ASN B 602 " " NAG R 1 " - " ASN B 691 " " NAG S 1 " - " ASN B 783 " " NAG T 1 " - " ASN B 699 " " NAG U 1 " - " ASN B1080 " " NAG V 1 " - " ASN B1116 " " NAG W 1 " - " ASN C 65 " " NAG X 1 " - " ASN C 269 " " NAG Y 1 " - " ASN C 318 " " NAG Z 1 " - " ASN C 691 " " NAG a 1 " - " ASN C 699 " " NAG b 1 " - " ASN C 783 " " NAG c 1 " - " ASN C1116 " " NAG d 1 " - " ASN C 602 " " NAG e 1 " - " ASN C1080 " Time building additional restraints: 12.95 Conformation dependent library (CDL) restraints added in 4.9 seconds 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6390 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 45 sheets defined 31.6% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 602 through 613 removed outlier: 3.606A pdb=" N HIS A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 724 removed outlier: 3.639A pdb=" N TYR A 723 " --> pdb=" O ASP A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 736 removed outlier: 3.627A pdb=" N ALA A 732 " --> pdb=" O SER A 728 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 765 removed outlier: 3.584A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 806 removed outlier: 4.117A pdb=" N ASN A 806 " --> pdb=" O ASP A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 864 removed outlier: 3.607A pdb=" N SER A 861 " --> pdb=" O ALA A 857 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 864 " --> pdb=" O VAL A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 872 removed outlier: 3.857A pdb=" N GLY A 871 " --> pdb=" O GLY A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 890 removed outlier: 3.552A pdb=" N PHE A 888 " --> pdb=" O MET A 884 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN A 889 " --> pdb=" O ALA A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 901 removed outlier: 4.167A pdb=" N LEU A 898 " --> pdb=" O THR A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 923 removed outlier: 4.063A pdb=" N THR A 921 " --> pdb=" O GLN A 917 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR A 923 " --> pdb=" O SER A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 947 removed outlier: 3.520A pdb=" N VAL A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 938 " --> pdb=" O VAL A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 962 through 966 removed outlier: 3.658A pdb=" N LEU A 966 " --> pdb=" O LEU A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 1014 removed outlier: 3.855A pdb=" N VAL A 973 " --> pdb=" O PRO A 969 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR A 988 " --> pdb=" O GLN A 984 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A1002 " --> pdb=" O ALA A 998 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A1012 " --> pdb=" O ALA A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1129 removed outlier: 4.135A pdb=" N ASP A1128 " --> pdb=" O PRO A1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 removed outlier: 3.513A pdb=" N LYS B 287 " --> pdb=" O LEU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 372 through 377 removed outlier: 3.612A pdb=" N LEU B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 397 removed outlier: 4.153A pdb=" N ARG B 395 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 425 through 430 Processing helix chain 'B' and resid 488 through 491 Processing helix chain 'B' and resid 602 through 612 Processing helix chain 'B' and resid 720 through 725 Processing helix chain 'B' and resid 728 through 736 removed outlier: 3.612A pdb=" N ALA B 732 " --> pdb=" O SER B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 739 No H-bonds generated for 'chain 'B' and resid 737 through 739' Processing helix chain 'B' and resid 740 through 764 removed outlier: 4.183A pdb=" N GLN B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU B 749 " --> pdb=" O LEU B 745 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 761 " --> pdb=" O ASP B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 808 removed outlier: 3.886A pdb=" N ASN B 806 " --> pdb=" O ASP B 802 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 864 Processing helix chain 'B' and resid 867 through 872 Processing helix chain 'B' and resid 879 through 891 removed outlier: 3.623A pdb=" N ARG B 887 " --> pdb=" O GLN B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 900 Processing helix chain 'B' and resid 901 through 923 removed outlier: 3.626A pdb=" N SER B 914 " --> pdb=" O ASN B 910 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR B 923 " --> pdb=" O SER B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 947 removed outlier: 3.743A pdb=" N GLN B 931 " --> pdb=" O LEU B 927 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN B 939 " --> pdb=" O ASN B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 950 No H-bonds generated for 'chain 'B' and resid 948 through 950' Processing helix chain 'B' and resid 958 through 965 removed outlier: 3.735A pdb=" N ILE B 962 " --> pdb=" O VAL B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 1014 removed outlier: 4.281A pdb=" N VAL B 973 " --> pdb=" O PRO B 969 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP B 976 " --> pdb=" O GLU B 972 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 988 " --> pdb=" O GLN B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1123 through 1127 removed outlier: 3.730A pdb=" N GLU B1126 " --> pdb=" O LEU B1123 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 604 through 613 Processing helix chain 'C' and resid 729 through 735 Processing helix chain 'C' and resid 736 through 739 removed outlier: 4.301A pdb=" N GLY C 739 " --> pdb=" O LEU C 736 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 736 through 739' Processing helix chain 'C' and resid 740 through 765 removed outlier: 3.508A pdb=" N GLN C 744 " --> pdb=" O SER C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 807 removed outlier: 3.769A pdb=" N ASN C 806 " --> pdb=" O ASP C 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 864 removed outlier: 3.744A pdb=" N ALA C 864 " --> pdb=" O VAL C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 873 Processing helix chain 