Starting phenix.real_space_refine on Wed Feb 21 14:02:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a95_15270/02_2024/8a95_15270.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a95_15270/02_2024/8a95_15270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a95_15270/02_2024/8a95_15270.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a95_15270/02_2024/8a95_15270.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a95_15270/02_2024/8a95_15270.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a95_15270/02_2024/8a95_15270.pdb" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.064 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 135 5.16 5 C 19600 2.51 5 N 5065 2.21 5 O 6066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 30866 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 8292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8292 Classifications: {'peptide': 1062} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 55, 'TRANS': 1006} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 8289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8289 Classifications: {'peptide': 1062} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 55, 'TRANS': 1006} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 8221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1054, 8221 Classifications: {'peptide': 1054} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 54, 'TRANS': 999} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 943 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "O" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "S" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 943 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "P" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "T" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 943 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "Q" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 98} 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: "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: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Time building chain proxies: 16.30, per 1000 atoms: 0.53 Number of scatterers: 30866 At special positions: 0 Unit cell: (160.59, 167.66, 203.01, 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 135 16.00 O 6066 8.00 N 5065 7.00 C 19600 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.01 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.01 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.05 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.05 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 89 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 89 " distance=2.03 Simple disulfide: pdb=" SG CYS T 22 " - pdb=" SG CYS T 96 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 89 " 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=2, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " 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-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 717 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1098 " " NAG A1309 " - " ASN A1134 " " NAG A1310 " - " ASN A 149 " " NAG A1311 " - " ASN A 616 " " NAG A1312 " - " ASN A 165 " " NAG A1314 " - " ASN A 801 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B1098 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 61 " " NAG B1309 " - " ASN B 149 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B 234 " " NAG B1312 " - " ASN B 165 " " NAG B1313 " - " ASN B 603 " " NAG B1315 " - " ASN B 801 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C1134 " " NAG C1310 " - " ASN C 149 " " NAG C1313 " - " ASN C 61 " " NAG C1314 " - " ASN C 165 " " NAG C1315 " - " ASN C 234 " " NAG C1316 " - " ASN C 801 " " NAG G 1 " - " ASN A 61 " " NAG J 1 " - " ASN A 234 " " NAG K 1 " - " ASN B 17 " " NAG L 1 " - " ASN B 122 " " NAG M 1 " - " ASN C 17 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.84 Conformation dependent library (CDL) restraints added in 5.8 seconds 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7178 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 65 sheets defined 20.4% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.10 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.814A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.653A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.883A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.300A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 966 Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 372 removed outlier: 4.242A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 removed outlier: 4.294A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.618A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.549A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.026A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.751A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.507A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.671A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.273A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.163A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 