Starting phenix.real_space_refine on Wed Sep 25 11:36:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyb_27073/09_2024/8cyb_27073.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyb_27073/09_2024/8cyb_27073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyb_27073/09_2024/8cyb_27073.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyb_27073/09_2024/8cyb_27073.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyb_27073/09_2024/8cyb_27073.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyb_27073/09_2024/8cyb_27073.cif" } resolution = 2.7 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= 0.001 sd= 0.037 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: 5 Type Number sf(0) Gaussians S 121 5.16 5 C 17866 2.51 5 N 4555 2.21 5 O 5687 1.98 5 H 25897 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 54126 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 16912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1102, 16912 Classifications: {'peptide': 1102} Link IDs: {'CIS': 2, 'PTRANS': 55, 'TRANS': 1044} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 16923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1102, 16923 Classifications: {'peptide': 1102} Link IDs: {'CIS': 2, 'PTRANS': 55, 'TRANS': 1044} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 16900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1102, 16900 Classifications: {'peptide': 1102} Link IDs: {'CIS': 2, 'PTRANS': 55, 'TRANS': 1044} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1913 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 70 Unusual residues: {'BMA': 1, 'FUC': 2, 'GAL': 1, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "W" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "X" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 165 Unusual residues: {'AH2': 1, 'NAG': 11} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 19.00, per 1000 atoms: 0.35 Number of scatterers: 54126 At special positions: 0 Unit cell: (164.796, 159.48, 195.363, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 121 16.00 O 5687 8.00 N 4555 7.00 C 17866 6.00 H 25897 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 38 " - pdb=" SG CYS D 112 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA J 3 " - " MAN J 4 " " BMA M 3 " - " MAN M 4 " " BMA O 3 " - " MAN O 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " " BMA J 3 " - " MAN J 5 " " BMA M 3 " - " MAN M 5 " " BMA O 3 " - " MAN O 5 " " BMA V 3 " - " MAN V 5 " BETA1-2 " GAL I 3 " - " FUC I 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... BETA1-3 " NAG N 1 " - " FUC N 4 " " NAG X 1 " - " FUC X 2 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 5 " " FUC I 2 " - " GAL I 3 " " NAG I 5 " - " BMA I 6 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " 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 N 2 " - " BMA N 3 " " 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 R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " 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 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " BETA1-6 " NAG I 1 " - " FUC I 2 " NAG-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 122 " " NAG A1304 " - " ASN A 149 " " NAG A1305 " - " ASN A 165 " " NAG A1306 " - " ASN A 234 " " NAG A1307 " - " ASN A 282 " " NAG A1308 " - " ASN A 343 " " NAG A1309 " - " ASN A 603 " " NAG A1310 " - " ASN A 616 " " NAG A1311 " - " ASN A 657 " " NAG B1301 " - " ASN B 657 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 234 " " NAG B1307 " - " ASN B 165 " " NAG B1308 " - " ASN B 149 " " NAG B1309 " - " ASN B 122 " " NAG B1310 " - " ASN B 61 " " NAG B1311 " - " ASN B 17 " " NAG C1301 " - " ASN C 17 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 149 " " NAG C1305 " - " ASN C 165 " " NAG C1306 " - " ASN C 234 " " NAG C1307 " - " ASN C 282 " " NAG C1308 " - " ASN C 343 " " NAG C1309 " - " ASN C 603 " " NAG C1310 " - " ASN C 657 " " NAG E 1 " - " ASN A 331 " " NAG F 1 " - " ASN A 709 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN B1074 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 709 " " NAG R 1 " - " ASN B 331 " " NAG S 1 " - " ASN C 331 " " NAG T 1 " - " ASN C 616 " " NAG U 1 " - " ASN C 709 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 801 " " NAG X 1 " - " ASN C1074 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " Time building additional restraints: 11.81 Conformation dependent library (CDL) restraints added in 3.6 seconds 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6412 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 51 sheets defined 25.3% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.89 Creating SS restraints... Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 293 through 304 removed outlier: 4.080A pdb=" N SER A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 371 removed outlier: 4.216A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.933A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.187A pdb=" N GLN A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 619 through 623 Processing helix chain 'A' and resid 629 through 633 removed outlier: 3.734A pdb=" N TRP A 633 " --> pdb=" O THR A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.795A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.502A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 854 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.189A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.048A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 200 removed outlier: 4.166A pdb=" N GLY B 199 " --> pdb=" O ASN B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.773A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 4.094A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 390 removed outlier: 4.535A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 632 through 638 removed outlier: 3.549A pdb=" N THR B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.728A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.075A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 941 removed outlier: 6.149A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.321A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.590A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 200 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.571A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.922A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 removed outlier: 4.435A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.990A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 542 through 546 Processing helix chain 'C' and resid 616 through 623 removed outlier: 3.777A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Proline residue: C 621 - end of helix Processing helix chain 'C' and resid 629 through 638 removed outlier: 3.952A pdb=" N ARG C 634 " --> pdb=" O THR C 630 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.520A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.926A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.843A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.346A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.872A pdb=" N ASP C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 48 removed outlier: 3.524A pdb=" N ASN D 47 " --> pdb=" O THR D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 107 removed outlier: 3.764A pdb=" N THR D 107 " --> pdb=" O ALA D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 128 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.663A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE A 68 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG A 78 " --> pdb=" O ILE A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.663A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 212 " --> pdb=" O PHE A 186 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASN A 188 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE A 210 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ARG A 190 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N THR A 208 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N PHE A 192 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LYS A 206 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N PHE A 194 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N TYR A 204 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.929A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 171 removed outlier: 6.265A pdb=" N TRP A 152 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N HIS A 146 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 10.785A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 10.247A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 245 through 246 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 317 removed outlier: 6.824A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 326 through 328 removed outlier: 3.752A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.145A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.741A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 712 through 715 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.038A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.406A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.608A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE B 68 " --> pdb=" O ARG B 78 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG B 78 " --> pdb=" O ILE B 68 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.608A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 212 " --> pdb=" O PHE B 186 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASN B 188 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ILE B 210 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ARG B 190 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR B 208 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N PHE B 192 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LYS B 206 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N PHE B 194 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N TYR B 204 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.964A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 