'C' and resid 879 through 892 removed outlier: 3.827A pdb=" N ARG C 887 " --> pdb=" O GLN C 883 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE C 888 " --> pdb=" O MET C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 901 removed outlier: 4.339A pdb=" N LEU C 898 " --> pdb=" O THR C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 920 removed outlier: 3.511A pdb=" N ALA C 912 " --> pdb=" O GLN C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 950 removed outlier: 3.620A pdb=" N VAL C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER C 949 " --> pdb=" O VAL C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 966 Processing helix chain 'C' and resid 967 through 1016 removed outlier: 3.691A pdb=" N ALA C 971 " --> pdb=" O ASP C 967 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU C 972 " --> pdb=" O PRO C 968 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL C 973 " --> pdb=" O PRO C 969 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE C 975 " --> pdb=" O ALA C 971 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP C 976 " --> pdb=" O GLU C 972 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY C 981 " --> pdb=" O ARG C 977 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA C1002 " --> pdb=" O ALA C 998 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER C1003 " --> pdb=" O GLU C 999 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N CYS C1014 " --> pdb=" O LYS C1010 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL C1015 " --> pdb=" O MET C1011 " (cutoff:3.500A) Processing helix chain 'C' and resid 1123 through 1127 Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.640A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 82 removed outlier: 3.635A pdb=" N MET D 82 " --> pdb=" O THR D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.609A pdb=" N LEU D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.721A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 129 removed outlier: 3.536A pdb=" N SER D 128 " --> pdb=" O SER D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.503A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL D 172 " --> pdb=" O TRP D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 194 Proline residue: D 178 - end of helix removed outlier: 3.771A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 218 through 252 removed outlier: 3.644A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.577A pdb=" N ALA D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 293 through 298 removed outlier: 3.770A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 317 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.627A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.516A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 400 through 406 Processing helix chain 'D' and resid 406 through 412 Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 465 removed outlier: 3.683A pdb=" N ASN D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU D 450 " --> pdb=" O ILE D 446 " (cutoff:3.500A) Proline residue: D 451 - end of helix Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 503 through 508 removed outlier: 3.590A pdb=" N SER D 507 " --> pdb=" O LEU D 503 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN D 508 " --> pdb=" O PHE D 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 503 through 508' Processing helix chain 'D' and resid 513 through 534 removed outlier: 3.787A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 557 removed outlier: 3.625A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33 removed outlier: 4.049A pdb=" N THR A 31 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 251 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS A 180 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 47 removed outlier: 6.035A pdb=" N PHE A 47 " --> pdb=" O ARG C 553 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLY C 552 " --> pdb=" O ASP C 560 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR C 539 " --> pdb=" O ASP C 572 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 59 Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 82 removed outlier: 7.437A pdb=" N ASN A 129 " --> pdb=" O CYS A 159 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N CYS A 159 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLU A 131 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N PHE A 157 " --> pdb=" O GLU A 131 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N CYS A 133 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 9.841A pdb=" N ASN A 155 " --> pdb=" O CYS A 133 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N ASN A 135 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE A 153 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET A 151 " --> pdb=" O PHE A 137 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 139 " --> pdb=" O HIS A 149 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N SER A 141 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLN A 147 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 82 removed outlier: 12.873A pdb=" N PHE A 231 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 12.467A pdb=" N LEU A 132 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 12.963A pdb=" N ALA A 233 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 10.037A pdb=" N ASP A 134 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 9.990A pdb=" N LEU A 235 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ALA A 237 " --> pdb=" O PRO A 136 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N PHE A 138 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER A 239 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL A 140 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ASN A 129 " --> pdb=" O CYS A 159 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N CYS A 159 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLU A 131 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N PHE A 157 " --> pdb=" O GLU A 131 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N CYS A 133 