479 through 483 removed outlier: 4.036A pdb=" N GLY C 482 " --> pdb=" O PRO C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.969A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.013A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.571A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.182A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'R' and resid 27 through 32 removed outlier: 3.982A pdb=" N THR R 31 " --> pdb=" O GLY R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 91 removed outlier: 3.928A pdb=" N THR R 91 " --> pdb=" O TYR R 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.893A pdb=" N THR S 91 " --> pdb=" O TYR S 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 33 removed outlier: 4.259A pdb=" N SER P 32 " --> pdb=" O VAL P 29 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR P 33 " --> pdb=" O SER P 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 29 through 33' Processing helix chain 'T' and resid 27 through 32 removed outlier: 4.115A pdb=" N THR T 31 " --> pdb=" O GLY T 27 " (cutoff:3.500A) Processing helix chain 'T' and resid 87 through 91 removed outlier: 3.946A pdb=" N THR T 91 " --> pdb=" O TYR T 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.942A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.376A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.878A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.903A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.664A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.580A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.452A pdb=" N ILE A 434 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.029A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.192A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 7.004A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.536A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.536A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.306A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.034A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.239A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.502A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.716A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.716A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.441A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.734A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.713A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.713A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.110A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.666A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.545A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.545A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.398A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.300A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.298A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 83 through 85 removed outlier: 12.707A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.117A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU C 141 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 9.711A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.740A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.481A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.870A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 660 removed outlier: 4.977A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.353A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.353A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.514A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF4, first strand: chain 'R' and resid 9 through 11 removed outlier: 3.689A pdb=" N THR R 120 " --> pdb=" O GLU R 10 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY R 49 " --> pdb=" O TRP R 36 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG R 50 " --> pdb=" O ASN R 59 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN R 59 " --> pdb=" O ARG R 50 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 9 through 11 removed outlier: 3.689A pdb=" N THR R 120 " --> pdb=" O GLU R 10 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR R 112 " --> pdb=" O ARG R 98 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'R' and resid 18 through 23 removed outlier: 3.577A pdb=" N VAL R 18 " --> pdb=" O LEU R 83 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'O' and resid 4 through 6 Processing sheet with id=AF8, first strand: chain 'O' and resid 45 through 49 removed outlier: 6.304A pdb=" N TRP O 36 " --> pdb=" O LEU O 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'O' and resid 64 through 65 Processing sheet with id=AG1, first strand: chain 'S' and resid 9 through 11 removed outlier: 3.950A pdb=" N THR S 120 " --> pdb=" O GLU S 10 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE S 34 " --> pdb=" O ARG S 50 