151 through 160 removed outlier: 6.582A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 13.123A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.746A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 10.062A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 143 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N TYR B 145 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 151 through 160 removed outlier: 6.582A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 13.123A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.746A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 10.062A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 143 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N TYR B 145 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 318 removed outlier: 5.489A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 538 through 543 removed outlier: 4.605A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.129A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.964A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.762A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.926A pdb=" N ILE C 68 " --> pdb=" O ARG C 78 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG C 78 " --> pdb=" O ILE C 68 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.748A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ASN C 188 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE C 210 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ARG C 190 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N THR C 208 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N PHE C 192 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LYS C 206 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N PHE C 194 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N TYR C 204 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.928A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 153 through 171 removed outlier: 5.216A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE C 140 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 10.581A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 9.939A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 8.884A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 245 through 246 Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 317 removed outlier: 7.030A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 539 through 541 removed outlier: 3.811A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.100A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.921A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AF3, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.613A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF5, first strand: chain 'D' and resid 19 through 23 Processing sheet with id=AF6, first strand: chain 'D' and resid 27 through 29 removed outlier: 6.894A pdb=" N MET D 50 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N SER D 66 " --> pdb=" O MET D 50 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP D 52 " --> pdb=" O VAL D 64 " (cutoff:3.500A) 1078 hydrogen bonds defined for protein. 2901 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 23.03 Time building geometry restraints manager: 14.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 25888 1.03 - 1.23: 95 1.23 - 1.42: 12197 1.42 - 1.62: 16423 1.62 - 1.82: 153 Bond restraints: 54756 Sorted by residual: bond pdb=" C1 MAN M 4 " pdb=" C2 MAN M 4 " ideal model delta sigma weight residual 1.526 1.611 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C1 MAN M 4 " pdb=" O5 MAN M 4 " ideal model delta sigma weight residual 1.399 1.480 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" C1 MAN H 4 " pdb=" C2 MAN H 4 " ideal model delta sigma weight residual 1.526 1.592 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" C1 BMA Z 3 " pdb=" C2 BMA Z 3 " ideal model delta sigma weight residual 1.519 1.579 -0.060 2.00e-02 2.50e+03 9.10e+00 bond pdb=" C1 BMA I 6 " pdb=" C2 BMA I 6 " ideal model delta sigma weight residual 1.519 1.578 -0.059 2.00e-02 2.50e+03 8.65e+00 ... (remaining 54751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.34: 97868 7.34 - 14.68: 2 14.68 - 22.02: 1 22.02 - 29.36: 3 29.36 - 36.69: 17 Bond angle restraints: 97891 Sorted by residual: angle pdb=" C ASP A 253 " pdb=" CA ASP A 253 " pdb=" HA ASP A 253 " ideal model delta sigma weight residual 109.00 72.31 36.69 3.00e+00 1.11e-01 1.50e+02 angle pdb=" C ASP B 253 " pdb=" CA ASP B 253 " pdb=" HA ASP B 253 " ideal model delta sigma weight residual 109.00 72.32 36.68 3.00e+00 1.11e-01 1.49e+02 angle pdb=" C ASP C 253 " pdb=" CA ASP C 253 " pdb=" HA ASP C 253 " ideal model delta sigma weight residual 109.00 72.69 36.31 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C ALA B 292 " pdb=" CA ALA B 292 " pdb=" HA ALA B 292 " ideal model delta sigma weight residual 109.00 73.28 35.72 3.00e+00 1.11e-01 1.42e+02 angle pdb=" C ALA A 292 " pdb=" CA ALA A 292 " pdb=" HA ALA A 292 " ideal model delta sigma weight residual 109.00 