Starting phenix.real_space_refine on Mon Feb 19 23:25:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vrv_32107/02_2024/7vrv_32107.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vrv_32107/02_2024/7vrv_32107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vrv_32107/02_2024/7vrv_32107.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vrv_32107/02_2024/7vrv_32107.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vrv_32107/02_2024/7vrv_32107.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vrv_32107/02_2024/7vrv_32107.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 16623 2.51 5 N 4277 2.21 5 O 5137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A TYR 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 741": "OE1" <-> "OE2" Residue "A ASP 789": "OD1" <-> "OD2" Residue "A ASP 929": "OD1" <-> "OD2" Residue "A GLU 1024": "OE1" <-> "OE2" Residue "A PHE 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 861": "OE1" <-> "OE2" Residue "B PHE 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 981": "OE1" <-> "OE2" Residue "B GLU 1024": "OE1" <-> "OE2" Residue "B TYR 1060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1065": "OE1" <-> "OE2" Residue "B ASP 1111": "OD1" <-> "OD2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 749": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 812": "OE1" <-> "OE2" Residue "C GLU 911": "OE1" <-> "OE2" Residue "C TYR 1040": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1111": "OD1" <-> "OD2" Residue "C GLU 1137": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26151 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 8457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8457 Classifications: {'peptide': 1087} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 53, 'TRANS': 1033} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 8485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1091, 8485 Classifications: {'peptide': 1091} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 54, 'TRANS': 1036} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 8411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8411 Classifications: {'peptide': 1079} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 52, 'TRANS': 1026} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 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: "O" 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 13.22, per 1000 atoms: 0.51 Number of scatterers: 26151 At special positions: 0 Unit cell: (154.96, 160.16, 193.44, 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 114 16.00 O 5137 8.00 N 4277 7.00 C 16623 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 731 " - pdb=" SG CYS A 753 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A1025 " - pdb=" SG CYS A1036 " distance=2.03 Simple disulfide: pdb=" SG CYS A1075 " - pdb=" SG CYS A1119 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.02 Simple disulfide: pdb=" SG CYS B 731 " - pdb=" SG CYS B 753 " distance=2.04 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B1025 " - pdb=" SG CYS B1036 " distance=2.03 Simple disulfide: pdb=" SG CYS B1075 " - pdb=" SG CYS B1119 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 731 " - pdb=" SG CYS C 753 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C1025 " - pdb=" SG CYS C1036 " distance=2.03 Simple disulfide: pdb=" SG CYS C1075 " - pdb=" SG CYS C1119 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 702 " " NAG A1310 " - " ASN A1067 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 702 " " NAG B1309 " - " ASN B 710 " " NAG B1310 " - " ASN B1067 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 702 " " NAG C1310 " - " ASN C1067 " " NAG C1311 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 710 " " NAG F 1 " - " ASN A 794 " " NAG G 1 " - " ASN A1091 " " NAG H 1 " - " ASN A1127 " " NAG I 1 " - " ASN B 282 " " NAG J 1 " - " ASN B 794 " " NAG K 1 " - " ASN B1091 " " NAG L 1 " - " ASN B1127 " " NAG M 1 " - " ASN C 710 " " NAG N 1 " - " ASN C 794 " " NAG O 1 " - " ASN C1091 " " NAG P 1 " - " ASN C1127 " Time building additional restraints: 11.07 Conformation dependent library (CDL) restraints added in 4.9 seconds 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6090 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 44 sheets defined 23.4% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.31 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.722A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.898A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 removed outlier: 4.387A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.576A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 removed outlier: 4.298A pdb=" N ILE A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 736 Processing helix chain 'A' and resid 739 through 750 Processing helix chain 'A' and resid 751 through 776 removed outlier: 3.869A pdb=" N PHE A 775 " --> pdb=" O THR A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 819 removed outlier: 3.896A pdb=" N LEU A 814 " --> pdb=" O PHE A 810 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 815 " --> pdb=" O ILE A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 removed outlier: 3.673A pdb=" N PHE A 848 " --> pdb=" O CYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 