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ARG S 50 " --> pdb=" O ILE S 34 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TRP S 36 " --> pdb=" O MET S 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'S' and resid 9 through 11 removed outlier: 3.950A pdb=" N THR S 120 " --> pdb=" O GLU S 10 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR S 112 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'S' and resid 18 through 23 removed outlier: 3.538A pdb=" N VAL S 18 " --> pdb=" O LEU S 83 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 45 through 47 Processing sheet with id=AG5, first strand: chain 'P' and resid 63 through 65 Processing sheet with id=AG6, first strand: chain 'P' and resid 90 through 91 Processing sheet with id=AG7, first strand: chain 'T' and resid 10 through 11 removed outlier: 4.153A pdb=" N THR T 120 " --> pdb=" O GLU T 10 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY T 49 " --> pdb=" O TRP T 36 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN T 59 " --> pdb=" O ARG T 50 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'T' and resid 18 through 23 removed outlier: 3.613A pdb=" N VAL T 18 " --> pdb=" O LEU T 83 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET T 81 " --> pdb=" O VAL T 20 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Q' and resid 4 through 6 Processing sheet with id=AH1, first strand: chain 'Q' and resid 45 through 51 removed outlier: 6.207A pdb=" N TRP Q 36 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TYR Q 50 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU Q 34 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL Q 86 " --> pdb=" O GLN Q 39 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Q' and resid 63 through 65 1207 hydrogen bonds defined for protein. 3288 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: 15.97 Time building geometry restraints manager: 13.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.34: 9444 1.34 - 1.51: 11660 1.51 - 1.69: 10279 1.69 - 1.86: 178 1.86 - 2.04: 1 Bond restraints: 31562 Sorted by residual: bond pdb=" CD2 PHE A 377 " pdb=" CE2 PHE A 377 " ideal model delta sigma weight residual 1.382 2.035 -0.653 3.00e-02 1.11e+03 4.74e+02 bond pdb=" C LEU A 368 " pdb=" N TYR A 369 " ideal model delta sigma weight residual 1.333 1.586 -0.253 1.41e-02 5.03e+03 3.21e+02 bond pdb=" C1 NAG A1313 " pdb=" O5 NAG A1313 " ideal model delta sigma weight residual 1.406 1.748 -0.342 2.00e-02 2.50e+03 2.92e+02 bond pdb=" N TYR A 369 " pdb=" CA TYR A 369 " ideal model delta sigma weight residual 1.460 1.653 -0.193 1.27e-02 6.20e+03 2.30e+02 bond pdb=" CA TYR A 369 " pdb=" C TYR A 369 " ideal model delta sigma weight residual 1.520 1.693 -0.173 1.37e-02 5.33e+03 1.59e+02 ... (remaining 31557 not shown) Histogram of bond angle deviations from ideal: 74.98 - 92.04: 2 92.04 - 109.09: 3060 109.09 - 126.14: 39389 126.14 - 143.20: 483 143.20 - 160.25: 4 Bond angle restraints: 42938 Sorted by residual: angle pdb=" C TYR A 369 " pdb=" CA TYR A 369 " pdb=" CB TYR A 369 " ideal model delta sigma weight residual 109.16 74.98 34.18 1.29e+00 6.01e-01 7.02e+02 angle pdb=" C LEU A 368 " pdb=" N TYR A 369 " pdb=" CA TYR A 369 " ideal model delta sigma weight residual 121.52 160.25 -38.73 1.74e+00 3.30e-01 4.95e+02 angle pdb=" CA TYR A 369 " pdb=" CB TYR A 369 " pdb=" CG TYR A 369 " ideal model delta sigma weight residual 113.90 145.21 -31.31 1.80e+00 3.09e-01 3.03e+02 angle pdb=" CD2 PHE A 377 " pdb=" CE2 PHE A 377 " pdb=" CZ PHE A 377 " ideal model delta sigma weight residual 120.00 89.06 30.94 1.80e+00 3.09e-01 2.96e+02 angle pdb=" CG PHE A 377 " pdb=" CD2 PHE A 377 " pdb=" CE2 PHE A 377 " ideal model delta sigma weight residual 120.70 143.76 -23.06 1.70e+00 3.46e-01 1.84e+02 ... (remaining 42933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.59: 18390 24.59 - 49.18: 932 49.18 - 73.77: 111 73.77 - 98.36: 48 98.36 - 122.94: 13 Dihedral angle restraints: 19494 sinusoidal: 8290 harmonic: 11204 Sorted by residual: dihedral pdb=" C TYR A 369 " pdb=" N TYR A 369 " pdb=" CA TYR A 369 " pdb=" CB TYR A 369 " ideal model delta harmonic sigma weight residual -122.60 -91.91 -30.69 0 2.50e+00 1.60e-01 1.51e+02 dihedral pdb=" C VAL A 367 " pdb=" N VAL A 367 " pdb=" CA VAL A 367 " pdb=" CB VAL A 367 " ideal model delta harmonic sigma weight residual -122.00 -141.06 19.06 0 2.50e+00 1.60e-01 5.81e+01 dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual -86.00 -150.26 64.26 1 1.00e+01 1.00e-02 5.43e+01 ... (remaining 19491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.348: 4948 0.348 - 0.696: 30 0.696 - 1.044: 6 1.044 - 1.392: 2 1.392 - 1.740: 1 Chirality restraints: 4987 Sorted by residual: chirality pdb=" C1 NAG C1315 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C1315 " pdb=" O5 NAG C1315 " both_signs ideal model delta sigma weight residual False -2.40 -0.66 -1.74 2.00e-01 2.50e+01 7.57e+01 chirality pdb=" C4 NAG A1313 " pdb=" C3 NAG A1313 " pdb=" C5 NAG A1313 " pdb=" O4 NAG A1313 " both_signs ideal model delta sigma weight residual