Starting phenix.real_space_refine on Sat Apr 13 04:54:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymx_33946/04_2024/7ymx_33946.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymx_33946/04_2024/7ymx_33946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymx_33946/04_2024/7ymx_33946.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymx_33946/04_2024/7ymx_33946.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymx_33946/04_2024/7ymx_33946.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymx_33946/04_2024/7ymx_33946.pdb" } resolution = 4.44 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= -0.005 sd= 0.117 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 153 5.16 5 C 17602 2.51 5 N 4511 2.21 5 O 5509 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1148": "OE1" <-> "OE2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 911": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 27775 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 9020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9020 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 57, 'TRANS': 1108} Chain breaks: 5 Chain: "B" Number of atoms: 9020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9020 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 57, 'TRANS': 1108} Chain breaks: 5 Chain: "C" Number of atoms: 9020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9020 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 57, 'TRANS': 1108} Chain breaks: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} 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: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 14.81, per 1000 atoms: 0.53 Number of scatterers: 27775 At special positions: 0 Unit cell: (151.8, 170.5, 179.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 153 16.00 O 5509 8.00 N 4511 7.00 C 17602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 654 " distance=2.03 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.03 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.03 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 736 " distance=2.02 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.03 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.03 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.03 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.05 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.02 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.04 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 654 " distance=2.03 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.03 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.03 Simple disulfide: pdb=" SG CYS B 806 " - pdb=" SG CYS B 828 " distance=2.03 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.03 Simple disulfide: pdb=" SG CYS B 912 " - pdb=" SG CYS B 925 " distance=2.03 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.03 Simple disulfide: pdb=" SG CYS B1156 " - pdb=" SG CYS B1164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.03 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.03 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 654 " distance=2.03 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.03 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 736 " distance=2.03 Simple disulfide: pdb=" SG CYS C 806 " - pdb=" SG CYS C 828 " distance=2.03 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.03 Simple disulfide: pdb=" SG CYS C 912 " - pdb=" SG CYS C 925 " distance=2.05 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.03 Simple disulfide: pdb=" SG CYS C1156 " - pdb=" SG CYS C1164 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA I 3 " - " MAN I 4 " " BMA O 3 " - " MAN O 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA I 3 " - " MAN I 5 " " BMA O 3 " - " MAN O 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A1401 " - " ASN A 222 " " NAG A1402 " - " ASN A 236 " " NAG A1403 " - " ASN A 244 " " NAG A1404 " - " ASN A 619 " " NAG A1405 " - " ASN A 719 " " NAG A1406 " - " ASN A 774 " " NAG A1407 " - " ASN A 785 " " NAG B1401 " - " ASN B 619 " " NAG B1402 " - " ASN B 774 " " NAG B1403 " - " ASN B 785 " " NAG B1404 " - " ASN B 244 " " NAG B1405 " - " ASN B 66 " " NAG B1406 " - " ASN B 719 " " NAG C1401 " - " ASN C 719 " " NAG C1402 " - " ASN C 870 " " NAG C1403 " - " ASN C 785 " " NAG C1404 " - " ASN C 166 " " NAG C1405 " - " ASN C 244 " " NAG C1406 " - " ASN C 619 " " NAG C1407 " - " ASN C 66 " " NAG D 1 " - " ASN A 66 " " NAG E 1 " - " ASN A 125 " " NAG F 1 " - " ASN A 166 " " NAG G 1 " - " ASN A 870 " " NAG H 1 " - " ASN A1213 " " NAG I 1 " - " ASN B 125 " " NAG J 1 " - " ASN B1213 " " NAG K 1 " - " ASN B 870 " " NAG L 1 " - " ASN B 222 " " NAG M 1 " - " ASN C1213 " " NAG N 1 " - " ASN C 222 " " NAG O 1 " - " ASN C 125 " Time building additional restraints: 11.81 Conformation dependent library (CDL) restraints added in 4.8 seconds 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6510 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 54 sheets defined 25.2% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.29 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 224 through 230 Processing helix chain 'A' and resid 342 through 352 Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 395 through 399 removed outlier: 3.813A pdb=" N PHE A 399 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 415 Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 431 through 436 Processing helix chain 'A' and resid 449 through 457 removed outlier: 3.556A pdb=" N MET A 452 " --> pdb=" O PRO A 449 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N SER A 454 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER A 457 " --> pdb=" O SER A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.873A pdb=" N SER A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 529 " --> pdb=" O PRO A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 596 through 600 removed outlier: 4.164A pdb=" N LEU A 600 " --> pdb=" O ALA A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 812 Processing helix chain 'A' and resid 814 through 822 Processing helix chain 'A' and resid 825 through 854 removed outlier: 4.411A pdb=" N SER A 829 " --> pdb=" O GLY A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 875 Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 