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 9.841A pdb=" N ASN A 155 " --> pdb=" O CYS A 133 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N ASN A 135 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE A 153 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET A 151 " --> pdb=" O PHE A 137 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 139 " --> pdb=" O HIS A 149 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N SER A 141 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLN A 147 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 615 through 616 removed outlier: 4.138A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ASN A 304 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLY A 579 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY A 580 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 524 through 525 removed outlier: 3.881A pdb=" N THR A 539 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER A 561 " --> pdb=" O GLY A 552 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 528 through 529 Processing sheet with id=AA9, first strand: chain 'A' and resid 640 through 641 removed outlier: 6.295A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 693 through 695 Processing sheet with id=AB2, first strand: chain 'A' and resid 699 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 699 through 704 removed outlier: 5.886A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AB5, first strand: chain 'A' and resid 821 through 823 Processing sheet with id=AB6, first strand: chain 'A' and resid 1062 through 1064 Processing sheet with id=AB7, first strand: chain 'A' and resid 1068 through 1072 removed outlier: 4.262A pdb=" N ALA A1069 " --> pdb=" O SER A1105 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 31 through 34 removed outlier: 7.805A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LEU B 194 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 51 through 59 removed outlier: 3.991A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 81 through 82 removed outlier: 6.591A pdb=" N VAL B 123 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TYR B 163 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE B 125 " --> pdb=" O PHE B 161 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE B 161 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA B 127 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N CYS B 159 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN B 155 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N CYS B 133 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE B 153 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ASN B 135 " --> pdb=" O MET B 151 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N MET B 151 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N PHE B 137 " --> pdb=" O HIS B 149 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N HIS B 149 " --> pdb=" O PHE B 137 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA B 139 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLN B 147 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 81 through 82 removed outlier: 12.960A pdb=" N PHE B 231 " --> pdb=" O PHE B 130 " (cutoff:3.500A) removed outlier: 12.841A pdb=" N LEU B 132 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 13.034A pdb=" N ALA B 233 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 10.178A pdb=" N ASP B 134 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 10.034A pdb=" N LEU B 235 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA B 237 " --> pdb=" O PRO B 136 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE B 138 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N SER B 239 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL B 140 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL B 123 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TYR B 163 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE B 125 " --> pdb=" O PHE B 161 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE B 161 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA B 127 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N CYS B 159 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN B 155 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N CYS B 133 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE B 153 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ASN B 135 " --> pdb=" O MET B 151 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N MET B 151 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N PHE B 137 " --> pdb=" O HIS B 149 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N HIS B 149 " --> pdb=" O PHE B 137 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA B 139 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLN B 147 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 615 through 616 removed outlier: 3.657A pdb=" N THR B 616 " --> pdb=" O ARG B 306 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ILE B 299 " --> pdb=" O THR B 585 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR B 585 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N GLN B 301 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 583 " --> pdb=" O GLN B 301 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N SER B 303 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 581 " --> pdb=" O SER B 303 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY B 579 " --> pdb=" O PHE B 305 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 312 through 314 removed outlier: 6.461A pdb=" N VAL B 313 " --> pdb=" O ASN B 528 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER B 574 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR B 539 " --> pdb=" O ASP B 572 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 343 through 345 removed outlier: 3.583A pdb=" N TRP B 423 " --> pdb=" O ARG B 495 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 439 through 441 Processing sheet with id=AC7, first strand: chain 'B' and resid 640 through 646 removed outlier: 6.024A pdb=" N GLU B 640 