False -2.53 -1.24 -1.29 2.00e-01 2.50e+01 4.19e+01 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.22 -1.18 2.00e-01 2.50e+01 3.48e+01 ... (remaining 4984 not shown) Planarity restraints: 5531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 377 " -0.180 2.00e-02 2.50e+03 1.69e-01 5.00e+02 pdb=" CG PHE A 377 " 0.210 2.00e-02 2.50e+03 pdb=" CD1 PHE A 377 " -0.154 2.00e-02 2.50e+03 pdb=" CD2 PHE A 377 " 0.254 2.00e-02 2.50e+03 pdb=" CE1 PHE A 377 " 0.072 2.00e-02 2.50e+03 pdb=" CE2 PHE A 377 " -0.170 2.00e-02 2.50e+03 pdb=" CZ PHE A 377 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 108 " -0.041 2.00e-02 2.50e+03 6.85e-02 9.37e+01 pdb=" CG TYR S 108 " 0.164 2.00e-02 2.50e+03 pdb=" CD1 TYR S 108 " -0.069 2.00e-02 2.50e+03 pdb=" CD2 TYR S 108 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR S 108 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR S 108 " -0.032 2.00e-02 2.50e+03 pdb=" CZ TYR S 108 " -0.026 2.00e-02 2.50e+03 pdb=" OH TYR S 108 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 367 " 0.038 2.00e-02 2.50e+03 7.41e-02 5.49e+01 pdb=" C VAL A 367 " -0.128 2.00e-02 2.50e+03 pdb=" O VAL A 367 " 0.049 2.00e-02 2.50e+03 pdb=" N LEU A 368 " 0.042 2.00e-02 2.50e+03 ... (remaining 5528 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 340 2.61 - 3.19: 25350 3.19 - 3.76: 48401 3.76 - 4.33: 66277 4.33 - 4.90: 110519 Nonbonded interactions: 250887 Sorted by model distance: nonbonded pdb=" CE2 PHE A 377 " pdb=" O7 NAG A1313 " model vdw 2.042 2.672 nonbonded pdb=" OG1 THR R 120 " pdb=" O SER R 122 " model vdw 2.191 2.440 nonbonded pdb=" OG1 THR S 120 " pdb=" O SER S 122 " model vdw 2.195 2.440 nonbonded pdb=" OG1 THR T 120 " pdb=" O SER T 122 " model vdw 2.208 2.440 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.242 2.440 ... (remaining 250882 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 14 through 68 or resid 76 through 531 or (resid 532 throug \ h 533 and (name N or name CA or name C or name O or name CB )) or resid 534 thro \ ugh 577 or resid 584 through 1146 or resid 1301 through 1314)) selection = (chain 'B' and (resid 14 through 68 or resid 76 through 532 or (resid 533 and (n \ ame N or name CA or name C or name O or name CB )) or resid 534 through 577 or r \ esid 584 through 1146 or resid 1301 through 1314)) selection = (chain 'C' and (resid 14 through 1146 or resid 1301 through 1314)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.460 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: 0.000 Extract box with map and model: 28.500 Check model and map are aligned: 0.480 Set scattering table: 0.300 Process input model: 87.600 Find NCS groups from input model: 2.520 Set up NCS constraints: 0.320 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:11.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5162 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 : 0.010 0.653 31562 Z= 0.671 Angle : 1.303 38.729 42938 Z= 0.708 Chirality : 0.092 1.740 4987 Planarity : 0.009 0.169 5485 Dihedral : 14.676 122.945 12190 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.38 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.25 % 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: -0.39 (0.14), residues: 3812 helix: 2.31 (0.20), residues: 675 sheet: 0.09 (0.17), residues: 906 loop : -1.28 (0.13), residues: 2231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP C 886 HIS 0.027 0.002 HIS C 66 PHE 0.254 0.005 PHE A 377 TYR 0.164 0.004 TYR S 108 ARG 0.039 0.002 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 3.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: -0.0382 (mtt) cc_final: -0.1307 (mpp) REVERT: Q 87 TYR cc_start: 0.5786 (m-80) cc_final: 0.5189 (m-10) REVERT: Q 97 ARG cc_start: 0.4468 (mtp180) cc_final: 0.4177 (mmt180) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 1.5427 time to fit residues: 482.3855 Evaluate side-chains 128 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 3.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 323 optimal weight: 10.0000 chunk 290 optimal weight: 4.9990 chunk 161 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 195 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 300 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 223 optimal weight: 1.9990 chunk 347 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 955 ASN B1005 GLN B1011 GLN B1071 GLN C 146 HIS C 394 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C1002 GLN R 59 ASN S 6 GLN ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 39 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5343 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.209 31562 Z= 0.271 Angle : 0.759 26.597 42938 Z= 0.375 Chirality : 0.054 0.848 4987 Planarity : 0.005 0.082 5485 Dihedral : 9.899 106.530 5409 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.12 % Favored : 95.83 % Rotamer: Outliers : 1.05 % Allowed : 8.19 % Favored : 90.76 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.14), residues: 3812 helix: 2.26 (0.20), residues: 689 sheet: 0.20 (0.17), residues: 862 loop : -1.18 (0.13), residues: 2261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP Q 36 HIS 0.007 0.001 HIS C 519 PHE 0.076 0.002 PHE A 377 TYR 0.052 0.002 TYR S 108 ARG 0.008 0.001 ARG C 995 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 135 time to evaluate : 3.