907 through 915 Processing helix chain 'A' and resid 926 through 931 removed outlier: 4.082A pdb=" N ALA A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 959 removed outlier: 4.876A pdb=" N ALA A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLY A 957 " --> pdb=" O GLY A 953 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 959 " --> pdb=" O ILE A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 983 Processing helix chain 'A' and resid 986 through 993 removed outlier: 3.803A pdb=" N LEU A 990 " --> pdb=" O THR A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1008 removed outlier: 3.585A pdb=" N ILE A 997 " --> pdb=" O ASN A 993 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET A1008 " --> pdb=" O ALA A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1040 removed outlier: 3.717A pdb=" N LEU A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1058 Processing helix chain 'A' and resid 1059 through 1106 removed outlier: 3.981A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 removed outlier: 4.153A pdb=" N PHE B 40 " --> pdb=" O GLN B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.556A pdb=" N TYR B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 removed outlier: 3.676A pdb=" N ARG B 307 " --> pdb=" O GLN B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 352 Processing helix chain 'B' and resid 395 through 399 removed outlier: 3.656A pdb=" N PHE B 399 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 457 removed outlier: 3.980A pdb=" N MET B 452 " --> pdb=" O PRO B 449 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N SER B 454 " --> pdb=" O SER B 451 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 457 " --> pdb=" O SER B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 removed outlier: 3.587A pdb=" N ASN B 468 " --> pdb=" O ILE B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 529 Processing helix chain 'B' and resid 546 through 550 Processing helix chain 'B' and resid 591 through 595 removed outlier: 4.088A pdb=" N LYS B 595 " --> pdb=" O ASN B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 600 removed outlier: 4.044A pdb=" N LEU B 600 " --> pdb=" O ALA B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 812 removed outlier: 3.615A pdb=" N TYR B 809 " --> pdb=" O ASP B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 820 Processing helix chain 'B' and resid 826 through 854 Processing helix chain 'B' and resid 888 through 898 removed outlier: 3.505A pdb=" N VAL B 898 " --> pdb=" O LEU B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 907 through 915 removed outlier: 3.846A pdb=" N GLN B 914 " --> pdb=" O ASP B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 959 removed outlier: 4.688A pdb=" N ALA B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N GLY B 957 " --> pdb=" O GLY B 953 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY B 959 " --> pdb=" O ILE B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 984 removed outlier: 3.698A pdb=" N GLY B 984 " --> pdb=" O LEU B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 993 removed outlier: 3.614A pdb=" N LEU B 990 " --> pdb=" O THR B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1008 removed outlier: 3.640A pdb=" N ILE B 997 " --> pdb=" O ASN B 993 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N MET B1008 " --> pdb=" O ALA B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1039 removed outlier: 3.699A pdb=" N LEU B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1042 No H-bonds generated for 'chain 'B' and resid 1040 through 1042' Processing helix chain 'B' and resid 1050 through 1058 Processing helix chain 'B' and resid 1059 through 1107 removed outlier: 4.152A pdb=" N ALA B1065 " --> pdb=" O PRO B1061 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL B1107 " --> pdb=" O VAL B1103 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 342 through 352 Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'C' and resid 395 through 399 removed outlier: 3.908A pdb=" N PHE C 399 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 418 Processing helix chain 'C' and resid 431 through 436 Processing helix chain 'C' and resid 452 through 457 Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 524 through 529 Processing helix chain 'C' and resid 546 through 550 Processing helix chain 'C' and resid 591 through 600 removed outlier: 3.591A pdb=" N THR C 594 " --> pdb=" O ALA C 591 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS C 595 " --> pdb=" O ASN C 592 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILE C 596 " --> pdb=" O ASP C 593 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA C 597 " --> pdb=" O THR C 594 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU C 600 " --> pdb=" O ALA C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 812 Processing helix chain 'C' and resid 814 through 822 Processing helix chain 'C' and resid 826 through 853 Processing helix chain 'C' and resid 888 through 898 Processing helix chain 'C' and resid 908 through 912 Processing helix chain 'C' and resid 926 through 931 removed outlier: 3.835A pdb=" N ALA C 930 " --> pdb=" O ALA C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 955 Processing helix chain 'C' and resid 971 through 983 removed outlier: 3.545A pdb=" N VAL C 983 " --> pdb=" O ARG C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 993 removed outlier: 3.749A pdb=" N LEU C 990 " --> pdb=" O THR C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1008 removed outlier: 4.013A pdb=" N MET C1008 " --> pdb=" O ALA C1004 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1038 removed outlier: 3.887A pdb=" N LEU C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) Processing helix chain 'C' and resid 1039 through 1042 Processing helix chain 'C' and resid 1050 through 1058 Processing helix chain 'C' and resid 1059 through 1106 removed outlier: 3.944A pdb=" N ALA C1065 " --> pdb=" O PRO C1061 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 75 removed outlier: 4.368A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 89 removed outlier: 7.473A pdb=" N SER A 88 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N THR A 206 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 removed outlier: 4.719A pdb=" N ALA A 146 