878 Processing helix chain 'A' and resid 879 through 884 Processing helix chain 'A' and resid 890 through 902 Processing helix chain 'A' and resid 905 through 911 removed outlier: 3.973A pdb=" N LEU A 909 " --> pdb=" O THR A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 934 removed outlier: 3.657A pdb=" N THR A 934 " --> pdb=" O SER A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 959 removed outlier: 4.102A pdb=" N GLN A 942 " --> pdb=" O LEU A 938 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 959 " --> pdb=" O LEU A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 977 removed outlier: 3.828A pdb=" N SER A 975 " --> pdb=" O ASN A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 1025 removed outlier: 3.673A pdb=" N VAL A 984 " --> pdb=" O PRO A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1113 Processing helix chain 'A' and resid 1134 through 1140 removed outlier: 3.839A pdb=" N SER A1140 " --> pdb=" O PRO A1136 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.641A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.913A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 730 through 736 removed outlier: 3.786A pdb=" N TYR B 734 " --> pdb=" O ASP B 730 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE B 735 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 749 removed outlier: 3.733A pdb=" N ASN B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR B 749 " --> pdb=" O LEU B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 775 removed outlier: 3.716A pdb=" N PHE B 775 " --> pdb=" O THR B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 819 removed outlier: 3.535A pdb=" N LEU B 814 " --> pdb=" O PHE B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 removed outlier: 3.715A pdb=" N LYS B 847 " --> pdb=" O ILE B 843 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE B 848 " --> pdb=" O CYS B 844 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 843 through 848' Processing helix chain 'B' and resid 859 through 876 Processing helix chain 'B' and resid 879 through 883 removed outlier: 3.900A pdb=" N GLY B 882 " --> pdb=" O TRP B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 903 Processing helix chain 'B' and resid 906 through 912 removed outlier: 3.712A pdb=" N TYR B 910 " --> pdb=" O GLN B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 934 removed outlier: 4.020A pdb=" N THR B 934 " --> pdb=" O SER B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 958 Processing helix chain 'B' and resid 959 through 961 No H-bonds generated for 'chain 'B' and resid 959 through 961' Processing helix chain 'B' and resid 969 through 977 Processing helix chain 'B' and resid 978 through 1026 removed outlier: 4.859A pdb=" N VAL B 984 " --> pdb=" O PRO B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1133 through 1140 removed outlier: 3.987A pdb=" N GLU B1137 " --> pdb=" O PRO B1133 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER B1140 " --> pdb=" O PRO B1136 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.689A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 739 through 749 Processing helix chain 'C' and resid 751 through 776 Processing helix chain 'C' and resid 809 through 818 removed outlier: 4.124A pdb=" N ASN C 817 " --> pdb=" O ASP C 813 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS C 818 " --> pdb=" O LEU C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 877 Processing helix chain 'C' and resid 879 through 884 removed outlier: 4.091A pdb=" N ALA C 883 " --> pdb=" O TRP C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 890 through 903 Processing helix chain 'C' and resid 905 through 934 removed outlier: 4.347A pdb=" N LEU C 909 " --> pdb=" O THR C 905 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS C 914 " --> pdb=" O TYR C 910 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU C 915 " --> pdb=" O GLU C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 958 removed outlier: 4.100A pdb=" N GLN C 942 " --> pdb=" O LEU C 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 977 removed outlier: 3.534A pdb=" N ILE C 973 " --> pdb=" O VAL C 969 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG C 976 " --> pdb=" O ASP C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 1025 removed outlier: 4.701A pdb=" N VAL C 984 " --> pdb=" O PRO C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 1134 through 1139 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 8.521A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR A 266 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY A 89 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.642A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 104 removed outlier: 4.270A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 120 Processing sheet with id=AA6, first strand: chain 'A' and resid 142 through 145 removed outlier: 5.666A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 314 through 317 removed outlier: 6.406A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 595 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 327 through 328 removed outlier: 3.823A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.930A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 376 through 378 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB3, first