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: -0.0672 (mtt) cc_final: -0.1897 (mpp) REVERT: R 54 MET cc_start: 0.4521 (OUTLIER) cc_final: 0.4273 (pmm) outliers start: 35 outliers final: 9 residues processed: 153 average time/residue: 1.4832 time to fit residues: 268.4520 Evaluate side-chains 121 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 3.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 54 MET Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain Q residue 49 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 193 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 289 optimal weight: 0.0570 chunk 236 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 348 optimal weight: 9.9990 chunk 376 optimal weight: 40.0000 chunk 310 optimal weight: 2.9990 chunk 345 optimal weight: 20.0000 chunk 118 optimal weight: 10.0000 chunk 279 optimal weight: 3.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 360 ASN B 388 ASN B 540 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN P 39 GLN P 43 GLN ** T 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5720 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.218 31562 Z= 0.401 Angle : 0.811 21.594 42938 Z= 0.413 Chirality : 0.056 1.142 4987 Planarity : 0.005 0.070 5485 Dihedral : 8.223 94.134 5409 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.72 % Favored : 94.23 % Rotamer: Outliers : 2.56 % Allowed : 10.72 % Favored : 86.72 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.13), residues: 3812 helix: 1.95 (0.20), residues: 685 sheet: -0.28 (0.17), residues: 854 loop : -1.34 (0.12), residues: 2273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP T 47 HIS 0.005 0.001 HIS C 146 PHE 0.100 0.003 PHE A 374 TYR 0.038 0.003 TYR R 109 ARG 0.015 0.001 ARG Q 97 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 122 time to evaluate : 3.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 166 CYS cc_start: 0.4403 (OUTLIER) cc_final: 0.3474 (m) REVERT: C 177 MET cc_start: -0.0494 (mtt) cc_final: -0.1702 (mpt) REVERT: R 54 MET cc_start: 0.4498 (mpp) cc_final: 0.4159 (pmm) REVERT: T 30 ASN cc_start: 0.8198 (OUTLIER) cc_final: 0.7737 (p0) REVERT: T 91 THR cc_start: 0.7105 (p) cc_final: 0.6544 (t) REVERT: Q 2 ILE cc_start: 0.1605 (OUTLIER) cc_final: 0.0929 (tt) REVERT: Q 11 LEU cc_start: 0.6465 (OUTLIER) cc_final: 0.6146 (pt) outliers start: 85 outliers final: 29 residues processed: 186 average time/residue: 1.2582 time to fit residues: 286.2331 Evaluate side-chains 135 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 102 time to evaluate : 3.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 30 ASN Chi-restraints excluded: chain T residue 38 ARG Chi-restraints excluded: chain T residue 50 ARG Chi-restraints excluded: chain Q residue 2 ILE Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 90 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 344 optimal weight: 20.0000 chunk 261 optimal weight: 0.7980 chunk 180 optimal weight: 0.1980 chunk 38 optimal weight: 10.0000 chunk 166 optimal weight: 2.9990 chunk 233 optimal weight: 0.6980 chunk 349 optimal weight: 5.9990 chunk 370 optimal weight: 9.9990 chunk 182 optimal weight: 0.6980 chunk 331 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN C 52 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 606 ASN C 613 GLN C 755 GLN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5640 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 31562 Z= 0.191 Angle : 0.652 16.430 42938 Z= 0.322 Chirality : 0.049 0.508 4987 Planarity : 0.004 0.074 5485 Dihedral : 7.377 83.595 5409 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.49 % Favored : 95.49 % Rotamer: Outliers : 1.63 % Allowed : 12.76 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.13), residues: 3812 helix: 2.32 (0.20), residues: 678 sheet: -0.18 (0.17), residues: 863 loop : -1.30 (0.12), residues: 2271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP S 36 HIS 0.003 0.001 HIS B 66 PHE 0.036 0.001 PHE C 456 TYR 0.025 0.001 TYR A 369 ARG 0.015 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 116 time to evaluate : 3.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: -0.0732 (mtt) cc_final: -0.1843 (mpt) REVERT: R 51 ILE cc_start: 0.2688 (OUTLIER) cc_final: 0.2460 (mt) REVERT: R 54 MET cc_start: 0.4613 (OUTLIER) cc_final: 0.4411 (pmm) REVERT: Q 92 TYR cc_start: 0.5552 (OUTLIER) cc_final: 0.4790 (m-80) outliers start: 54 outliers final: 14 residues processed: 149 average time/residue: 1.3972 time to fit residues: 250.5684 Evaluate side-chains 120 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 3.