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 279 through 284 removed outlier: 4.980A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 126 through 129 removed outlier: 4.087A pdb=" N SER A 126 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 359 through 362 removed outlier: 4.097A pdb=" N THR A 669 " --> pdb=" O ASP A 664 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 373 through 374 removed outlier: 6.207A pdb=" N VAL A 374 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL A 639 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL A 631 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 400 through 404 removed outlier: 6.542A pdb=" N THR A 483 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N VAL A 420 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 513 through 515 removed outlier: 4.937A pdb=" N SER A 498 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL A 561 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE A 500 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N SER A 559 " --> pdb=" O ILE A 500 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 723 through 724 removed outlier: 3.635A pdb=" N GLY A 732 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ALA A 737 " --> pdb=" O PRO A 730 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 768 through 769 removed outlier: 5.814A pdb=" N ILE A 768 " --> pdb=" O SER B 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 778 through 796 removed outlier: 6.870A pdb=" N LYS A 779 " --> pdb=" O VAL A1150 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A1150 " --> pdb=" O LYS A 779 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N SER A 781 " --> pdb=" O GLU A1148 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLU A1148 " --> pdb=" O SER A 781 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N HIS A1146 " --> pdb=" O PRO A 783 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY A1133 " --> pdb=" O ASN A1129 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ASN A1129 " --> pdb=" O GLY A1133 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TYR A1135 " --> pdb=" O VAL A1127 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL A1127 " --> pdb=" O TYR A1135 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N MET A1137 " --> pdb=" O SER A1125 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER A1125 " --> pdb=" O MET A1137 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL A1139 " --> pdb=" O ILE A1123 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A1121 " --> pdb=" O TYR A1141 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AB6, first strand: chain 'A' and resid 857 through 858 removed outlier: 3.544A pdb=" N SER A 858 " --> pdb=" O ILE C 768 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1202 through 1204 removed outlier: 6.164A pdb=" N CYS A1156 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1170 through 1173 Processing sheet with id=AB9, first strand: chain 'B' and resid 67 through 75 removed outlier: 4.327A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 92 through 93 removed outlier: 3.518A pdb=" N THR B 93 " --> pdb=" O THR B 96 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 110 through 111 removed outlier: 3.510A pdb=" N LYS B 110 " --> pdb=" O TYR B 293 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ALA B 146 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 110 through 111 removed outlier: 3.510A pdb=" N LYS B 110 " --> pdb=" O TYR B 293 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ALA B 146 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 279 through 284 removed outlier: 5.209A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 127 through 129 Processing sheet with id=AC6, first strand: chain 'B' and resid 359 through 362 removed outlier: 3.655A pdb=" N TYR B 663 " --> pdb=" O GLY B 359 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR B 669 " --> pdb=" O ASP B 664 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 373 through 375 Processing sheet with id=AC8, first strand: chain 'B' and resid 400 through 404 removed outlier: 6.748A pdb=" N THR B 477 " --> pdb=" O CYS B 425 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N CYS B 425 " --> pdb=" O THR B 477 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU B 479 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE B 423 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU B 481 " --> pdb=" O ASN B 421 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER B 419 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 513 through 515 removed outlier: 4.682A pdb=" N SER B 498 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL B 561 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ILE B 500 " --> pdb=" O SER B 559 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N SER B 559 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER B 504 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL B 555 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 506 " --> pdb=" O TRP B 553 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 618 through 620 removed outlier: 3.977A pdb=" N TYR B 648 " --> pdb=" O CYS B 620 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL B 631 " --> pdb=" O VAL B 639 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 724 removed outlier: 6.416A pdb=" N VAL B 718 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N SER B 761 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 9.805A pdb=" N SER B 720 " --> pdb=" O SER B 761 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 768 through 769 removed outlier: 5.451A pdb=" N ILE B 768 " --> pdb=" O SER C 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 778 through 782 Processing sheet with id=AD5, first strand: chain 'B' and resid 785 through 795 removed outlier: 7.020A pdb=" N TYR B1135 " --> pdb=" O VAL B1127 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL B1127 " --> pdb=" O TYR B1135 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N MET B1137 " --> pdb=" O SER B1125 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N SER B1125 " --> pdb=" O MET B1137 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL B1139 " --> pdb=" O ILE B1123 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR B1121 " --> pdb=" O TYR B1141 