strand: chain 'A' and resid 551 through 553 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.627A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 695 through 697 Processing sheet with id=AB6, first strand: chain 'A' and resid 704 through 720 removed outlier: 6.825A pdb=" N SER A 704 " --> pdb=" O THR A1069 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N THR A1069 " --> pdb=" O SER A 704 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA A 706 " --> pdb=" O ASN A1067 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN A1067 " --> pdb=" O ALA A 706 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU A1065 " --> pdb=" O PRO A 708 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN A 710 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET A1043 " --> pdb=" O VAL A1058 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N TYR A1060 " --> pdb=" O HIS A1041 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N HIS A1041 " --> pdb=" O TYR A1060 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 704 through 720 removed outlier: 6.825A pdb=" N SER A 704 " --> pdb=" O THR A1069 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N THR A1069 " --> pdb=" O SER A 704 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA A 706 " --> pdb=" O ASN A1067 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN A1067 " --> pdb=" O ALA A 706 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU A1065 " --> pdb=" O PRO A 708 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN A 710 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHE A1088 " --> pdb=" O ALA A1071 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 728 through 729 Processing sheet with id=AB9, first strand: chain 'A' and resid 1080 through 1081 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.590A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.872A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.812A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 152 through 158 removed outlier: 6.510A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.640A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 327 removed outlier: 6.581A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 5.205A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 660 removed outlier: 3.665A pdb=" N VAL B 656 " --> pdb=" O ALA B 687 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR B 689 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ASN B 658 " --> pdb=" O THR B 689 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 704 through 713 removed outlier: 6.360A pdb=" N GLN B1064 " --> pdb=" O THR B 709 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE B 711 " --> pdb=" O PRO B1062 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE B 713 " --> pdb=" O TYR B1060 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N TYR B1060 " --> pdb=" O ILE B 713 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TYR B1060 " --> pdb=" O HIS B1041 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N HIS B1041 " --> pdb=" O TYR B1060 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 716 through 720 removed outlier: 4.174A pdb=" N THR B1069 " --> pdb=" O SER B1090 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE B1088 " --> pdb=" O ALA B1071 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1113 through 1116 removed outlier: 4.004A pdb=" N CYS B1075 " --> pdb=" O VAL B1126 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 29 through 30 removed outlier: 5.146A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 53 removed outlier: 3.881A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.571A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 141 through 145 removed outlier: 6.507A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.549A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL C 597 " --> pdb=" O TYR C 313 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 327 removed outlier: 5.896A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 356 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 655 through 656 removed outlier: 4.419A pdb=" N THR C 689 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 704 through 713 removed outlier: 7.147A pdb=" N SER C 704 " --> pdb=" O THR C1069 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR C1069 " --> pdb=" O SER C 704 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA C 706 " --> pdb=" O ASN C1067 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASN C1067 " --> pdb=" O ALA C 706 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU C1065 " --> pdb=" O PRO C 708 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN C 710 " --> pdb=" O ALA C1063 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 704 through 713 removed outlier: 7.147A pdb=" N SER C 704 " --> pdb=" O THR C1069 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR C1069 " --> pdb=" O SER C 704 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA C 706 " --> pdb=" O ASN C1067 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASN C1067 " --> pdb=" O ALA C 706 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU C1065 " --> pdb=" O PRO C 708 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN C 710 " --> pdb=" O ALA C1063 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLY C1052 " --> pdb=" O SER C1048 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N SER C1048 " --> pdb=" O GLY C1052 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL C1054 " --> pdb=" O PRO C1046 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU C1056 " --> pdb=" O SER C1044 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER C1044 " --> pdb=" O LEU C1056 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL C1058 " --> pdb=" O LEU C1042 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1074 through 1075 Processing sheet with id=AE7, first strand: chain 'C' and resid 1082 through 1083 Processing sheet with id=AE8, first strand: chain 'C' and resid 1087 through 1089 913 hydrogen bonds defined for protein. 