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N THR B 678 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 9.434A pdb=" N VAL B 642 " --> pdb=" O THR B 678 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE B 656 " --> pdb=" O ILE B 652 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.629A pdb=" N GLN B1053 " --> pdb=" O THR B 698 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N PHE B 700 " --> pdb=" O PRO B1051 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE B 702 " --> pdb=" O TYR B1049 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N TYR B1049 " --> pdb=" O ILE B 702 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE B 704 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL B1047 " --> pdb=" O ILE B 704 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR B 706 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU B1045 " --> pdb=" O THR B 706 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 708 " --> pdb=" O VAL B1043 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL B1043 " --> pdb=" O VAL B 708 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLY B1041 " --> pdb=" O PRO B 710 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N GLY B1041 " --> pdb=" O ALA B1037 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ALA B1037 " --> pdb=" O GLY B1041 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL B1043 " --> pdb=" O PRO B1035 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU B1045 " --> pdb=" O SER B1033 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER B1033 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL B1047 " --> pdb=" O LEU B1031 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.629A pdb=" N GLN B1053 " --> pdb=" O THR B 698 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N PHE B 700 " --> pdb=" O PRO B1051 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE B 702 " --> pdb=" O TYR B1049 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N TYR B1049 " --> pdb=" O ILE B 702 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE B 704 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL B1047 " --> pdb=" O ILE B 704 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR B 706 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU B1045 " --> pdb=" O THR B 706 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 708 " --> pdb=" O VAL B1043 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL B1043 " --> pdb=" O VAL B 708 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLY B1041 " --> pdb=" O PRO B 710 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N THR B1058 " --> pdb=" O PHE B1079 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 716 through 718 Processing sheet with id=AD2, first strand: chain 'B' and resid 778 through 779 Processing sheet with id=AD3, first strand: chain 'B' and resid 821 through 822 removed outlier: 3.510A pdb=" N ALA B 834 " --> pdb=" O GLU B 821 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1102 through 1107 removed outlier: 4.914A pdb=" N VAL B1104 " --> pdb=" O PHE B1071 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N PHE B1071 " --> pdb=" O VAL B1104 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLY B1106 " --> pdb=" O ALA B1069 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS B1065 " --> pdb=" O LYS B1068 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR B1070 " --> pdb=" O ILE B1063 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE B1063 " --> pdb=" O TYR B1070 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 31 through 33 removed outlier: 4.086A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU C 194 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LYS C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N TYR C 200 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N THR C 215 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 52 through 59 removed outlier: 3.842A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 81 through 82 removed outlier: 12.018A pdb=" N LEU C 132 " --> pdb=" O PHE C 231 " (cutoff:3.500A) removed outlier: 12.654A pdb=" N ALA C 233 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N ASP C 134 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 10.240A pdb=" N LEU C 235 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ALA C 237 " --> pdb=" O PRO C 136 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N PHE C 138 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER C 239 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N VAL C 140 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ASN C 135 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE C 152 " --> pdb=" O ASN C 135 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N PHE C 137 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N THR C 150 " --> pdb=" O PHE C 137 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA C 139 " --> pdb=" O THR C 148 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.500A pdb=" N PHE C 161 " --> pdb=" O ALA C 127 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 615 through 616 removed outlier: 4.261A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASN C 304 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLY C 579 " --> pdb=" O ASN C 304 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLY C 580 " --> pdb=" O GLN C 599 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 640 through 646 removed outlier: 5.894A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N VAL C 642 " --> pdb=" O THR C 678 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 693 through 695 removed outlier: 4.638A pdb=" N THR C1058 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE C1077 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 699 through 710 removed outlier: 7.341A pdb=" N GLY C1041 " --> pdb=" O ALA C1037 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ALA C1037 " --> pdb=" O GLY C1041 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL C1043 " --> pdb=" O PRO C1035 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU C1045 " --> pdb=" O SER C1033 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER C1033 " --> pdb=" O LEU C1045 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL C1047 " --> pdb=" O LEU C1031 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 716 through 718 Processing sheet with id=AE5, first strand: chain 'C' and resid 821 through 822 Processing sheet with id=AE6, first strand: chain 'C' and resid 1102 through 1104 removed outlier: 3.598A pdb=" N TYR C1070 " --> pdb=" O ILE C1063 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE C1063 " --> pdb=" O TYR C1070 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AE8, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.457A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'D' and resid 347 through 352 removed outlier: 3.741A pdb=" N LEU D 351 " --> pdb=" O ASP D 355 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 1111 hydrogen bonds defined for protein. 3057 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: 11.85 Time building geometry restraints manager: 13.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8730 1.34 - 1.46: 7226 1.46 - 1.59: 12312 1.59 - 1.71: 3 1.71 - 1.83: 214 Bond restraints: 28485 Sorted by residual: bond pdb=" C GLN B1124 " pdb=" N PRO B1125 " ideal model delta sigma weight residual 1.337 1.390 -0.053 9.80e-03 1.04e+04 2.93e+01 bond pdb=" N PRO B 493 " pdb=" CD PRO B 493 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" C5 MAN I 4 " pdb=" O5 MAN I 4 " ideal model delta sigma weight residual 1.418 1.483 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C1 MAN U 4 " pdb=" C2 MAN U 4 " ideal model delta sigma weight residual 1.526 1.588 -0.062 2.00e-02 2.50e+03 9.54e+00 bond pdb=" C5 MAN e 4 " pdb=" O5 MAN e 4 " ideal model delta sigma weight residual 1.418 1.473 -0.055 2.00e-02 2.50e+03 7.55e+00 ... (remaining 28480 not shown) Histogram of bond angle deviations from ideal: 98.93 - 106.43: 852 106.43 - 113.94: 16692 113.94 - 121.45: 14098 121.45 - 128.96: 6939 128.96 - 136.47: 154 Bond angle restraints: 38735 Sorted by residual: angle pdb=" N SER D 502 " pdb=" CA SER D 502 " pdb=" C SER D 502 " ideal model delta sigma weight residual 111.82 100.82 11.00 1.16e+00 7.43e-01 8.99e+01 angle pdb=" N PHE D 504 " pdb=" CA PHE D 504 " pdb=" C PHE D 504 " ideal model delta sigma weight residual 112.38 119.63 -7.25 1.22e+00 6.72e-01 3.53e+01 angle pdb=" C VAL B1022 " pdb=" N ASP B1023 " pdb=" CA ASP B1023 " ideal model delta sigma weight residual 121.54 131.32 -9.78 1.91e+00 2.74e-01 2.62e+01 angle pdb=" C SER B 346 " pdb=" N ASN B 347 " pdb=" CA ASN B 347 " ideal model delta sigma weight residual 121.54 130.80 -9.26 1.91e+00 2.74e-01 2.35e+01 angle pdb=" N PRO A 968 " pdb=" CA PRO A 968 " pdb=" C PRO A 968 " ideal model delta sigma weight residual 110.70 116.49 -5.79 1.22e+00 6.72e-01 2.26e+01 ... (remaining 38730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.33: 16704 16.33 - 32.66: 613 32.66 - 48.99: 172 48.99 - 65.32: 32 65.32 - 81.64: 10 Dihedral angle restraints: 17531 sinusoidal: 7616 harmonic: 9915 Sorted by residual: dihedral pdb=" CA PHE C 83 " pdb=" C PHE C 83 " pdb=" N LYS C 84 " pdb=" CA LYS C 84 " ideal model delta harmonic sigma weight residual -180.00 -134.02 -45.98 0 5.00e+00 4.00e-02 8.45e+01 dihedral pdb=" CB CYS B 467 " pdb=" SG CYS B 467 " pdb=" SG CYS B 474 " pdb=" CB CYS B 474 " ideal model delta sinusoidal sigma weight residual -86.00 -167.64 81.64 1 1.00e+01 1.00e-02 8.20e+01 dihedral pdb=" CB CYS C1014 " pdb=" SG CYS C1014 " pdb=" SG CYS C1025 " pdb=" CB CYS C1025 " ideal model delta sinusoidal sigma weight residual 93.00 167.37 -74.37 1 1.00e+01 1.00e-02 7.01e+01 ... (remaining 17528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3811 0.073 - 0.146: 716 0.146 - 0.219: 63 0.219 - 0.293: 21 0.293 - 0.366: 13 Chirality restraints: 4624 Sorted by residual: chirality pdb=" C1 NAG Z 1 " pdb=" ND2 ASN C 691 " pdb=" C2 NAG Z 1 " pdb=" O5 NAG Z 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CB ILE C 955 " pdb=" CA ILE C 955 " pdb=" CG1 ILE C 955 " pdb=" CG2 ILE C 955 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.59 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 4621 not shown) Planarity restraints: 4914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 83 " 0.021 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C PHE C 83 " -0.071 2.00e-02 2.50e+03 pdb=" O PHE C 83 " 0.027 2.00e-02 2.50e+03 pdb=" N LYS C 84 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 83 " 0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C PHE A 83 " -0.069 2.00e-02 2.50e+03 pdb=" O PHE A 83 " 0.026 2.00e-02 2.50e+03 pdb=" N LYS A 84 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 83 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.38e+00 pdb=" C PHE B 83 " -0.050 2.00e-02 2.50e+03 pdb=" O PHE B 83 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS B 84 " 0.017 2.00e-02 2.50e+03 ... (remaining 4911 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 264 2.56 - 3.14: 21901 3.14 - 3.73: 42955 3.73 - 4.31: 59734 4.31 - 4.90: 95606 Nonbonded interactions: 220460 Sorted by model distance: nonbonded pdb=" OG1 THR B 425 " pdb=" O PRO B 493 " model vdw 1.972 2.440 nonbonded pdb=" O LEU A 966 " pdb=" OD1 ASP A 967 " model vdw 2.018 3.040 nonbonded pdb=" O ASP C 727 " pdb=" OD1 ASP C 727 " model vdw 2.033 3.040 nonbonded pdb=" O ASP D 499 " pdb=" OG SER D 502 " model vdw 2.084 2.440 nonbonded pdb=" O VAL B 354 " pdb=" OG SER B 358 " model vdw 2.237 2.440 ... (remaining 220455 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 18 through 318 or (resid 515 and (name N or name CA or nam \ e C or name O or name CB )) or resid 516 through 1129 or resid 1301 through 1308 \ )) selection = (chain 'C' and (resid 18 through 663 or resid 672 through 808 or resid 818 throu \ gh 1129 or resid 1309 through 1320)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'N' selection = chain 'R' selection = chain 'Y' selection = chain 'Z' selection = chain 'c' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'P' selection = chain 'S' selection = chain 