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 802 through 804 Processing sheet with id=AD7, first strand: chain 'B' and resid 1202 through 1205 removed outlier: 3.873A pdb=" N CYS B1164 " --> pdb=" O VAL B1205 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N CYS B1156 " --> pdb=" O ILE B1214 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1170 through 1173 Processing sheet with id=AD9, first strand: chain 'C' and resid 67 through 75 removed outlier: 4.457A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AE2, first strand: chain 'C' and resid 279 through 284 removed outlier: 5.202A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG C 119 " --> pdb=" O TYR C 314 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR C 314 " --> pdb=" O ARG C 119 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AE4, first strand: chain 'C' and resid 232 through 235 Processing sheet with id=AE5, first strand: chain 'C' and resid 232 through 235 Processing sheet with id=AE6, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AE7, first strand: chain 'C' and resid 206 through 208 removed outlier: 6.182A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 359 through 361 removed outlier: 4.008A pdb=" N THR C 669 " --> pdb=" O ASP C 664 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 373 through 374 removed outlier: 6.543A pdb=" N VAL C 374 " --> pdb=" O SER C 607 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 400 through 405 removed outlier: 6.312A pdb=" N THR C 483 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VAL C 420 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 407 through 409 removed outlier: 3.621A pdb=" N CYS C 585 " --> pdb=" O CYS C 407 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 513 through 515 removed outlier: 5.129A pdb=" N SER C 498 " --> pdb=" O VAL C 561 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL C 561 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE C 500 " --> pdb=" O SER C 559 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N SER C 559 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL C 555 " --> pdb=" O SER C 504 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU C 506 " --> pdb=" O TRP C 553 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TRP C 553 " --> pdb=" O LEU C 506 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP C 539 " --> pdb=" O GLY C 558 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 618 through 619 removed outlier: 7.217A pdb=" N VAL C 631 " --> pdb=" O VAL C 639 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 717 through 724 removed outlier: 3.568A pdb=" N VAL C 718 " --> pdb=" O MET C 757 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU C 759 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER C 720 " --> pdb=" O LEU C 759 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N SER C 761 " --> pdb=" O SER C 720 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU C 722 " --> pdb=" O SER C 761 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 778 through 795 removed outlier: 7.069A pdb=" N ASN C1145 " --> pdb=" O THR C 784 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N PHE C 786 " --> pdb=" O PRO C1143 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N PHE C 788 " --> pdb=" O TYR C1141 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N TYR C1141 " --> pdb=" O PHE C 788 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL C 790 " --> pdb=" O VAL C1139 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL C1139 " --> pdb=" O VAL C 790 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLN C 792 " --> pdb=" O MET C1137 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N MET C1137 " --> pdb=" O GLN C 792 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TYR C 794 " --> pdb=" O TYR C1135 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TYR C1135 " --> pdb=" O TYR C 794 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N TYR C1141 " --> pdb=" O HIS C1122 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N HIS C1122 " --> pdb=" O TYR C1141 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 802 through 804 Processing sheet with id=AF8, first strand: chain 'C' and resid 1202 through 1205 removed outlier: 3.795A pdb=" N CYS C1164 " --> pdb=" O VAL C1205 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1170 through 1174 1019 hydrogen bonds defined for protein. 2715 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: 12.45 Time building geometry restraints manager: 12.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8619 1.34 - 1.46: 7225 1.46 - 1.59: 12356 1.59 - 1.71: 1 1.71 - 1.84: 204 Bond restraints: 28405 Sorted by residual: bond pdb=" CA ASP B 213 " pdb=" C ASP B 213 " ideal model delta sigma weight residual 1.522 1.465 0.057 1.36e-02 5.41e+03 1.77e+01 bond pdb=" CA GLY C 908 " pdb=" C GLY C 908 " ideal model delta sigma weight residual 1.515 1.466 0.049 1.25e-02 6.40e+03 1.52e+01 bond pdb=" CA CYS B 214 " pdb=" C CYS B 214 " ideal model delta sigma weight residual 1.522 1.480 0.042 1.20e-02 6.94e+03 1.23e+01 bond pdb=" C1 MAN O 4 " pdb=" C2 MAN O 4 " ideal model delta sigma weight residual 1.526 1.594 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" CA ASP C 911 " pdb=" C ASP C 911 " ideal model delta sigma weight residual 1.522 1.478 0.044 1.32e-02 5.74e+03 1.11e+01 ... (remaining 28400 not shown) Histogram of bond angle deviations from ideal: 97.43 - 104.82: 509 104.82 - 112.20: 13904 112.20 - 119.59: 9624 119.59 - 126.98: 14371 126.98 - 134.36: 234 Bond angle restraints: 38642 Sorted by residual: angle pdb=" N ASP C 911 " pdb=" CA ASP C 911 " pdb=" C ASP C 911 " ideal model delta sigma weight residual 113.50 102.10 11.40 1.23e+00 6.61e-01 8.59e+01 angle pdb=" N GLY C 908 " pdb=" CA GLY C 908 " pdb=" C GLY C 908 " ideal model delta sigma weight residual 113.37 101.58 11.79 1.34e+00 5.57e-01 7.74e+01 angle pdb=" N CYS C 912 " pdb=" CA CYS C 912 " pdb=" C CYS C 912 " ideal model delta sigma weight residual 113.16 103.20 9.96 1.24e+00 6.50e-01 6.45e+01 angle pdb=" N MET C 913 " pdb=" CA MET C 913 " pdb=" C MET C 913 " ideal model delta sigma weight residual 112.92 103.35 9.57 1.23e+00 6.61e-01 6.05e+01 angle pdb=" N TYR C 909 " pdb=" CA TYR C 909 " pdb=" C TYR C 909 " ideal model delta sigma weight residual 111.36 103.90 7.46 1.09e+00 