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 54 MET Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 50 ARG Chi-restraints excluded: chain Q residue 92 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 308 optimal weight: 0.6980 chunk 210 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 275 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 315 optimal weight: 5.9990 chunk 255 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 2.9990 chunk 332 optimal weight: 40.0000 chunk 93 optimal weight: 5.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 957 GLN A1088 HIS B 87 ASN C 146 HIS ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5954 moved from start: 0.5968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 31562 Z= 0.465 Angle : 0.836 14.834 42938 Z= 0.424 Chirality : 0.053 0.492 4987 Planarity : 0.006 0.075 5485 Dihedral : 7.448 60.853 5409 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.74 % Favored : 93.21 % Rotamer: Outliers : 2.35 % Allowed : 13.73 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.13), residues: 3812 helix: 1.79 (0.20), residues: 675 sheet: -0.59 (0.16), residues: 885 loop : -1.41 (0.12), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP S 36 HIS 0.005 0.001 HIS B 66 PHE 0.031 0.003 PHE C 106 TYR 0.073 0.003 TYR A 369 ARG 0.013 0.001 ARG R 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 112 time to evaluate : 3.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 51 ILE cc_start: 0.2946 (OUTLIER) cc_final: 0.2591 (mt) REVERT: R 54 MET cc_start: 0.4905 (OUTLIER) cc_final: 0.4547 (pmm) REVERT: Q 91 GLN cc_start: 0.4686 (pm20) cc_final: 0.4366 (pm20) REVERT: Q 92 TYR cc_start: 0.5916 (OUTLIER) cc_final: 0.5171 (m-80) outliers start: 78 outliers final: 28 residues processed: 174 average time/residue: 1.2487 time to fit residues: 265.2150 Evaluate side-chains 126 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 95 time to evaluate : 3.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 54 MET Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 55 PHE Chi-restraints excluded: chain Q residue 92 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 124 optimal weight: 4.9990 chunk 333 optimal weight: 20.0000 chunk 73 optimal weight: 0.0870 chunk 217 optimal weight: 8.9990 chunk 91 optimal weight: 0.6980 chunk 370 optimal weight: 6.9990 chunk 307 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 122 optimal weight: 0.0470 chunk 194 optimal weight: 0.9990 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 188 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN C 121 ASN C 239 GLN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN C 953 ASN P 94 ASN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5835 moved from start: 0.5976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 31562 Z= 0.184 Angle : 0.678 15.900 42938 Z= 0.332 Chirality : 0.050 0.504 4987 Planarity : 0.004 0.075 5485 Dihedral : 6.808 57.523 5409 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.46 % Favored : 95.51 % Rotamer: Outliers : 1.93 % Allowed : 14.60 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.13), residues: 3812 helix: 2.31 (0.20), residues: 675 sheet: -0.44 (0.17), residues: 861 loop : -1.35 (0.12), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Q 36 HIS 0.004 0.001 HIS B 66 PHE 0.036 0.002 PHE A 374 TYR 0.061 0.002 TYR A 369 ARG 0.006 0.001 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 104 time to evaluate : 3.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 166 CYS cc_start: 0.4744 (OUTLIER) cc_final: 0.3464 (m) REVERT: R 51 ILE cc_start: 0.2755 (OUTLIER) cc_final: 0.2459 (mt) REVERT: R 54 MET cc_start: 0.4714 (OUTLIER) cc_final: 0.4466 (pmm) REVERT: P 78 ARG cc_start: 0.8578 (tpm170) cc_final: 0.8369 (tpm170) REVERT: T 51 ILE cc_start: 0.5347 (OUTLIER) cc_final: 0.5054 (pp) REVERT: Q 11 LEU cc_start: 0.6530 (OUTLIER) cc_final: 0.6210 (pt) REVERT: Q 92 TYR cc_start: 0.5970 (OUTLIER) cc_final: 0.5225 (m-80) outliers start: 64 outliers final: 23 residues processed: 157 average time/residue: 1.2667 time to fit residues: 243.8703 Evaluate side-chains 127 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 98 time to evaluate : 3.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 54 MET Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 51 ILE Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 92 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 357 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 211 optimal weight: 0.9980 chunk 270 optimal weight: 3.9990 chunk 209 optimal weight: 0.9990 chunk 311 optimal weight: 5.9990 chunk 206 optimal weight: 0.8980 chunk 369 optimal weight: 20.0000 chunk 231 optimal weight: 7.9990 chunk 225 optimal weight: 7.9990 chunk 170 optimal weight: 6.