2499 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: 10.47 Time building geometry restraints manager: 11.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8334 1.34 - 1.47: 6757 1.47 - 1.59: 11513 1.59 - 1.71: 0 1.71 - 1.83: 144 Bond restraints: 26748 Sorted by residual: bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.57e+00 bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.64e+00 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.61e+00 bond pdb=" C1 NAG A1306 " pdb=" O5 NAG A1306 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.08e+00 bond pdb=" C1 NAG O 1 " pdb=" O5 NAG O 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.08e+00 ... (remaining 26743 not shown) Histogram of bond angle deviations from ideal: 98.67 - 105.73: 565 105.73 - 112.80: 14491 112.80 - 119.86: 8244 119.86 - 126.92: 12874 126.92 - 133.98: 255 Bond angle restraints: 36429 Sorted by residual: angle pdb=" N VAL C 130 " pdb=" CA VAL C 130 " pdb=" C VAL C 130 " ideal model delta sigma weight residual 112.29 106.77 5.52 9.40e-01 1.13e+00 3.44e+01 angle pdb=" N VAL C 213 " pdb=" CA VAL C 213 " pdb=" C VAL C 213 " ideal model delta sigma weight residual 112.96 109.50 3.46 1.00e+00 1.00e+00 1.19e+01 angle pdb=" N VAL C 722 " pdb=" CA VAL C 722 " pdb=" C VAL C 722 " ideal model delta sigma weight residual 113.71 110.60 3.11 9.50e-01 1.11e+00 1.07e+01 angle pdb=" C ALA B 570 " pdb=" N ASP B 571 " pdb=" CA ASP B 571 " ideal model delta sigma weight residual 121.54 127.21 -5.67 1.91e+00 2.74e-01 8.80e+00 angle pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " ideal model delta sigma weight residual 114.40 120.53 -6.13 2.30e+00 1.89e-01 7.11e+00 ... (remaining 36424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 15050 17.47 - 34.95: 1269 34.95 - 52.42: 225 52.42 - 69.89: 68 69.89 - 87.37: 27 Dihedral angle restraints: 16639 sinusoidal: 7158 harmonic: 9481 Sorted by residual: dihedral pdb=" CB CYS A 731 " pdb=" SG CYS A 731 " pdb=" SG CYS A 753 " pdb=" CB CYS A 753 " ideal model delta sinusoidal sigma weight residual -86.00 -0.49 -85.51 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -5.96 -80.04 1 1.00e+01 1.00e-02 7.94e+01 dihedral pdb=" CB CYS B 736 " pdb=" SG CYS B 736 " pdb=" SG CYS B 742 " pdb=" CB CYS B 742 " ideal model delta sinusoidal sigma weight residual 93.00 166.64 -73.64 1 1.00e+01 1.00e-02 6.90e+01 ... (remaining 16636 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3831 0.079 - 0.159: 440 0.159 - 0.238: 12 0.238 - 0.318: 6 0.318 - 0.397: 4 Chirality restraints: 4293 Sorted by residual: chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 4290 not shown) Planarity restraints: 4697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 664 " 0.069 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO B 665 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO B 665 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO B 665 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 603 " 0.031 2.00e-02 2.50e+03 3.07e-02 1.18e+01 pdb=" CG ASN B 603 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN B 603 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B 603 " -0.042 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B1049 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO B1050 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B1050 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B1050 " -0.033 5.00e-02 4.00e+02 ... (remaining 4694 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 424 2.64 - 3.20: 25246 3.20 - 3.77: 39970 3.77 - 4.33: 54712 4.33 - 4.90: 87006 Nonbonded interactions: 207358 Sorted by model distance: nonbonded pdb=" O VAL B1033 " pdb=" OG SER C1023 " model vdw 2.071 2.440 nonbonded pdb=" OG SER B 751 " pdb=" OG1 THR B 754 " model vdw 2.127 2.440 nonbonded pdb=" OG1 THR A 430 " pdb=" O PHE A 515 " model vdw 2.140 2.440 nonbonded pdb=" O LEU A 959 " pdb=" OG SER A 968 " model vdw 2.143 2.440 nonbonded pdb=" O ASP B 290 " pdb=" OG SER B 297 " model vdw 2.156 2.440 ... (remaining 207353 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 332 or (resid 333 and (name N or name CA or nam \ e C or name O or name CB )) or resid 334 through 465 or (resid 466 and (name N o \ r name CA or name C or name O or name CB )) or resid 467 through 527 or (resid 5 \ 28 through 529 and (name N or name CA or name C or name O or name CB )) or resid \ 530 through 553 or (resid 554 and (name N or name CA or name C or name O or nam \ e CB )) or resid 555 through 582 or (resid 583 and (name N or name CA or name C \ or