8.42e-01 4.69e+01 ... (remaining 38637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.82: 16323 22.82 - 45.65: 1056 45.65 - 68.47: 148 68.47 - 91.29: 79 91.29 - 114.11: 19 Dihedral angle restraints: 17625 sinusoidal: 7434 harmonic: 10191 Sorted by residual: dihedral pdb=" CB CYS C 811 " pdb=" SG CYS C 811 " pdb=" SG CYS C 817 " pdb=" CB CYS C 817 " ideal model delta sinusoidal sigma weight residual -86.00 -161.15 75.15 1 1.00e+01 1.00e-02 7.14e+01 dihedral pdb=" CB CYS B 912 " pdb=" SG CYS B 912 " pdb=" SG CYS B 925 " pdb=" CB CYS B 925 " ideal model delta sinusoidal sigma weight residual 93.00 162.93 -69.93 1 1.00e+01 1.00e-02 6.31e+01 dihedral pdb=" CB CYS B 811 " pdb=" SG CYS B 811 " pdb=" SG CYS B 817 " pdb=" CB CYS B 817 " ideal model delta sinusoidal sigma weight residual -86.00 -155.88 69.88 1 1.00e+01 1.00e-02 6.30e+01 ... (remaining 17622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 4380 0.136 - 0.271: 93 0.271 - 0.407: 2 0.407 - 0.542: 1 0.542 - 0.678: 1 Chirality restraints: 4477 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN B 222 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.15e+01 chirality pdb=" CA ASN B 222 " pdb=" N ASN B 222 " pdb=" C ASN B 222 " pdb=" CB ASN B 222 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.41e+00 chirality pdb=" CB VAL A 86 " pdb=" CA VAL A 86 " pdb=" CG1 VAL A 86 " pdb=" CG2 VAL A 86 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.03e+00 ... (remaining 4474 not shown) Planarity restraints: 4972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 212 " -0.023 2.00e-02 2.50e+03 4.78e-02 2.28e+01 pdb=" C THR B 212 " 0.083 2.00e-02 2.50e+03 pdb=" O THR B 212 " -0.031 2.00e-02 2.50e+03 pdb=" N ASP B 213 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 928 " 0.014 2.00e-02 2.50e+03 2.68e-02 1.43e+01 pdb=" CG TYR C 928 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR C 928 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR C 928 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR C 928 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 928 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR C 928 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR C 928 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 84 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.27e+00 pdb=" C MET A 84 " -0.053 2.00e-02 2.50e+03 pdb=" O MET A 84 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR A 85 " 0.018 2.00e-02 2.50e+03 ... (remaining 4969 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5461 2.77 - 3.30: 26658 3.30 - 3.84: 48568 3.84 - 4.37: 53419 4.37 - 4.90: 89487 Nonbonded interactions: 223593 Sorted by model distance: nonbonded pdb=" O SER A 350 " pdb=" OG SER B 829 " model vdw 2.240 2.440 nonbonded pdb=" OD1 ASN B 421 " pdb=" OG1 THR B 483 " model vdw 2.245 2.440 nonbonded pdb=" OD2 ASP C 664 " pdb=" OG1 THR C 667 " model vdw 2.250 2.440 nonbonded pdb=" O GLN B 346 " pdb=" OG SER B 350 " model vdw 2.252 2.440 nonbonded pdb=" OD2 ASP B 664 " pdb=" OG1 THR B 667 " model vdw 2.260 2.440 ... (remaining 223588 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 1223 or resid 1401 through 1406)) selection = chain 'B' selection = (chain 'C' and (resid 19 through 1223 or resid 1401 through 1406)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 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: 0.030 Extract box with map and model: 5.140 Check model and map are aligned: 0.390 Set scattering table: 0.240 Process input model: 74.590 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.230 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: 0.010 Load rotamer database and sin/cos tables:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 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 0.068 28405 Z= 0.293 Angle : 0.825 11.857 38642 Z= 0.434 Chirality : 0.054 0.678 4477 Planarity : 0.006 0.073 4940 Dihedral : 15.809 114.115 10971 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.86 % Favored : 94.08 % Rotamer: Outliers : 0.33 % Allowed : 0.60 % Favored : 99.07 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.13), residues: 3462 helix: 0.24 (0.19), residues: 686 sheet: -0.18 (0.20), residues: 584 loop : -1.36 (0.12), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 553 HIS 0.005 0.001 HIS A 264 PHE 0.027 0.002 PHE B1136 TYR 0.062 0.002 TYR C 928 ARG 0.008 0.000 ARG C 505 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 3.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 ASN cc_start: 0.9770 (t0) cc_final: 0.9502 (p0) REVERT: A 452 MET cc_start: 0.1376 (ttp) cc_final: 0.0946 (ptt) REVERT: B 673 LEU cc_start: 0.9082 (mp) cc_final: 0.8840 (tp) REVERT: B 943 MET cc_start: 0.8514 (mmm) cc_final: 0.7951 (tmm) REVERT: C 169 LEU cc_start: 0.9397 (tp) cc_final: 0.9113 (mt) REVERT: C 563 MET cc_start: 0.8087 (mmt) cc_final: 0.7526 (mmp) REVERT: C 569 MET cc_start: 0.9270 (pmm) cc_final: 0.8672 (pmm) REVERT: C 943 MET cc_start: 0.8368 (ppp) cc_final: 0.7956 (ppp) outliers start: 10 outliers final: 2 residues processed: 112 average time/residue: 0.3968 time to fit residues: 74.6090 Evaluate side-chains 79 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 3.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 8.9990 chunk 263 optimal weight: 8.9990 chunk 146 optimal weight: 30.0000 chunk 90 optimal weight: 0.5980 chunk 177 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 272 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 chunk 165 optimal weight: 30.0000 chunk 203 optimal weight: 50.0000 chunk 316 optimal weight: 9.9990 overall best weight: 7.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN A 708 GLN A 833 GLN ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 GLN A1085 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 GLN B 833 GLN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1129 ASN ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 GLN C1028 ASN ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1145 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28405 Z= 0.253 Angle : 0.610 10.597 38642 Z= 0.315 Chirality : 0.043 0.502 4477 Planarity : 0.004 0.063 4940 Dihedral : 9.064 110.380 4881 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.72 % Favored : 94.25 % Rotamer: Outliers : 0.10 % Allowed : 5.55 % Favored : 94.