73.93 35.07 3.00e+00 1.11e-01 1.37e+02 ... (remaining 97886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.21: 26145 24.21 - 48.42: 1161 48.42 - 72.63: 333 72.63 - 96.84: 164 96.84 - 121.05: 114 Dihedral angle restraints: 27917 sinusoidal: 15922 harmonic: 11995 Sorted by residual: dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 155.59 -62.59 1 1.00e+01 1.00e-02 5.18e+01 dihedral pdb=" CA ASN C 149 " pdb=" C ASN C 149 " pdb=" N LYS C 150 " pdb=" CA LYS C 150 " ideal model delta harmonic sigma weight residual 180.00 148.20 31.80 0 5.00e+00 4.00e-02 4.05e+01 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual 93.00 131.19 -38.19 1 1.00e+01 1.00e-02 2.05e+01 ... (remaining 27914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 4217 0.079 - 0.157: 533 0.157 - 0.236: 8 0.236 - 0.314: 17 0.314 - 0.393: 5 Chirality restraints: 4780 Sorted by residual: chirality pdb=" CA ALA A 292 " pdb=" N ALA A 292 " pdb=" C ALA A 292 " pdb=" CB ALA A 292 " both_signs ideal model delta sigma weight residual False 2.48 2.09 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CA ALA B 292 " pdb=" N ALA B 292 " pdb=" C ALA B 292 " pdb=" CB ALA B 292 " both_signs ideal model delta sigma weight residual False 2.48 2.10 0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" CA ASP C 253 " pdb=" N ASP C 253 " pdb=" C ASP C 253 " pdb=" CB ASP C 253 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.47e+00 ... (remaining 4777 not shown) Planarity restraints: 8233 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 38 " -0.044 5.00e-02 4.00e+02 6.63e-02 7.02e+00 pdb=" N PRO B 39 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 84 " -0.040 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO C 85 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 85 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 85 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 630 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO B 631 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 631 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 631 " -0.028 5.00e-02 4.00e+02 ... (remaining 8230 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 2434 2.18 - 2.79: 105860 2.79 - 3.39: 145480 3.39 - 4.00: 194095 4.00 - 4.60: 296328 Nonbonded interactions: 744197 Sorted by model distance: nonbonded pdb=" HE ARG B 457 " pdb=" OD2 ASP B 467 " model vdw 1.575 2.450 nonbonded pdb=" O VAL C 36 " pdb=" H LEU C 223 " model vdw 1.585 2.450 nonbonded pdb=" O ASN C 334 " pdb=" H VAL C 362 " model vdw 1.597 2.450 nonbonded pdb=" H ALA A 292 " pdb=" HA ALA A 292 " model vdw 1.599 1.816 nonbonded pdb=" O VAL B 327 " pdb="HD22 ASN B 532 " model vdw 1.601 2.450 ... (remaining 744192 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 199 or (resid 200 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH or name H or name HA or name HB2 or name HB3 or name H \ D1 or name HD2 or name HE1 or name HE2)) or resid 201 through 230 or (resid 231 \ and (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or \ name CD1 or name HA or name HB or name HG12 or name HG13 or name HG21 or name H \ G22 or name HG23 or name HD11 or name HD12 or name HD13)) or resid 232 through 3 \ 56 or (resid 357 and (name N or name CA or name C or name O or name CB or name C \ G or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE or name HH11 or name HH12 or name HH21)) or resid 358 through 527 or (resid 5 \ 28 through 529 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name CE or name NZ or name H or name HA )) or resid 530 or (resid \ 531 and (name N or name CA or name C or name O or name H or name HA )) or resid \ 532 through 562 or (resid 563 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name \ HB3 or name HG2 or name HG3 or name HE21 or name HE22)) or resid 564 through 11 \ 47 or resid 1301 through 1310)) selection = (chain 'B' and (resid 13 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ or name H or \ name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 \ or name HE2 or name HE3)) or resid 42 through 168 or (resid 169 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ OE2 or name HA or name HB2 or name HB3 or name HG2 or name HG3)) or resid 170 th \ rough 230 or (resid 231 and (name N or name CA or name C or name O or name CB or \ name CG1 or name CG2 or name CD1 or name HA or name HB or name HG12 or name HG1 \ 3 or name HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name HD13) \ ) or resid 232 through 290 or (resid 291 and (name N or name CA or name C or nam \ e O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resi \ d 292 through 300 or (resid 301 and (name N or name CA or name C or name O or na \ me CB or name SG or name H or name HA or name HB2 or name HB3)) or resid 302 thr \ ough 320 or (resid 321 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 322 through 527 or (resid 528 through 529 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD or name CE o \ r name NZ or name H or name HA )) or resid 530 or (resid 531 and (name N or name \ CA or name C or name O or name H or name HA )) or resid 532 through 1147 or res \ id 1301 through 1310)) selection = (chain 'C' and (resid 13 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ or name H or \ name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 \ or name HE2 or name HE3)) or resid 42 through 168 or (resid 169 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ OE2 or name HA or name HB2 or name HB3 or name HG2 or name HG3)) or resid 170 th \ rough 199 or (resid 200 and (name N or name CA or name C or name O or name CB or \ name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH o \ r name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 \ or name HE2)) or resid 201 through 290 or (resid 291 and (name N or name CA or n \ ame C or name O or name CB or name SG or name H or name HA or name HB2 or name H \ B3)) or resid 292 through 300 or (resid 301 and (name N or name CA or name C or \ name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or r \ esid 302 through 320 or (resid 321 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 322 through 356 or (resid 357 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD or name NE o \ r name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 o \ r name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name H \ H12 or name HH21)) or resid 358 through 537 or (resid 538 and (name N or name CA \ or name C or name O or name CB or name SG or name H or name HA or name HB2 or n \ ame HB3)) or resid 539 through 562 or (resid 563 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HE21 or name HE22)) or r \ esid 564 through 589 or (resid 590 and (name N or name CA or name C or name O or \ name CB or name SG or name H or name HA or name HB2 or name HB3)) or resid 591 \ through 1063 or (resid 1064 and (name N or name CA or name C or name O or name C \ B or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name H \ A or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 1065 th \ rough 1147 or resid 1301 through 1310)) } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'M' selection = chain 'O' selection = chain 'V' } ncs_group { reference = (chain 'L' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'Z' and resid 1) } ncs_group { reference = (chain 'N' and resid 1 through 3) selection = (chain 'W' and resid 1 through 3) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.450 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: 0.690 Extract box with map and model: 1.450 Check model and map are aligned: 0.300 Set scattering table: 0.370 Process input model: 94.030 Find NCS groups from input model: 2.400 Set up NCS constraints: 0.270 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: 0.020 Load rotamer database and sin/cos tables:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 28859 Z= 0.241 Angle : 0.616 7.616 39296 Z= 0.272 Chirality : 0.049 0.393 4780 Planarity : 0.003 0.066 4926 Dihedral : 19.332 121.046 12071 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.04 % Favored : 94.70 % Rotamer: Outliers : 0.20 % Allowed : 0.37 % Favored : 99.43 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.15), residues: 3412 helix: 2.50 (0.22), residues: 674 sheet: 0.29 (0.18), residues: 751 loop : -1.21 (0.14), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 152 HIS 0.002 0.000 HIS C 207 PHE 0.012 0.001 PHE C 541 TYR 0.010 0.001 TYR C 265 ARG 0.001 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 200 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue THR 531 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 172 time to evaluate : 3.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8460 (tp-100) outliers start: 6 outliers final: 7 residues processed: 178 average time/residue: 1.7713 time to fit residues: 391.7382 Evaluate side-chains 124 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 3.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 754 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 288 optimal weight: 0.8980 chunk 259 optimal weight: 20.0000 chunk 143 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 chunk 174 optimal weight: 0.7980 chunk 138 optimal weight: 0.7980 chunk 268 optimal weight: 20.0000 chunk 103 optimal weight: 0.9980 chunk 162 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 310 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 239 GLN ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28859 Z= 0.192 Angle : 0.566 8.816 39296 Z= 0.272 Chirality : 0.048 0.393 4780 Planarity : 0.004 0.064 4926 Dihedral : 15.740 124.286 6021 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.28 % Favored : 94.46 % Rotamer: Outliers : 0.37 % Allowed : 4.17 % Favored : 95.46 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.15), residues: 3412 helix: 2.55 (0.21), residues: 681 sheet: 0.16 (0.18), residues: 784 loop : -1.34 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 64 HIS 0.003 0.001 HIS A1064 PHE 0.020 0.001 PHE C 318 TYR 0.011 0.001 TYR C1067 ARG 0.004 0.000 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 200 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue THR 531 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 3.050 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: A 52 GLN cc_start: 0.8774 (tm-30) cc_final: 0.8570 (tp40) outliers start: 11 outliers final: 8 residues processed: 138 average time/residue: 1.8590 time to fit residues: 321.4566 Evaluate side-chains 120 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 754 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 172 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 258 optimal weight: 10.0000 chunk 211 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 311 optimal weight: 1.9990 chunk 336 optimal weight: 40.0000 chunk 277 optimal weight: 0.0870 chunk 308 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 249 optimal weight: 2.