name O or name CB )) or resid 584 through 621 or resid 640 through 645 or (re \ sid 646 through 647 and (name N or name CA or name C or name O or name CB )) or \ resid 648 through 820 or resid 845 through 1140 or resid 1301 through 1310)) selection = (chain 'B' and (resid 27 through 416 or (resid 417 and (name N or name CA or nam \ e C or name O or name CB )) or resid 418 through 423 or (resid 424 and (name N o \ r name CA or name C or name O or name CB )) or resid 425 through 453 or (resid 4 \ 54 and (name N or name CA or name C or name O or name CB )) or resid 455 through \ 456 or (resid 457 and (name N or name CA or name C or name O or name CB )) or r \ esid 458 through 465 or (resid 466 and (name N or name CA or name C or name O or \ name CB )) or resid 467 through 621 or resid 640 through 645 or (resid 646 thro \ ugh 647 and (name N or name CA or name C or name O or name CB )) or resid 648 th \ rough 820 or resid 845 through 1140 or resid 1301 through 1310)) selection = (chain 'C' and (resid 27 through 332 or (resid 333 and (name N or name CA or nam \ e C or name O or name CB )) or resid 334 through 416 or (resid 417 and (name N o \ r name CA or name C or name O or name CB )) or resid 418 through 423 or (resid 4 \ 24 and (name N or name CA or name C or name O or name CB )) or resid 425 through \ 453 or (resid 454 and (name N or name CA or name C or name O or name CB )) or r \ esid 455 through 456 or (resid 457 and (name N or name CA or name C or name O or \ name CB )) or resid 458 through 527 or (resid 528 through 529 and (name N or na \ me CA or name C or name O or name CB )) or resid 530 through 553 or (resid 554 a \ nd (name N or name CA or name C or name O or name CB )) or resid 555 through 582 \ or (resid 583 and (name N or name CA or name C or name O or name CB )) or resid \ 584 through 621 or resid 640 through 1099 or (resid 1100 and (name N or name CA \ or name C or name O or name CB )) or resid 1101 through 1140 or resid 1301 thro \ ugh 1310)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.770 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 69.810 Find NCS groups from input model: 2.100 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26748 Z= 0.270 Angle : 0.674 8.602 36429 Z= 0.364 Chirality : 0.048 0.397 4293 Planarity : 0.005 0.103 4653 Dihedral : 13.403 87.365 10432 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.14), residues: 3239 helix: 0.61 (0.21), residues: 645 sheet: -1.12 (0.20), residues: 636 loop : -2.19 (0.13), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 436 HIS 0.011 0.001 HIS A 66 PHE 0.035 0.002 PHE C 392 TYR 0.019 0.001 TYR A 866 ARG 0.009 0.001 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 3.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.5670 (mtt180) cc_final: 0.5417 (mtt180) REVERT: A 237 ARG cc_start: 0.8303 (mtt180) cc_final: 0.7979 (mtp85) REVERT: A 516 GLU cc_start: 0.7566 (pm20) cc_final: 0.7359 (pm20) REVERT: C 700 TYR cc_start: 0.8375 (t80) cc_final: 0.8091 (t80) REVERT: C 848 PHE cc_start: 0.6649 (t80) cc_final: 0.6397 (t80) REVERT: C 1043 MET cc_start: 0.7802 (ptp) cc_final: 0.7483 (ptp) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.3420 time to fit residues: 145.5106 Evaluate side-chains 153 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 3.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 6.9990 chunk 245 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 83 optimal weight: 0.2980 chunk 165 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 chunk 253 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 154 optimal weight: 0.0770 chunk 189 optimal weight: 0.8980 chunk 294 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 239 GLN ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1081 HIS B1094 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.0748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26748 Z= 0.160 Angle : 0.551 9.112 36429 Z= 0.288 Chirality : 0.045 0.372 4293 Planarity : 0.004 0.073 4653 Dihedral : 7.494 58.610 4690 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.27 % Favored : 93.70 % Rotamer: Outliers : 0.07 % Allowed : 4.39 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.15), residues: 3239 helix: 1.14 (0.21), residues: 656 sheet: -0.98 (0.20), residues: 646 loop : -2.00 (0.14), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 436 HIS 0.010 0.001 HIS A 66 PHE 0.021 0.001 PHE C 238 TYR 0.016 0.001 TYR A1060 ARG 0.005 0.000 ARG C 758 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 240 time to evaluate : 3.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.8387 (mtt180) cc_final: 0.8184 (mtp85) REVERT: A 402 ILE cc_start: 0.9084 (pt) cc_final: 0.8826 (tt) REVERT: A 490 PHE cc_start: 0.7542 (t80) cc_final: 0.7181 (t80) REVERT: B 770 ASN cc_start: 0.8791 (m-40) cc_final: 0.8518 (m-40) REVERT: B 1044 SER cc_start: 0.8728 (m) cc_final: 0.8486 (p) REVERT: C 405 ASP cc_start: 0.7569 (t0) cc_final: 0.7232 (p0) REVERT: C 700 TYR cc_start: 0.8319 (t80) cc_final: 0.7983 (t80) outliers start: 2 outliers final: 1 residues processed: 242 average time/residue: 0.3309 time to fit residues: 136.7767 Evaluate side-chains 159 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 3.