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.14), residues: 3462 helix: 1.29 (0.20), residues: 719 sheet: -0.49 (0.19), residues: 670 loop : -1.17 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 960 HIS 0.006 0.001 HIS B 264 PHE 0.017 0.002 PHE B 850 TYR 0.020 0.002 TYR B 351 ARG 0.005 0.001 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 3.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 406 ASN cc_start: 0.9764 (t0) cc_final: 0.9541 (p0) REVERT: A 452 MET cc_start: 0.0675 (ttp) cc_final: 0.0386 (ptt) REVERT: B 278 MET cc_start: 0.7288 (mmp) cc_final: 0.7030 (mmp) REVERT: C 169 LEU cc_start: 0.9398 (tp) cc_final: 0.9073 (pp) REVERT: C 563 MET cc_start: 0.8507 (mmt) cc_final: 0.8072 (mmt) REVERT: C 1169 ASN cc_start: 0.8152 (t0) cc_final: 0.7871 (t0) outliers start: 3 outliers final: 1 residues processed: 85 average time/residue: 0.3678 time to fit residues: 54.9181 Evaluate side-chains 72 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 3.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 175 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 263 optimal weight: 7.9990 chunk 215 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 316 optimal weight: 20.0000 chunk 342 optimal weight: 20.0000 chunk 281 optimal weight: 2.9990 chunk 313 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 253 optimal weight: 3.9990 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 708 GLN A 766 HIS ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 GLN B 194 HIS ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 GLN B 792 GLN B 808 GLN B 848 ASN B1072 ASN ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1122 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28405 Z= 0.213 Angle : 0.575 11.783 38642 Z= 0.295 Chirality : 0.042 0.418 4477 Planarity : 0.004 0.062 4940 Dihedral : 8.387 111.796 4881 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.89 % Favored : 94.08 % Rotamer: Outliers : 0.03 % Allowed : 4.59 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.14), residues: 3462 helix: 1.35 (0.20), residues: 727 sheet: -0.50 (0.19), residues: 696 loop : -1.13 (0.14), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 44 HIS 0.005 0.001 HIS A 766 PHE 0.018 0.001 PHE C 850 TYR 0.017 0.001 TYR B 689 ARG 0.004 0.000 ARG A1088 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 3.390 Fit side-chains revert: symmetry clash REVERT: A 406 ASN cc_start: 0.9769 (t0) cc_final: 0.9547 (p0) REVERT: A 452 MET cc_start: 0.1332 (ttp) cc_final: 0.0321 (ptp) REVERT: B 84 MET cc_start: 0.8126 (tpt) cc_final: 0.7888 (tpt) REVERT: B 171 LEU cc_start: 0.9516 (tp) cc_final: 0.9163 (pp) REVERT: B 278 MET cc_start: 0.7023 (mmp) cc_final: 0.6795 (mmp) REVERT: B 913 MET cc_start: 0.9521 (mtm) cc_final: 0.9080 (mtt) REVERT: C 171 LEU cc_start: 0.9675 (tp) cc_final: 0.9191 (pp) REVERT: C 569 MET cc_start: 0.9255 (pmm) cc_final: 0.8302 (pmm) REVERT: C 1169 ASN cc_start: 0.8178 (t0) cc_final: 0.7895 (t0) outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.3816 time to fit residues: 55.2207 Evaluate side-chains 68 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 3.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 312 optimal weight: 20.0000 chunk 238 optimal weight: 8.9990 chunk 164 optimal weight: 50.0000 chunk 35 optimal weight: 20.0000 chunk 151 optimal weight: 7.9990 chunk 212 optimal weight: 9.9990 chunk 317 optimal weight: 30.0000 chunk 336 optimal weight: 10.0000 chunk 165 optimal weight: 8.9990 chunk 301 optimal weight: 20.0000 chunk 90 optimal weight: 30.0000 overall best weight: 9.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN ** A1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1028 ASN ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 ASN ** C 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 833 GLN ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 28405 Z= 0.300 Angle : 0.643 12.555 38642 Z= 0.334 Chirality : 0.043 0.459 4477 Planarity : 0.004 0.059 4940 Dihedral : 7.730 114.268 4881 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 24.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.76 % Favored : 93.21 % Rotamer: Outliers : 0.03 % Allowed : 4.69 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3462 helix: 1.20 (0.20), residues: 739 sheet: -0.63 (0.19), residues: 707 loop : -1.20 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 535 HIS 0.007 0.002 HIS B1146 PHE 0.028 0.002 PHE C 164 TYR 0.020 0.002 TYR C 361 ARG 0.005 0.001 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 3.181 Fit side-chains REVERT: A 452 MET cc_start: 0.1564 (ttp) cc_final: 0.1070 (ptp) REVERT: B 84 MET cc_start: 0.8482 (tpt) cc_final: 0.8181 (tpt) REVERT: B 171 LEU cc_start: 0.9504 (tp) cc_final: 0.9133 (pp) REVERT: B 913 MET cc_start: 0.9598 (mtm) cc_final: 0.9230 (mtt) REVERT: B 943 MET cc_start: 0.8696 (tpt) cc_final: 0.8204 (tpt) REVERT: C 171 LEU cc_start: 0.9668 (tp) cc_final: 0.9115 (pp) REVERT: C 563 MET cc_start: 0.9052 (mmm) cc_final: 0.8494 (mmt) REVERT: C 569 MET cc_start: 0.9284 (pmm) cc_final: 0.8372 (pmm) REVERT: C 943 MET cc_start: 0.8949 (ppp) cc_final: 0.8375 (ppp) REVERT: C 1169 ASN cc_start: 0.8419 (t0) cc_final: 0.8046 (t0) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.3995 time to fit residues: 52.5922 Evaluate side-chains 63 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 3.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 280 optimal weight: 9.9990 chunk 190 optimal weight: 20.0000 chunk 4 optimal weight: 7.9990 chunk 250 optimal weight: 30.0000 chunk 138 optimal weight: 0.9990 chunk 287 optimal weight: 5.9990 chunk 232 optimal weight: 40.0000 chunk 0 optimal weight: 50.0000 chunk 171 optimal weight: 50.0000 chunk 301 optimal weight: 7.9990 chunk 84 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1129 ASN ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN ** C 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 28405 Z= 0.227 Angle : 0.584 12.242 38642 Z= 0.300 Chirality : 0.043 0.438 4477 Planarity : 0.004 0.070 4940 Dihedral : 7.559 113.711 4881 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 20.