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN C 49 HIS C 239 GLN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C 777 ASN C 949 GLN C 953 ASN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5971 moved from start: 0.6666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 31562 Z= 0.359 Angle : 0.733 15.378 42938 Z= 0.364 Chirality : 0.050 0.521 4987 Planarity : 0.005 0.091 5485 Dihedral : 6.718 57.888 5409 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.43 % Favored : 93.55 % Rotamer: Outliers : 1.93 % Allowed : 15.38 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.13), residues: 3812 helix: 2.28 (0.20), residues: 670 sheet: -0.59 (0.16), residues: 882 loop : -1.37 (0.13), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP S 47 HIS 0.004 0.001 HIS C 49 PHE 0.049 0.002 PHE P 72 TYR 0.037 0.002 TYR A 369 ARG 0.007 0.001 ARG P 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 97 time to evaluate : 3.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.0438 (mpt) cc_final: -0.0688 (mpt) REVERT: A 472 ILE cc_start: 0.1091 (OUTLIER) cc_final: 0.0712 (tt) REVERT: B 166 CYS cc_start: 0.4844 (OUTLIER) cc_final: 0.3516 (m) REVERT: C 177 MET cc_start: 0.0296 (mpt) cc_final: 0.0065 (mpp) REVERT: R 51 ILE cc_start: 0.2718 (OUTLIER) cc_final: 0.2400 (mt) REVERT: R 54 MET cc_start: 0.4873 (OUTLIER) cc_final: 0.4581 (pmm) REVERT: P 78 ARG cc_start: 0.8572 (tpm170) cc_final: 0.8337 (tpm170) REVERT: Q 11 LEU cc_start: 0.6538 (OUTLIER) cc_final: 0.5949 (pt) REVERT: Q 92 TYR cc_start: 0.5902 (OUTLIER) cc_final: 0.5331 (m-80) outliers start: 64 outliers final: 29 residues processed: 152 average time/residue: 1.2572 time to fit residues: 235.7308 Evaluate side-chains 126 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 91 time to evaluate : 3.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 54 MET Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain P residue 13 LEU Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 69 THR Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 92 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 228 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 220 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 234 optimal weight: 20.0000 chunk 251 optimal weight: 20.0000 chunk 182 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 290 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN B 544 ASN C 239 GLN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN C 953 ASN C1002 GLN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5958 moved from start: 0.6976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31562 Z= 0.274 Angle : 0.678 14.709 42938 Z= 0.336 Chirality : 0.049 0.508 4987 Planarity : 0.004 0.052 5485 Dihedral : 6.537 59.380 5409 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.33 % Favored : 94.65 % Rotamer: Outliers : 1.69 % Allowed : 15.77 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.13), residues: 3812 helix: 2.46 (0.20), residues: 667 sheet: -0.59 (0.16), residues: 889 loop : -1.38 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 104 HIS 0.004 0.001 HIS B 66 PHE 0.040 0.002 PHE A 374 TYR 0.031 0.002 TYR A 369 ARG 0.004 0.000 ARG T 50 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 98 time to evaluate : 3.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 472 ILE cc_start: 0.1152 (OUTLIER) cc_final: 0.0782 (tt) REVERT: B 166 CYS cc_start: 0.4489 (OUTLIER) cc_final: 0.3160 (m) REVERT: C 177 MET cc_start: 0.0399 (mpt) cc_final: 0.0087 (mpp) REVERT: R 51 ILE cc_start: 0.2675 (OUTLIER) cc_final: 0.2343 (mt) REVERT: R 54 MET cc_start: 0.5124 (OUTLIER) cc_final: 0.4832 (pmm) REVERT: P 78 ARG cc_start: 0.8637 (tpm170) cc_final: 0.8421 (tpm170) REVERT: T 51 ILE cc_start: 0.5318 (OUTLIER) cc_final: 0.4990 (pp) REVERT: Q 11 LEU cc_start: 0.6451 (OUTLIER) cc_final: 0.6087 (pt) REVERT: Q 92 TYR cc_start: 0.5970 (OUTLIER) cc_final: 0.5380 (m-80) outliers start: 56 outliers final: 29 residues processed: 141 average time/residue: 1.2346 time to fit residues: 214.7413 Evaluate side-chains 128 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 92 time to evaluate : 3.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 54 MET Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 51 ILE Chi-restraints excluded: chain T residue 69 THR Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 92 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 335 optimal weight: 10.0000 chunk 353 optimal weight: 8.9990 chunk 322 optimal weight: 9.9990 chunk 344 optimal weight: 0.0370 chunk 207 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 270 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 310 optimal weight: 4.9990 chunk 325 optimal weight: 0.6980 chunk 342 optimal weight: 6.9990 overall best weight: 2.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN C 196 ASN C 544 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN ** T 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 0.7570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 31562 Z= 0.359 Angle : 0.740 16.454 42938 Z= 0.370 Chirality : 0.050 0.517 4987 Planarity : 0.005 0.054 5485 Dihedral : 6.558 57.575 5409 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.87 % Favored : 93.10 % Rotamer: Outliers : 1.48 % Allowed : 16.16 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.13), residues: 3812 helix: 2.40 (0.20), residues: 667 sheet: -0.70 (0.17), residues: 885 loop : -1.39 (0.13), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP S 36 HIS 0.004 0.001 HIS B 66 PHE 0.035 0.002 PHE A 374 TYR 0.061 0.002 TYR A 369 ARG 0.014 0.001 ARG R 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 101 time to evaluate : 3.