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 244 optimal weight: 0.7980 chunk 200 optimal weight: 0.0070 chunk 81 optimal weight: 6.9990 chunk 294 optimal weight: 4.9990 chunk 318 optimal weight: 9.9990 chunk 262 optimal weight: 0.9990 chunk 292 optimal weight: 0.3980 chunk 100 optimal weight: 1.9990 chunk 236 optimal weight: 7.9990 overall best weight: 0.8402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 683 GLN A 865 GLN A 985 GLN A1016 ASN A1029 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 995 GLN ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26748 Z= 0.160 Angle : 0.537 9.360 36429 Z= 0.279 Chirality : 0.044 0.365 4293 Planarity : 0.004 0.061 4653 Dihedral : 6.946 59.523 4690 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.04 % Allowed : 3.72 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.15), residues: 3239 helix: 1.25 (0.21), residues: 658 sheet: -0.87 (0.20), residues: 677 loop : -1.95 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 879 HIS 0.009 0.001 HIS A 66 PHE 0.018 0.001 PHE C 238 TYR 0.019 0.001 TYR B 897 ARG 0.004 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 251 time to evaluate : 3.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.8302 (mtt180) cc_final: 0.8022 (mtp85) REVERT: A 987 ASP cc_start: 0.8495 (m-30) cc_final: 0.8189 (m-30) REVERT: B 770 ASN cc_start: 0.8723 (m-40) cc_final: 0.8491 (m-40) REVERT: B 1044 SER cc_start: 0.8890 (m) cc_final: 0.8589 (p) REVERT: C 317 ASN cc_start: 0.8125 (t0) cc_final: 0.7735 (t0) REVERT: C 402 ILE cc_start: 0.8647 (mm) cc_final: 0.8437 (mm) REVERT: C 405 ASP cc_start: 0.7413 (t0) cc_final: 0.7113 (p0) REVERT: C 770 ASN cc_start: 0.8781 (m-40) cc_final: 0.8478 (m-40) outliers start: 1 outliers final: 0 residues processed: 252 average time/residue: 0.3252 time to fit residues: 137.7245 Evaluate side-chains 155 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 5.9990 chunk 221 optimal weight: 40.0000 chunk 152 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 140 optimal weight: 4.9990 chunk 197 optimal weight: 7.9990 chunk 295 optimal weight: 3.9990 chunk 313 optimal weight: 0.7980 chunk 154 optimal weight: 0.0020 chunk 280 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 overall best weight: 2.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 958 GLN ** C 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26748 Z= 0.231 Angle : 0.569 9.223 36429 Z= 0.295 Chirality : 0.045 0.380 4293 Planarity : 0.004 0.057 4653 Dihedral : 6.793 58.989 4690 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.07 % Allowed : 4.00 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.15), residues: 3239 helix: 1.16 (0.21), residues: 663 sheet: -0.79 (0.20), residues: 650 loop : -1.99 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 104 HIS 0.009 0.001 HIS A 66 PHE 0.020 0.001 PHE B 275 TYR 0.021 0.001 TYR A1060 ARG 0.007 0.000 ARG A1012 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 238 time to evaluate : 3.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.8306 (mtt180) cc_final: 0.8034 (mtp85) REVERT: A 881 PHE cc_start: 0.8380 (p90) cc_final: 0.8126 (p90) REVERT: A 983 GLU cc_start: 0.6515 (tm-30) cc_final: 0.5853 (tp30) REVERT: B 1044 SER cc_start: 0.8855 (m) cc_final: 0.8520 (p) REVERT: C 317 ASN cc_start: 0.8165 (t0) cc_final: 0.7765 (t0) REVERT: C 402 ILE cc_start: 0.8645 (mm) cc_final: 0.8412 (mm) REVERT: C 405 ASP cc_start: 0.7430 (t0) cc_final: 0.7156 (p0) REVERT: C 895 MET cc_start: 0.8654 (tpp) cc_final: 0.8432 (tpt) REVERT: C 1043 MET cc_start: 0.8398 (ptp) cc_final: 0.8121 (ptp) outliers start: 2 outliers final: 1 residues processed: 240 average time/residue: 0.3217 time to fit residues: 131.4021 Evaluate side-chains 152 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 2.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 10.0000 chunk 177 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 233 optimal weight: 10.0000 chunk 129 optimal weight: 20.0000 chunk 267 optimal weight: 6.9990 chunk 216 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 281 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS B 919 GLN ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26748 Z= 0.215 Angle : 0.566 9.289 36429 Z= 0.293 Chirality : 0.045 0.374 4293 Planarity : 0.004 0.055 4653 Dihedral : 6.664 59.181 4690 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.15), residues: 3239 helix: 1.11 (0.21), residues: 669 sheet: -0.79 (0.20), residues: 680 loop : -1.97 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 104 HIS 0.014 0.001 HIS B1041 PHE 0.021 0.001 PHE B 201 TYR 0.020 0.001 TYR A1060 ARG 0.005 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 3.045 Fit side-chains revert: symmetry clash REVERT: A 237 ARG cc_start: 0.8326 (mtt180) cc_final: 0.8042 (mtp85) REVERT: A 881 PHE cc_start: 0.8371 (p90) cc_final: 0.8157 (p90) REVERT: B 723 SER cc_start: 0.8958 (t) cc_final: 0.8185 (t) REVERT: B 767 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8309 (mm-40) REVERT: C 317 ASN cc_start: 0.8131 (t0) cc_final: 0.7663 (t0) REVERT: C 402 ILE cc_start: 0.8555 (mm) cc_final: 0.8292 (mm) REVERT: C 405 ASP cc_start: 0.7526 (t0) cc_final: 0.7266 (p0) REVERT: C 770 ASN cc_start: 0.8865 (m-40) cc_final: 0.8488 (m-40) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.3335 time to fit residues: 141.0642 Evaluate side-chains 155 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 3.