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.12 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 3462 helix: 1.29 (0.20), residues: 738 sheet: -0.79 (0.18), residues: 751 loop : -1.21 (0.14), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 535 HIS 0.007 0.001 HIS B1138 PHE 0.022 0.001 PHE C 164 TYR 0.018 0.002 TYR C 947 ARG 0.004 0.000 ARG C 629 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 3.424 Fit side-chains revert: symmetry clash REVERT: B 84 MET cc_start: 0.8580 (tpt) cc_final: 0.8229 (tpt) REVERT: B 171 LEU cc_start: 0.9516 (tp) cc_final: 0.9111 (pp) REVERT: B 278 MET cc_start: 0.6992 (mmp) cc_final: 0.6752 (mmp) REVERT: B 913 MET cc_start: 0.9573 (mtm) cc_final: 0.9141 (mtt) REVERT: B 943 MET cc_start: 0.8910 (tpt) cc_final: 0.8486 (tpp) REVERT: C 171 LEU cc_start: 0.9660 (tp) cc_final: 0.9071 (pp) REVERT: C 563 MET cc_start: 0.9160 (mmm) cc_final: 0.8874 (mmm) REVERT: C 569 MET cc_start: 0.9323 (pmm) cc_final: 0.8469 (pmm) REVERT: C 757 MET cc_start: 0.8115 (tpt) cc_final: 0.7845 (tpp) REVERT: C 939 MET cc_start: 0.8329 (tpt) cc_final: 0.8008 (tpt) REVERT: C 943 MET cc_start: 0.8792 (ppp) cc_final: 0.8569 (ppp) REVERT: C 1169 ASN cc_start: 0.8371 (t0) cc_final: 0.7991 (t0) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.4137 time to fit residues: 55.1173 Evaluate side-chains 68 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 113 optimal weight: 7.9990 chunk 302 optimal weight: 4.9990 chunk 66 optimal weight: 40.0000 chunk 197 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 chunk 336 optimal weight: 6.9990 chunk 279 optimal weight: 0.8980 chunk 155 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 111 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28405 Z= 0.176 Angle : 0.554 10.966 38642 Z= 0.282 Chirality : 0.043 0.447 4477 Planarity : 0.004 0.071 4940 Dihedral : 7.204 111.868 4881 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.01 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3462 helix: 1.30 (0.20), residues: 751 sheet: -0.72 (0.19), residues: 714 loop : -1.15 (0.14), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 535 HIS 0.005 0.001 HIS B1138 PHE 0.018 0.001 PHE C 164 TYR 0.032 0.001 TYR B 219 ARG 0.004 0.000 ARG A1113 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 3.385 Fit side-chains REVERT: A 265 LEU cc_start: 0.9582 (tp) cc_final: 0.9366 (tp) REVERT: A 452 MET cc_start: 0.1085 (ttp) cc_final: 0.0609 (ptp) REVERT: B 84 MET cc_start: 0.8475 (tpt) cc_final: 0.8164 (tpt) REVERT: B 171 LEU cc_start: 0.9521 (tp) cc_final: 0.9117 (pp) REVERT: B 913 MET cc_start: 0.9566 (mtm) cc_final: 0.9167 (mtt) REVERT: B 943 MET cc_start: 0.8897 (tpt) cc_final: 0.8485 (tpp) REVERT: C 171 LEU cc_start: 0.9654 (tp) cc_final: 0.9076 (pp) REVERT: C 563 MET cc_start: 0.9130 (mmm) cc_final: 0.8806 (mmm) REVERT: C 569 MET cc_start: 0.9321 (pmm) cc_final: 0.8450 (pmm) REVERT: C 1169 ASN cc_start: 0.8369 (t0) cc_final: 0.8007 (t0) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.3795 time to fit residues: 50.5147 Evaluate side-chains 66 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 3.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 324 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 191 optimal weight: 30.0000 chunk 245 optimal weight: 40.0000 chunk 190 optimal weight: 30.0000 chunk 283 optimal weight: 30.0000 chunk 188 optimal weight: 20.0000 chunk 335 optimal weight: 5.9990 chunk 209 optimal weight: 0.4980 chunk 204 optimal weight: 20.0000 chunk 154 optimal weight: 50.0000 overall best weight: 9.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 HIS ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 ASN ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 812 ASN ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 28405 Z= 0.298 Angle : 0.645 11.849 38642 Z= 0.336 Chirality : 0.043 0.469 4477 Planarity : 0.005 0.107 4940 Dihedral : 7.209 112.798 4881 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 27.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.08 % Favored : 92.89 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.14), residues: 3462 helix: 1.16 (0.20), residues: 744 sheet: -0.93 (0.18), residues: 745 loop : -1.24 (0.14), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 535 HIS 0.007 0.002 HIS B1138 PHE 0.020 0.002 PHE C1172 TYR 0.023 0.002 TYR B 219 ARG 0.008 0.001 ARG C 181 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 3.143 Fit side-chains REVERT: A 452 MET cc_start: 0.1699 (ttp) cc_final: 0.1177 (ptp) REVERT: A 1137 MET cc_start: 0.8134 (pmm) cc_final: 0.7910 (pmm) REVERT: B 171 LEU cc_start: 0.9522 (tp) cc_final: 0.9143 (pp) REVERT: B 913 MET cc_start: 0.9552 (mtm) cc_final: 0.9213 (mtt) REVERT: B 943 MET cc_start: 0.8920 (tpt) cc_final: 0.8414 (tpt) REVERT: C 171 LEU cc_start: 0.9662 (tp) cc_final: 0.8974 (pp) REVERT: C 569 MET cc_start: 0.9322 (pmm) cc_final: 0.8445 (pmm) REVERT: C 757 MET cc_start: 0.8201 (tpt) cc_final: 0.7880 (tpp) REVERT: C 1169 ASN cc_start: 0.8575 (t0) cc_final: 0.8197 (t0) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.3697 time to fit residues: 48.3173 Evaluate side-chains 63 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 3.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 207 optimal weight: 7.9990 chunk 133 optimal weight: 0.9990 chunk 200 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 64 optimal weight: 8.9990 chunk 213 optimal weight: 20.0000 chunk 228 optimal weight: 7.9990 chunk 165 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 263 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1084 GLN ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28405 Z= 0.208 Angle : 0.578 12.567 38642 Z= 0.296 Chirality : 0.043 0.471 4477 Planarity : 0.004 0.056 4940 Dihedral : 7.025 112.785 4881 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.41 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.14), residues: 3462 helix: 1.37 (0.20), residues: 733 sheet: -0.86 (0.18), residues: 728 loop : -1.22 (0.14), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 535 HIS 0.004 0.001 HIS B1138 PHE 0.016 0.001 PHE C 850 TYR 0.019 0.001 TYR B 219 ARG 0.004 0.000 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 3.