'U' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'e' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.470 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: 11.480 Check model and map are aligned: 0.430 Set scattering table: 0.260 Process input model: 76.220 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.440 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 28485 Z= 0.430 Angle : 0.971 11.474 38735 Z= 0.501 Chirality : 0.059 0.366 4624 Planarity : 0.006 0.060 4881 Dihedral : 9.584 74.763 11021 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.02 % Favored : 92.93 % Rotamer: Outliers : 0.24 % Allowed : 1.69 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.98 (0.12), residues: 3364 helix: -3.00 (0.11), residues: 953 sheet: -1.76 (0.19), residues: 659 loop : -2.81 (0.12), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP D 163 HIS 0.016 0.002 HIS A1030 PHE 0.025 0.003 PHE A 805 TYR 0.030 0.003 TYR B 481 ARG 0.010 0.001 ARG A 996 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 230 time to evaluate : 2.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 237 average time/residue: 0.4549 time to fit residues: 163.0032 Evaluate side-chains 123 residues out of total 2958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 2.800 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2323 time to fit residues: 4.2665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 286 optimal weight: 20.0000 chunk 256 optimal weight: 0.7980 chunk 142 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 173 optimal weight: 3.9990 chunk 137 optimal weight: 30.0000 chunk 265 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 161 optimal weight: 0.6980 chunk 197 optimal weight: 20.0000 chunk 307 optimal weight: 7.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN A 135 ASN A 201 GLN A 599 GLN A 733 ASN A 907 ASN A 974 GLN A 984 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN B 135 ASN B 201 GLN B 330 ASN B 473 ASN B 549 GLN B 733 ASN B 759 ASN B 806 ASN B 835 GLN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 935 ASN B 987 GLN B1088 GLN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 HIS ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN C 135 ASN C 201 GLN C 301 GLN C 523 GLN C 599 GLN C 630 GLN C 877 GLN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 939 GLN ** C 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 GLN D 33 ASN D 64 ASN D 239 HIS D 345 HIS D 526 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 28485 Z= 0.271 Angle : 0.695 9.145 38735 Z= 0.363 Chirality : 0.044 0.254 4624 Planarity : 0.005 0.077 4881 Dihedral : 7.698 58.806 4894 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.03 % Allowed : 2.64 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: -2.81 (0.13), residues: 3364 helix: -1.11 (0.15), residues: 977 sheet: -1.47 (0.19), residues: 636 loop : -2.51 (0.13), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 163 HIS 0.007 0.001 HIS D 239 PHE 0.017 0.002 PHE A 805 TYR 0.020 0.002 TYR D 385 ARG 0.009 0.001 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 2.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 157 average time/residue: 0.4461 time to fit residues: 111.4706 Evaluate side-chains 115 residues out of total 2958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 3.456 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2484 time to fit residues: 4.9920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 171 optimal weight: 8.9990 chunk 95 optimal weight: 0.4980 chunk 256 optimal weight: 5.9990 chunk 209 optimal weight: 20.0000 chunk 84 optimal weight: 4.9990 chunk 308 optimal weight: 30.0000 chunk 333 optimal weight: 0.0570 chunk 274 optimal weight: 9.9990 chunk 305 optimal weight: 30.0000 chunk 105 optimal weight: 7.9990 chunk 247 optimal weight: 0.0070 overall best weight: 2.3120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN A 599 GLN A1088 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN B 201 GLN B 549 GLN B 835 GLN B 883 GLN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 ASN B1088 GLN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 HIS ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 ASN C 301 GLN C 523 GLN C 599 GLN C 630 GLN C 917 GLN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 GLN D 345 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28485 Z= 0.192 Angle : 0.613 11.459 38735 Z= 0.316 Chirality : 0.043 0.212 4624 Planarity : 0.004 0.078 4881 Dihedral : 6.979 58.428 4894 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.07 % Allowed : 2.33 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.13), residues: 3364 helix: -0.38 (0.16), residues: 992 sheet: -1.46 (0.19), residues: 647 loop : -2.33 (0.13), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 478 HIS 0.004 0.001 HIS A1030 PHE 0.019 0.001 PHE A 805 TYR 0.018 0.001 TYR B 252 ARG 0.016 0.000 ARG A 965 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 144 time to evaluate : 3.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 146 average time/residue: 0.3966 time to fit residues: 95.6457 Evaluate side-chains 109 residues out of total 2958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 3.193 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2503 time to fit residues: 4.6320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 304 optimal weight: 50.0000 chunk 231 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 207 optimal weight: 20.0000 chunk 309 optimal weight: 40.0000 chunk 327 optimal weight: 40.0000 chunk 161 optimal weight: 0.6980 chunk 293 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 overall best weight: 7.