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 7.9990 chunk 282 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 313 optimal weight: 0.6980 chunk 260 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 26 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 164 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 564 GLN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26748 Z= 0.173 Angle : 0.541 9.202 36429 Z= 0.281 Chirality : 0.045 0.368 4293 Planarity : 0.004 0.053 4653 Dihedral : 6.467 59.150 4690 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.15), residues: 3239 helix: 1.24 (0.21), residues: 670 sheet: -0.74 (0.20), residues: 668 loop : -1.94 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 879 HIS 0.012 0.001 HIS C 66 PHE 0.019 0.001 PHE B 374 TYR 0.019 0.001 TYR B 897 ARG 0.007 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 3.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1023 SER cc_start: 0.8965 (m) cc_final: 0.8189 (t) REVERT: B 723 SER cc_start: 0.9043 (t) cc_final: 0.8274 (t) REVERT: B 767 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8424 (mm-40) REVERT: B 770 ASN cc_start: 0.8729 (m-40) cc_final: 0.8524 (t0) REVERT: B 1044 SER cc_start: 0.8715 (m) cc_final: 0.8387 (p) REVERT: C 317 ASN cc_start: 0.7596 (t0) cc_final: 0.7202 (p0) REVERT: C 402 ILE cc_start: 0.8531 (mm) cc_final: 0.8256 (mm) REVERT: C 534 VAL cc_start: 0.8396 (t) cc_final: 0.8130 (t) REVERT: C 552 LEU cc_start: 0.9090 (mm) cc_final: 0.8453 (mp) REVERT: C 770 ASN cc_start: 0.8825 (m-40) cc_final: 0.8376 (m-40) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.3258 time to fit residues: 140.8185 Evaluate side-chains 157 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 3.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 178 optimal weight: 0.7980 chunk 228 optimal weight: 6.9990 chunk 177 optimal weight: 0.9980 chunk 263 optimal weight: 0.0050 chunk 175 optimal weight: 5.9990 chunk 312 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 190 optimal weight: 0.9980 chunk 144 optimal weight: 6.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN ** B 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26748 Z= 0.184 Angle : 0.555 9.284 36429 Z= 0.285 Chirality : 0.045 0.359 4293 Planarity : 0.004 0.052 4653 Dihedral : 6.365 58.850 4690 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.15), residues: 3239 helix: 1.23 (0.21), residues: 672 sheet: -0.65 (0.21), residues: 622 loop : -1.90 (0.13), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 104 HIS 0.013 0.001 HIS B1041 PHE 0.017 0.001 PHE B 374 TYR 0.018 0.001 TYR A1060 ARG 0.009 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 3.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 987 ASP cc_start: 0.8530 (m-30) cc_final: 0.8185 (m-30) REVERT: B 723 SER cc_start: 0.9015 (t) cc_final: 0.8154 (t) REVERT: B 767 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8428 (mm-40) REVERT: B 770 ASN cc_start: 0.8733 (m-40) cc_final: 0.8516 (t0) REVERT: B 911 GLU cc_start: 0.8061 (pp20) cc_final: 0.7802 (pp20) REVERT: C 317 ASN cc_start: 0.7868 (t0) cc_final: 0.7291 (t0) REVERT: C 402 ILE cc_start: 0.8490 (mm) cc_final: 0.8232 (mm) REVERT: C 405 ASP cc_start: 0.7662 (t0) cc_final: 0.7250 (p0) REVERT: C 534 VAL cc_start: 0.8429 (t) cc_final: 0.8172 (t) REVERT: C 552 LEU cc_start: 0.9151 (mm) cc_final: 0.8563 (mp) REVERT: C 770 ASN cc_start: 0.8784 (m-40) cc_final: 0.8506 (m-40) REVERT: C 1043 MET cc_start: 0.8348 (ptp) cc_final: 0.8138 (ptp) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.3391 time to fit residues: 144.9355 Evaluate side-chains 158 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 3.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 1.9990 chunk 124 optimal weight: 30.0000 chunk 186 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 60 optimal weight: 0.0030 chunk 198 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 245 optimal weight: 0.0870 overall best weight: 0.6770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN ** A 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1029 GLN ** B 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 998 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 26748 Z= 0.161 Angle : 0.543 9.278 36429 Z= 0.280 Chirality : 0.045 0.351 4293 Planarity : 0.004 0.050 4653 Dihedral : 6.195 59.109 4690 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.15), residues: 3239 helix: 1.32 (0.21), residues: 671 sheet: -0.53 (0.21), residues: 622 loop : -1.88 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 879 HIS 0.011 0.001 HIS B1041 PHE 0.036 0.001 PHE B 816 TYR 0.016 0.001 TYR A1060 ARG 0.005 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 2.