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 472 ILE cc_start: 0.1112 (OUTLIER) cc_final: 0.0750 (tt) REVERT: B 166 CYS cc_start: 0.4767 (OUTLIER) cc_final: 0.3581 (m) REVERT: C 269 TYR cc_start: 0.4770 (OUTLIER) cc_final: 0.3407 (m-80) REVERT: R 51 ILE cc_start: 0.2809 (OUTLIER) cc_final: 0.2499 (mt) REVERT: R 54 MET cc_start: 0.5205 (OUTLIER) cc_final: 0.4872 (pmm) REVERT: T 115 GLN cc_start: 0.7879 (mp10) cc_final: 0.7553 (mp10) REVERT: Q 11 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6329 (pt) REVERT: Q 92 TYR cc_start: 0.6154 (OUTLIER) cc_final: 0.5626 (m-10) outliers start: 49 outliers final: 29 residues processed: 140 average time/residue: 1.2101 time to fit residues: 211.3958 Evaluate side-chains 129 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 93 time to evaluate : 3.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 54 MET Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 69 THR Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 92 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 225 optimal weight: 5.9990 chunk 363 optimal weight: 30.0000 chunk 222 optimal weight: 10.0000 chunk 172 optimal weight: 0.4980 chunk 252 optimal weight: 5.9990 chunk 381 optimal weight: 5.9990 chunk 351 optimal weight: 8.9990 chunk 303 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 chunk 234 optimal weight: 6.9990 chunk 186 optimal weight: 0.7980 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN ** T 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 62 GLN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6087 moved from start: 0.8269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 31562 Z= 0.399 Angle : 0.758 16.014 42938 Z= 0.381 Chirality : 0.051 0.505 4987 Planarity : 0.005 0.116 5485 Dihedral : 6.697 56.613 5409 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.82 % Favored : 94.07 % Rotamer: Outliers : 1.48 % Allowed : 16.29 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.88 (0.13), residues: 3812 helix: 2.23 (0.20), residues: 674 sheet: -0.75 (0.17), residues: 869 loop : -1.46 (0.12), residues: 2269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 104 HIS 0.020 0.001 HIS C 66 PHE 0.037 0.002 PHE C 490 TYR 0.077 0.002 TYR A 369 ARG 0.013 0.001 ARG R 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 97 time to evaluate : 3.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.0121 (mpt) cc_final: -0.0188 (mpt) REVERT: A 472 ILE cc_start: 0.1324 (OUTLIER) cc_final: 0.0908 (tt) REVERT: B 166 CYS cc_start: 0.4679 (OUTLIER) cc_final: 0.3424 (m) REVERT: C 269 TYR cc_start: 0.5173 (OUTLIER) cc_final: 0.3749 (m-80) REVERT: R 51 ILE cc_start: 0.2978 (OUTLIER) cc_final: 0.2645 (mt) REVERT: R 54 MET cc_start: 0.5509 (OUTLIER) cc_final: 0.5131 (pmm) REVERT: Q 11 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.5941 (pt) REVERT: Q 37 TYR cc_start: 0.3742 (m-80) cc_final: 0.3506 (m-80) REVERT: Q 92 TYR cc_start: 0.6203 (OUTLIER) cc_final: 0.5648 (m-80) outliers start: 49 outliers final: 25 residues processed: 134 average time/residue: 1.2163 time to fit residues: 202.6475 Evaluate side-chains 123 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 91 time to evaluate : 3.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 54 MET Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 92 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 241 optimal weight: 0.0980 chunk 323 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 280 optimal weight: 1.9990 chunk 44 optimal weight: 0.0370 chunk 84 optimal weight: 1.9990 chunk 304 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 312 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 overall best weight: 1.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.070689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.043762 restraints weight = 228930.339| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 8.35 r_work: 0.3173 rms_B_bonded: 7.43 restraints_weight: 2.0000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.8285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31562 Z= 0.217 Angle : 0.697 14.965 42938 Z= 0.346 Chirality : 0.049 0.499 4987 Planarity : 0.005 0.133 5485 Dihedral : 6.442 56.313 5409 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.82 % Favored : 94.12 % Rotamer: Outliers : 1.11 % Allowed : 16.74 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.74 (0.13), residues: 3812 helix: 2.43 (0.20), residues: 680 sheet: -0.66 (0.17), residues: 840 loop : -1.40 (0.13), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 104 HIS 0.005 0.001 HIS A 519 PHE 0.099 0.002 PHE C 490 TYR 0.088 0.001 TYR A 369 ARG 0.009 0.001 ARG R 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9776.60 seconds wall clock time: 177 minutes 49.51 seconds (10669.51 seconds total)