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 935 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28859 Z= 0.223 Angle : 0.537 8.134 39296 Z= 0.262 Chirality : 0.047 0.402 4780 Planarity : 0.004 0.052 4926 Dihedral : 12.296 122.565 6019 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.04 % Favored : 94.70 % Rotamer: Outliers : 0.54 % Allowed : 5.44 % Favored : 94.02 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3412 helix: 2.53 (0.21), residues: 676 sheet: 0.16 (0.18), residues: 804 loop : -1.35 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 64 HIS 0.004 0.001 HIS C1064 PHE 0.020 0.001 PHE C 392 TYR 0.015 0.001 TYR C1067 ARG 0.003 0.000 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 200 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue THR 531 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 3.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8819 (tm-30) cc_final: 0.8584 (tp40) REVERT: C 950 ASP cc_start: 0.8325 (m-30) cc_final: 0.8067 (m-30) outliers start: 16 outliers final: 11 residues processed: 131 average time/residue: 1.8223 time to fit residues: 300.4495 Evaluate side-chains 121 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 3.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 858 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 307 optimal weight: 0.9980 chunk 233 optimal weight: 20.0000 chunk 161 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 148 optimal weight: 40.0000 chunk 208 optimal weight: 0.9980 chunk 312 optimal weight: 2.9990 chunk 330 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 295 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 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 66 HIS B 49 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 804 GLN ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 28859 Z= 0.365 Angle : 0.585 11.507 39296 Z= 0.293 Chirality : 0.048 0.436 4780 Planarity : 0.004 0.055 4926 Dihedral : 10.999 124.841 6019 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.15 % Favored : 93.55 % Rotamer: Outliers : 0.87 % Allowed : 5.91 % Favored : 93.21 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.14), residues: 3412 helix: 2.10 (0.20), residues: 676 sheet: 0.01 (0.18), residues: 809 loop : -1.51 (0.13), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 64 HIS 0.008 0.001 HIS C1064 PHE 0.019 0.001 PHE C 541 TYR 0.016 0.001 TYR C1067 ARG 0.005 0.000 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 200 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue THR 531 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 133 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 107 time to evaluate : 3.002 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: A 52 GLN cc_start: 0.8906 (tm-30) cc_final: 0.8663 (tp40) REVERT: B 226 LEU cc_start: 0.7864 (mm) cc_final: 0.7650 (mm) outliers start: 26 outliers final: 19 residues processed: 127 average time/residue: 1.7289 time to fit residues: 275.9631 Evaluate side-chains 113 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 94 time to evaluate : 2.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1075 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 275 optimal weight: 3.9990 chunk 187 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 282 optimal weight: 10.0000 chunk 228 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 168 optimal weight: 0.9990 chunk 296 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 ASN ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28859 Z= 0.205 Angle : 0.527 7.964 39296 Z= 0.262 Chirality : 0.046 0.449 4780 Planarity : 0.004 0.054 4926 Dihedral : 10.394 122.833 6017 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.16 % Favored : 94.55 % Rotamer: Outliers : 0.71 % Allowed : 6.82 % Favored : 92.47 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.14), residues: 3412 helix: 2.32 (0.21), residues: 669 sheet: 0.10 (0.18), residues: 795 loop : -1.45 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 64 HIS 0.021 0.001 HIS A 66 PHE 0.014 0.001 PHE C 541 TYR 0.013 0.001 TYR C1067 ARG 0.003 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 200 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue THR 531 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 3.482 