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 ILE cc_start: 0.9075 (pt) cc_final: 0.8813 (tt) REVERT: B 723 SER cc_start: 0.9049 (t) cc_final: 0.8638 (t) REVERT: C 317 ASN cc_start: 0.7788 (t0) cc_final: 0.7385 (t0) REVERT: C 402 ILE cc_start: 0.8405 (mm) cc_final: 0.8151 (mm) REVERT: C 405 ASP cc_start: 0.7561 (t0) cc_final: 0.7261 (p0) REVERT: C 534 VAL cc_start: 0.8391 (t) cc_final: 0.8120 (t) REVERT: C 552 LEU cc_start: 0.9141 (mm) cc_final: 0.8549 (mp) REVERT: C 767 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8524 (mm-40) REVERT: C 770 ASN cc_start: 0.8657 (m-40) cc_final: 0.8404 (m-40) REVERT: C 1043 MET cc_start: 0.8339 (ptp) cc_final: 0.7930 (ptt) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.3261 time to fit residues: 144.7839 Evaluate side-chains 160 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 1.9990 chunk 299 optimal weight: 0.9990 chunk 272 optimal weight: 0.9990 chunk 291 optimal weight: 1.9990 chunk 175 optimal weight: 0.7980 chunk 126 optimal weight: 9.9990 chunk 228 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 262 optimal weight: 0.9980 chunk 275 optimal weight: 3.9990 chunk 289 optimal weight: 5.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN B 894 GLN ** B 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26748 Z= 0.170 Angle : 0.548 9.303 36429 Z= 0.282 Chirality : 0.045 0.350 4293 Planarity : 0.004 0.050 4653 Dihedral : 6.147 58.702 4690 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.15), residues: 3239 helix: 1.31 (0.21), residues: 669 sheet: -0.51 (0.21), residues: 631 loop : -1.85 (0.14), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.009 0.001 HIS C 66 PHE 0.031 0.001 PHE A 275 TYR 0.018 0.001 TYR B 265 ARG 0.004 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 3.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 ILE cc_start: 0.9074 (pt) cc_final: 0.8827 (tt) REVERT: B 1044 SER cc_start: 0.8913 (m) cc_final: 0.8711 (m) REVERT: C 317 ASN cc_start: 0.7902 (t0) cc_final: 0.7347 (t0) REVERT: C 402 ILE cc_start: 0.8350 (mm) cc_final: 0.8096 (mm) REVERT: C 405 ASP cc_start: 0.7543 (t0) cc_final: 0.7277 (p0) REVERT: C 534 VAL cc_start: 0.8390 (t) cc_final: 0.8130 (t) REVERT: C 552 LEU cc_start: 0.9160 (mm) cc_final: 0.8575 (mp) REVERT: C 767 GLN cc_start: 0.8790 (mm-40) cc_final: 0.8507 (mm-40) REVERT: C 770 ASN cc_start: 0.8609 (m-40) cc_final: 0.8368 (m-40) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.3269 time to fit residues: 135.8831 Evaluate side-chains 158 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 3.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 6.9990 chunk 307 optimal weight: 7.9990 chunk 187 optimal weight: 0.8980 chunk 145 optimal weight: 20.0000 chunk 213 optimal weight: 0.7980 chunk 322 optimal weight: 2.9990 chunk 297 optimal weight: 0.8980 chunk 257 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 198 optimal weight: 0.9980 chunk 157 optimal weight: 6.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 894 GLN ** B 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 GLN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 948 ASN ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26748 Z= 0.184 Angle : 0.552 9.322 36429 Z= 0.284 Chirality : 0.045 0.350 4293 Planarity : 0.004 0.051 4653 Dihedral : 6.141 58.567 4690 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.04 % Allowed : 0.42 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.15), residues: 3239 helix: 1.19 (0.21), residues: 682 sheet: -0.51 (0.21), residues: 634 loop : -1.85 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 104 HIS 0.011 0.001 HIS A 66 PHE 0.026 0.001 PHE B 816 TYR 0.017 0.001 TYR A1060 ARG 0.006 0.000 ARG A 976 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 243 time to evaluate : 3.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.7016 (ptp) cc_final: 0.6791 (ptp) REVERT: A 402 ILE cc_start: 0.9072 (pt) cc_final: 0.8831 (tt) REVERT: B 1044 SER cc_start: 0.8888 (m) cc_final: 0.8448 (p) REVERT: C 317 ASN cc_start: 0.7875 (t0) cc_final: 0.7344 (t0) REVERT: C 402 ILE cc_start: 0.8328 (mm) cc_final: 0.7954 (tt) REVERT: C 405 ASP cc_start: 0.7535 (t0) cc_final: 0.7273 (p0) REVERT: C 534 VAL cc_start: 0.8372 (t) cc_final: 0.8121 (t) REVERT: C 552 LEU cc_start: 0.9175 (mm) cc_final: 0.8582 (mp) REVERT: C 767 GLN cc_start: 0.8822 (mm-40) cc_final: 0.8503 (mm-40) REVERT: C 770 ASN cc_start: 0.8621 (m-40) cc_final: 0.8393 (m-40) outliers start: 1 outliers final: 0 residues processed: 244 average time/residue: 0.3364 time to fit residues: 139.6955 Evaluate side-chains 158 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 3.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 4.9990 chunk 273 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 237 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 264 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 912 ASN A 998 GLN B 894 GLN ** B 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.098061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.077472 restraints weight = 88567.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.076907 restraints weight = 76566.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.077485 restraints weight = 61893.629| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 26748 Z= 0.364 Angle : 0.676 9.466 36429 Z= 0.348 Chirality : 0.047 0.359 4293 Planarity : 0.004 0.056 4653 Dihedral : 6.761 59.578 4690 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.15), residues: 3239 helix: 0.81 (0.21), residues: 679 sheet: -0.71 (0.20), residues: 695 loop : -1.93 (0.14), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 104 HIS 0.012 0.002 HIS A 66 PHE 0.033 0.002 PHE A 275 TYR 0.032 0.002 TYR B 866 ARG 0.007 0.001 ARG A 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4514.95 seconds wall clock time: 84 minutes 51.04 seconds (5091.04 seconds total)