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 201 GLN A 987 GLN ** A1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 HIS ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 GLN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 GLN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 599 GLN ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 ASN ** C 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 947 GLN ** C 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 HIS D 394 ASN ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 28485 Z= 0.439 Angle : 0.828 11.096 38735 Z= 0.424 Chirality : 0.046 0.242 4624 Planarity : 0.005 0.061 4881 Dihedral : 7.326 58.917 4894 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 0.03 % Allowed : 3.42 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.13), residues: 3364 helix: -0.51 (0.15), residues: 1004 sheet: -1.36 (0.20), residues: 595 loop : -2.51 (0.13), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 619 HIS 0.011 0.002 HIS C 641 PHE 0.022 0.003 PHE A 782 TYR 0.026 0.003 TYR B 195 ARG 0.010 0.001 ARG A 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 3.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 123 average time/residue: 0.4204 time to fit residues: 85.0602 Evaluate side-chains 94 residues out of total 2958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 3.350 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 272 optimal weight: 0.9990 chunk 186 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 243 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 279 optimal weight: 6.9990 chunk 226 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 167 optimal weight: 10.0000 chunk 294 optimal weight: 20.0000 chunk 82 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN A 122 ASN A 201 GLN A 759 ASN A1088 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN B 381 ASN B 549 GLN B 835 GLN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1030 HIS B1088 GLN ** B1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 599 GLN ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 939 GLN ** C 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 GLN D 345 HIS ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28485 Z= 0.228 Angle : 0.635 11.562 38735 Z= 0.324 Chirality : 0.044 0.228 4624 Planarity : 0.004 0.049 4881 Dihedral : 6.825 58.970 4894 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.14), residues: 3364 helix: -0.06 (0.16), residues: 1001 sheet: -1.29 (0.20), residues: 614 loop : -2.37 (0.13), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 868 HIS 0.006 0.001 HIS C 641 PHE 0.026 0.002 PHE A 545 TYR 0.021 0.002 TYR D 217 ARG 0.006 0.000 ARG A 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 3.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.4213 time to fit residues: 90.5497 Evaluate side-chains 97 residues out of total 2958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 3.073 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 110 optimal weight: 8.9990 chunk 295 optimal weight: 40.0000 chunk 64 optimal weight: 6.9990 chunk 192 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 327 optimal weight: 40.0000 chunk 272 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 108 optimal weight: 20.0000 chunk 172 optimal weight: 9.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 ASN A 201 GLN A1088 GLN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN B 381 ASN B 546 GLN ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 883 GLN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 993 GLN B1088 GLN ** B1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 599 GLN ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 HIS ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 28485 Z= 0.308 Angle : 0.681 10.216 38735 Z= 0.347 Chirality : 0.043 0.212 4624 Planarity : 0.004 0.052 4881 Dihedral : 6.763 59.742 4894 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.14), residues: 3364 helix: 0.03 (0.16), residues: 986 sheet: -1.30 (0.20), residues: 615 loop : -2.39 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 868 HIS 0.008 0.001 HIS C1030 PHE 0.017 0.002 PHE A 545 TYR 0.019 0.002 TYR D 385 ARG 0.007 0.001 ARG A 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 2.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.4106 time to fit residues: 84.1585 Evaluate side-chains 97 residues out of total 2958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 2.934 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 316 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 186 optimal weight: 9.9990 chunk 239 optimal weight: 6.9990 chunk 185 optimal weight: 8.9990 chunk 276 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 326 optimal weight: 20.0000 chunk 204 optimal weight: 7.9990 chunk 199 optimal weight: 0.1980 chunk 150 optimal weight: 8.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN A 201 GLN A 993 GLN A1088 GLN B 201 GLN ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 838 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 GLN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 599 GLN ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 939 GLN ** C 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 HIS ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28485 Z= 0.241 Angle : 0.634 11.431 38735 Z= 0.324 Chirality : 0.043 0.201 4624 Planarity : 0.004 0.053 4881 Dihedral : 6.509 58.173 4894 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.25 % Favored : 92.72 % Rotamer: Outliers : 0.03 % Allowed : 1.76 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: -1.96 (0.14), residues: 3364 helix: 0.22 (0.16), residues: 989 sheet: -1.28 (0.20), residues: 620 loop : -2.27 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 271 HIS 0.006 0.001 HIS C 641 PHE 0.021 0.001 PHE B 262 TYR 0.014 0.001 TYR C 989 ARG 0.008 0.001 ARG C1001 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 3.