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: A 52 GLN cc_start: 0.8882 (tm-30) cc_final: 0.8646 (tp40) REVERT: B 661 GLU cc_start: 0.7997 (pp20) cc_final: 0.7647 (pp20) outliers start: 21 outliers final: 14 residues processed: 117 average time/residue: 1.8839 time to fit residues: 275.5008 Evaluate side-chains 106 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 603 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 111 optimal weight: 0.9980 chunk 297 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 330 optimal weight: 20.0000 chunk 274 optimal weight: 3.9990 chunk 153 optimal weight: 40.0000 chunk 27 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28859 Z= 0.277 Angle : 0.536 7.892 39296 Z= 0.268 Chirality : 0.047 0.462 4780 Planarity : 0.004 0.054 4926 Dihedral : 9.931 122.935 6017 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.86 % Favored : 93.87 % Rotamer: Outliers : 0.64 % Allowed : 7.19 % Favored : 92.17 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3412 helix: 2.25 (0.20), residues: 673 sheet: 0.09 (0.18), residues: 793 loop : -1.51 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 64 HIS 0.005 0.001 HIS C1064 PHE 0.014 0.001 PHE C 201 TYR 0.014 0.001 TYR C1067 ARG 0.009 0.000 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 200 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue THR 531 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 94 time to evaluate : 3.049 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: A 52 GLN cc_start: 0.8899 (tm-30) cc_final: 0.8657 (tp40) REVERT: B 661 GLU cc_start: 0.8008 (pp20) cc_final: 0.7659 (pp20) REVERT: C 177 MET cc_start: 0.4118 (mpt) cc_final: 0.2920 (pmm) outliers start: 19 outliers final: 18 residues processed: 112 average time/residue: 1.9126 time to fit residues: 274.9381 Evaluate side-chains 108 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 3.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 858 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 319 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 chunk 241 optimal weight: 3.9990 chunk 187 optimal weight: 0.2980 chunk 278 optimal weight: 0.3980 chunk 184 optimal weight: 1.9990 chunk 329 optimal weight: 2.9990 chunk 206 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 804 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 28859 Z= 0.168 Angle : 0.512 7.874 39296 Z= 0.255 Chirality : 0.046 0.471 4780 Planarity : 0.004 0.054 4926 Dihedral : 9.671 122.558 6017 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.30 % Favored : 94.46 % Rotamer: Outliers : 0.67 % Allowed : 7.19 % Favored : 92.14 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3412 helix: 2.40 (0.21), residues: 667 sheet: 0.12 (0.18), residues: 806 loop : -1.47 (0.14), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.003 0.001 HIS C1064 PHE 0.013 0.001 PHE C 541 TYR 0.014 0.001 TYR C 200 ARG 0.002 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 200 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue THR 531 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 3.041 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: A 52 GLN cc_start: 0.8891 (tm-30) cc_final: 0.8649 (tp40) REVERT: D 50 MET cc_start: 0.2399 (tpp) cc_final: 0.1665 (tpt) outliers start: 20 outliers final: 16 residues processed: 112 average time/residue: 1.7534 time to fit residues: 247.8787 Evaluate side-chains 109 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 3.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 603 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 203 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 196 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 209 optimal weight: 1.9990 chunk 224 optimal weight: 0.7980 chunk 162 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 259 optimal weight: 20.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN C1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 28859 Z= 0.278 Angle : 0.538 7.833 39296 Z= 0.269 Chirality : 0.046 0.486 4780 Planarity : 0.004 0.050 4926 Dihedral : 9.389 122.544 6017 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.01 % Favored : 93.76 % Rotamer: Outliers : 0.74 % Allowed : 7.33 % Favored : 91.94 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3412 helix: 2.31 (0.21), residues: 673 sheet: 0.02 (0.18), residues: 799 loop : -1.49 (0.14), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 886 HIS 0.005 0.001 HIS C1064 PHE 0.014 0.001 PHE C 855 TYR 0.014 0.001 TYR C1067 ARG 0.003 0.000 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 200 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue THR 531 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 3.063 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: A 52 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8660 (tp40) REVERT: B 661 GLU cc_start: 0.8152 (pm20) cc_final: 0.7929 (pp20) REVERT: C 177 MET cc_start: 0.4041 (mpt) cc_final: 0.2791 (pmm) REVERT: C 198 ASP cc_start: 0.7590 (p0) cc_final: 0.7219 (p0) outliers start: 22 outliers final: 21 residues processed: 112 average time/residue: 1.8091 time to fit residues: 255.4753 Evaluate side-chains 112 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 91 time to evaluate : 3.