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 LEU cc_start: 0.9639 (tp) cc_final: 0.9438 (tp) REVERT: A 452 MET cc_start: 0.1806 (ttp) cc_final: 0.1225 (ptp) REVERT: B 171 LEU cc_start: 0.9518 (tp) cc_final: 0.9091 (pp) REVERT: B 943 MET cc_start: 0.8899 (tpt) cc_final: 0.8382 (tpt) REVERT: C 452 MET cc_start: 0.8469 (pmm) cc_final: 0.8239 (pmm) REVERT: C 563 MET cc_start: 0.9210 (mmm) cc_final: 0.8718 (mmt) REVERT: C 569 MET cc_start: 0.9311 (pmm) cc_final: 0.8530 (pmm) REVERT: C 757 MET cc_start: 0.8073 (tpt) cc_final: 0.7794 (tpp) REVERT: C 943 MET cc_start: 0.9068 (ppp) cc_final: 0.8856 (ppp) REVERT: C 1169 ASN cc_start: 0.8506 (t0) cc_final: 0.8137 (t0) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.4015 time to fit residues: 50.7517 Evaluate side-chains 64 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 3.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 305 optimal weight: 3.9990 chunk 321 optimal weight: 20.0000 chunk 293 optimal weight: 20.0000 chunk 312 optimal weight: 10.0000 chunk 188 optimal weight: 30.0000 chunk 136 optimal weight: 5.9990 chunk 245 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 282 optimal weight: 50.0000 chunk 295 optimal weight: 10.0000 chunk 311 optimal weight: 6.9990 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28405 Z= 0.230 Angle : 0.591 12.054 38642 Z= 0.304 Chirality : 0.043 0.468 4477 Planarity : 0.004 0.053 4940 Dihedral : 6.873 111.623 4881 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 23.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.96 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.14), residues: 3462 helix: 1.42 (0.20), residues: 720 sheet: -0.87 (0.19), residues: 706 loop : -1.26 (0.14), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 535 HIS 0.006 0.001 HIS B1138 PHE 0.026 0.002 PHE A 895 TYR 0.018 0.002 TYR B 219 ARG 0.007 0.000 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 3.189 Fit side-chains revert: symmetry clash REVERT: A 265 LEU cc_start: 0.9655 (tp) cc_final: 0.9452 (tp) REVERT: A 452 MET cc_start: 0.2048 (ttp) cc_final: 0.1733 (ptp) REVERT: B 171 LEU cc_start: 0.9523 (tp) cc_final: 0.9096 (pp) REVERT: B 943 MET cc_start: 0.8906 (tpt) cc_final: 0.8376 (tpt) REVERT: C 171 LEU cc_start: 0.9661 (tp) cc_final: 0.9049 (pp) REVERT: C 563 MET cc_start: 0.9201 (mmm) cc_final: 0.8673 (mmt) REVERT: C 569 MET cc_start: 0.9285 (pmm) cc_final: 0.8521 (pmm) REVERT: C 696 MET cc_start: 0.8083 (tpt) cc_final: 0.7693 (tpt) REVERT: C 757 MET cc_start: 0.8122 (tpt) cc_final: 0.7754 (tpp) REVERT: C 1169 ASN cc_start: 0.8567 (t0) cc_final: 0.8207 (t0) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.4114 time to fit residues: 51.2411 Evaluate side-chains 64 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 3.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 8.9990 chunk 330 optimal weight: 9.9990 chunk 201 optimal weight: 30.0000 chunk 156 optimal weight: 8.9990 chunk 229 optimal weight: 5.9990 chunk 346 optimal weight: 5.9990 chunk 319 optimal weight: 0.9990 chunk 276 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 213 optimal weight: 20.0000 chunk 169 optimal weight: 50.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 GLN ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN ** C 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28405 Z= 0.217 Angle : 0.584 11.811 38642 Z= 0.301 Chirality : 0.043 0.464 4477 Planarity : 0.004 0.053 4940 Dihedral : 6.807 111.361 4881 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 22.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.64 % Favored : 93.33 % Rotamer: Outliers : 0.03 % Allowed : 0.30 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.14), residues: 3462 helix: 1.39 (0.20), residues: 720 sheet: -0.79 (0.19), residues: 705 loop : -1.24 (0.14), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 535 HIS 0.006 0.001 HIS C 167 PHE 0.018 0.001 PHE C 850 TYR 0.018 0.002 TYR B 219 ARG 0.008 0.000 ARG B 505 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 2.923 Fit side-chains revert: symmetry clash REVERT: A 452 MET cc_start: 0.2189 (ttp) cc_final: 0.1865 (ptp) REVERT: A 757 MET cc_start: 0.8264 (mmm) cc_final: 0.8048 (tpp) REVERT: B 171 LEU cc_start: 0.9510 (tp) cc_final: 0.9098 (pp) REVERT: B 943 MET cc_start: 0.8851 (tpt) cc_final: 0.8371 (tpt) REVERT: C 171 LEU cc_start: 0.9651 (tp) cc_final: 0.8980 (pp) REVERT: C 452 MET cc_start: 0.8486 (pmm) cc_final: 0.8283 (pmm) REVERT: C 563 MET cc_start: 0.9215 (mmm) cc_final: 0.8694 (mmt) REVERT: C 569 MET cc_start: 0.9289 (pmm) cc_final: 0.8534 (pmm) REVERT: C 696 MET cc_start: 0.7932 (tpt) cc_final: 0.7490 (tpt) REVERT: C 913 MET cc_start: 0.9476 (ptp) cc_final: 0.9267 (ppp) REVERT: C 1169 ASN cc_start: 0.8579 (t0) cc_final: 0.8229 (t0) outliers start: 1 outliers final: 0 residues processed: 71 average time/residue: 0.3673 time to fit residues: 46.2065 Evaluate side-chains 62 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 219 optimal weight: 9.9990 chunk 294 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 254 optimal weight: 20.0000 chunk 40 optimal weight: 50.0000 chunk 76 optimal weight: 6.9990 chunk 276 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 283 optimal weight: 30.0000 chunk 35 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 GLN ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1097 GLN C1122 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.022098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2258 r_free = 0.2258 target = 0.013906 restraints weight = 581610.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2280 r_free = 0.2280 target = 0.014283 restraints weight = 372076.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2300 r_free = 0.2300 target = 0.014594 restraints weight = 277625.758| |-----------------------------------------------------------------------------| r_work (final): 0.2302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28405 Z= 0.270 Angle : 0.625 11.989 38642 Z= 0.325 Chirality : 0.043 0.469 4477 Planarity : 0.004 0.053 4940 Dihedral : 6.866 111.835 4881 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 26.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.51 % Favored : 92.46 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.14), residues: 3462 helix: 1.21 (0.20), residues: 738 sheet: -0.89 (0.19), residues: 712 loop : -1.26 (0.14), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 310 HIS 0.006 0.002 HIS B 264 PHE 0.020 0.002 PHE C 850 TYR 0.020 0.002 TYR B 219 ARG 0.011 0.001 ARG B 758 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3695.21 seconds wall clock time: 72 minutes 5.15 seconds (4325.15 seconds total)