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.4055 time to fit residues: 85.4502 Evaluate side-chains 98 residues out of total 2958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 2.859 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 202 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 195 optimal weight: 7.9990 chunk 98 optimal weight: 20.0000 chunk 64 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 207 optimal weight: 9.9990 chunk 222 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 256 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN A 201 GLN A 984 GLN A1088 GLN B 201 GLN ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 835 GLN B 838 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 GLN B1090 ASN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 939 GLN ** C 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 GLN D 345 HIS D 505 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28485 Z= 0.192 Angle : 0.596 9.534 38735 Z= 0.303 Chirality : 0.042 0.193 4624 Planarity : 0.004 0.081 4881 Dihedral : 6.178 59.438 4894 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.03 % Allowed : 0.85 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: -1.80 (0.14), residues: 3364 helix: 0.45 (0.17), residues: 984 sheet: -1.33 (0.20), residues: 637 loop : -2.18 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 271 HIS 0.005 0.001 HIS C 641 PHE 0.020 0.001 PHE B 262 TYR 0.013 0.001 TYR A 886 ARG 0.006 0.000 ARG A 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 3.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.4265 time to fit residues: 95.2391 Evaluate side-chains 97 residues out of total 2958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 3.260 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 297 optimal weight: 20.0000 chunk 313 optimal weight: 1.9990 chunk 285 optimal weight: 8.9990 chunk 304 optimal weight: 8.9990 chunk 312 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 275 optimal weight: 7.9990 chunk 287 optimal weight: 20.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN A 201 GLN A1088 GLN B 201 GLN ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 835 GLN B 838 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 GLN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 939 GLN ** C 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 GLN D 345 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28485 Z= 0.195 Angle : 0.593 11.115 38735 Z= 0.300 Chirality : 0.042 0.192 4624 Planarity : 0.004 0.046 4881 Dihedral : 5.928 55.316 4894 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.03 % Allowed : 0.74 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: -1.70 (0.14), residues: 3364 helix: 0.54 (0.17), residues: 988 sheet: -1.35 (0.19), residues: 665 loop : -2.09 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 271 HIS 0.006 0.001 HIS B 149 PHE 0.020 0.001 PHE B 262 TYR 0.013 0.001 TYR C 989 ARG 0.005 0.000 ARG A 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 3.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.3778 time to fit residues: 82.7248 Evaluate side-chains 95 residues out of total 2958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 3.142 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 303 optimal weight: 9.9990 chunk 199 optimal weight: 10.0000 chunk 321 optimal weight: 30.0000 chunk 196 optimal weight: 30.0000 chunk 152 optimal weight: 9.9990 chunk 223 optimal weight: 9.9990 chunk 337 optimal weight: 30.0000 chunk 310 optimal weight: 30.0000 chunk 268 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 ASN A 201 GLN A 984 GLN ** A1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN B 437 ASN B 479 ASN ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 611 HIS ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 838 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 993 GLN B1088 GLN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 599 GLN ** C 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 28485 Z= 0.432 Angle : 0.801 10.393 38735 Z= 0.408 Chirality : 0.046 0.220 4624 Planarity : 0.005 0.054 4881 Dihedral : 6.697 53.488 4894 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 22.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 0.07 % Allowed : 0.41 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.14), residues: 3364 helix: 0.02 (0.16), residues: 999 sheet: -1.32 (0.21), residues: 581 loop : -2.32 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 271 HIS 0.011 0.002 HIS C 641 PHE 0.021 0.002 PHE C 545 TYR 0.025 0.002 TYR B 738 ARG 0.014 0.001 ARG A 965 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 3.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 112 average time/residue: 0.4125 time to fit residues: 80.3526 Evaluate side-chains 88 residues out of total 2958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 3.404 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 164 optimal weight: 0.9990 chunk 213 optimal weight: 0.9990 chunk 286 optimal weight: 20.0000 chunk 82 optimal weight: 0.3980 chunk 247 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 269 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 276 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN A 122 ASN A 201 GLN A1088 GLN B 201 GLN ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 835 GLN B 877 GLN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN B1088 GLN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN C 301 GLN C 523 GLN C 599 GLN C 917 GLN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 939 GLN ** C 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 993 GLN C1088 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.051187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.034339 restraints weight = 271954.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.035294 restraints weight = 169008.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.035824 restraints weight = 122614.430| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28485 Z= 0.167 Angle : 0.609 10.928 38735 Z= 0.305 Chirality : 0.043 0.183 4624 Planarity : 0.004 0.051 4881 Dihedral : 5.983 49.685 4894 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: -1.65 (0.14), residues: 3364 helix: 0.59 (0.17), residues: 986 sheet: -1.22 (0.20), residues: 635 loop : -2.10 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 868 HIS 0.005 0.001 HIS C 641 PHE 0.022 0.001 PHE B 262 TYR 0.015 0.001 TYR B 442 ARG 0.008 0.001 ARG A 965 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4200.39 seconds wall clock time: 79 minutes 35.81 seconds (4775.81 seconds total)