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 858 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 299 optimal weight: 0.8980 chunk 315 optimal weight: 1.9990 chunk 288 optimal weight: 1.9990 chunk 307 optimal weight: 0.9980 chunk 184 optimal weight: 1.9990 chunk 133 optimal weight: 8.9990 chunk 241 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 277 optimal weight: 0.5980 chunk 290 optimal weight: 0.9980 chunk 306 optimal weight: 0.0980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 28859 Z= 0.166 Angle : 0.512 7.715 39296 Z= 0.255 Chirality : 0.046 0.496 4780 Planarity : 0.003 0.049 4926 Dihedral : 9.020 122.272 6013 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.25 % Favored : 94.52 % Rotamer: Outliers : 0.67 % Allowed : 7.46 % Favored : 91.87 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 3412 helix: 2.39 (0.21), residues: 673 sheet: 0.12 (0.18), residues: 772 loop : -1.42 (0.14), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 64 HIS 0.004 0.001 HIS A 66 PHE 0.012 0.001 PHE C 541 TYR 0.017 0.001 TYR C 200 ARG 0.002 0.000 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 200 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue THR 531 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 3.017 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: A 52 GLN cc_start: 0.8868 (tm-30) cc_final: 0.8624 (tp40) REVERT: C 177 MET cc_start: 0.3985 (mpt) cc_final: 0.2756 (pmm) REVERT: C 198 ASP cc_start: 0.7629 (p0) cc_final: 0.7245 (p0) outliers start: 20 outliers final: 20 residues processed: 117 average time/residue: 1.7561 time to fit residues: 258.1763 Evaluate side-chains 111 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 91 time to evaluate : 2.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 754 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 201 optimal weight: 1.9990 chunk 324 optimal weight: 1.9990 chunk 198 optimal weight: 0.9980 chunk 154 optimal weight: 9.9990 chunk 225 optimal weight: 3.9990 chunk 340 optimal weight: 30.0000 chunk 313 optimal weight: 0.7980 chunk 271 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 209 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1002 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28859 Z= 0.215 Angle : 0.520 7.620 39296 Z= 0.259 Chirality : 0.046 0.507 4780 Planarity : 0.004 0.049 4926 Dihedral : 8.706 121.982 6013 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.66 % Favored : 94.11 % Rotamer: Outliers : 0.64 % Allowed : 7.53 % Favored : 91.83 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 3412 helix: 2.46 (0.21), residues: 668 sheet: 0.12 (0.18), residues: 778 loop : -1.44 (0.14), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 886 HIS 0.003 0.001 HIS C1064 PHE 0.029 0.001 PHE C 855 TYR 0.013 0.001 TYR C1067 ARG 0.003 0.000 ARG B 634 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 200 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue THR 531 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 94 time to evaluate : 3.060 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: A 52 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8633 (tp40) REVERT: C 177 MET cc_start: 0.3985 (mpt) cc_final: 0.2763 (pmm) REVERT: C 198 ASP cc_start: 0.7677 (p0) cc_final: 0.7280 (p0) REVERT: D 50 MET cc_start: 0.2501 (tpp) cc_final: 0.1715 (tpt) outliers start: 19 outliers final: 19 residues processed: 111 average time/residue: 1.7539 time to fit residues: 248.4846 Evaluate side-chains 110 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 3.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 754 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 215 optimal weight: 1.9990 chunk 289 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 250 optimal weight: 1.9990 chunk 40 optimal weight: 30.0000 chunk 75 optimal weight: 1.9990 chunk 271 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 279 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.150158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.084077 restraints weight = 170080.078| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.61 r_work: 0.2970 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28859 Z= 0.287 Angle : 0.538 8.907 39296 Z= 0.271 Chirality : 0.046 0.521 4780 Planarity : 0.004 0.049 4926 Dihedral : 8.594 122.048 6013 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.66 % Favored : 94.11 % Rotamer: Outliers : 0.71 % Allowed : 7.43 % Favored : 91.87 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.14), residues: 3412 helix: 2.34 (0.21), residues: 674 sheet: 0.05 (0.18), residues: 787 loop : -1.49 (0.13), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 886 HIS 0.005 0.001 HIS C1064 PHE 0.014 0.001 PHE C 823 TYR 0.019 0.001 TYR C 200 ARG 0.003 0.000 ARG C1039 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11057.83 seconds wall clock time: 189 minutes 46.87 seconds (11386.87 seconds total)