Starting phenix.real_space_refine on Tue Jun 10 06:42:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7txz_26162/06_2025/7txz_26162.cif Found real_map, /net/cci-nas-00/data/ceres_data/7txz_26162/06_2025/7txz_26162.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7txz_26162/06_2025/7txz_26162.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7txz_26162/06_2025/7txz_26162.map" model { file = "/net/cci-nas-00/data/ceres_data/7txz_26162/06_2025/7txz_26162.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7txz_26162/06_2025/7txz_26162.cif" } resolution = 3.2 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= 0.102 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 74 5.16 5 C 7238 2.51 5 N 1914 2.21 5 O 2077 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11303 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 3513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3513 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 7, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 125 Chain: "B" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3579 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 438} Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 7} Unresolved non-hydrogen planarities: 87 Chain: "E" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 882 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "F" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 835 Classifications: {'peptide': 110} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 102} Chain: "H" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 874 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "L" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 805 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 103} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 212 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 29} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 205 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 4, 'TRANS': 29} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 34 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: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "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: "Q" 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: "R" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.44, per 1000 atoms: 0.75 Number of scatterers: 11303 At special positions: 0 Unit cell: (101.85, 134.4, 143.85, 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 74 16.00 O 2077 8.00 N 1914 7.00 C 7238 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS C 146 " distance=2.03 Simple disulfide: pdb=" SG CYS A 158 " - pdb=" SG CYS D 162 " distance=2.06 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS D 158 " distance=2.04 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 601 " distance=2.02 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS A 240 " distance=2.12 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 295 " distance=2.05 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 499 " distance=2.03 Simple disulfide: pdb=" SG CYS A 493 " - pdb=" SG CYS A 503 " distance=2.03 Simple disulfide: pdb=" SG CYS A 565 " - pdb=" SG CYS A 574 " distance=2.03 Simple disulfide: pdb=" SG CYS B 146 " - pdb=" SG CYS D 146 " distance=2.03 Simple disulfide: pdb=" SG CYS B 158 " - pdb=" SG CYS C 162 " distance=2.07 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS C 158 " distance=2.04 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 601 " distance=2.02 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 240 " distance=2.02 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 295 " distance=2.04 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 499 " distance=2.11 Simple disulfide: pdb=" SG CYS B 493 " - pdb=" SG CYS B 503 " distance=2.06 Simple disulfide: pdb=" SG CYS B 565 " - pdb=" SG CYS B 574 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 98 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 92 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 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 Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " BETA1-6 " NAG J 1 " - " FUC J 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG R 1 " - " FUC R 3 " NAG-ASN " NAG A 701 " - " ASN A 378 " " NAG G 1 " - " ASN A 306 " " NAG I 1 " - " ASN A 417 " " NAG J 1 " - " ASN A 529 " " NAG K 1 " - " ASN A 481 " " NAG M 1 " - " ASN A 159 " " NAG N 1 " - " ASN B 306 " " NAG O 1 " - " ASN B 378 " " NAG P 1 " - " ASN B 417 " " NAG Q 1 " - " ASN B 481 " " NAG R 1 " - " ASN B 529 " " NAG S 1 " - " ASN B 159 " " NAG T 1 " - " ASN D 159 " " NAG U 1 " - " ASN C 159 " Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 1.4 seconds 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2718 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 30 sheets defined 9.9% alpha, 43.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 131 through 146 Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 204 through 207 Processing helix chain 'A' and resid 239 through 243 Processing helix chain 'A' and resid 327 through 330 Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 378 through 382 Processing helix chain 'A' and resid 393 through 398 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 327 through 331 Processing helix chain 'B' and resid 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 378 through 382 Processing helix chain 'B' and resid 393 through 398 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 57 Processing helix chain 'E' and resid 89 through 93 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'H' and resid 76 through 78 No H-bonds generated for 'chain 'H' and resid 76 through 78' Processing helix chain 'H' and resid 89 through 93 Processing helix chain 'D' and resid 133 through 146 Processing helix chain 'C' and resid 133 through 146 removed outlier: 3.571A pdb=" N ASN C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 154 removed outlier: 6.076A pdb=" N LEU A 153 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 153 " --> pdb=" O ILE C 160 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 161 Processing sheet with id=AA3, first strand: chain 'A' and resid 178 through 179 removed outlier: 6.826A pdb=" N ALA A 558 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR A 581 " --> pdb=" O ALA A 558 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LYS A 560 " --> pdb=" O GLU A 579 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 215 through 225 removed outlier: 6.405A pdb=" N SER A 232 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU A 222 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA A 230 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N MET A 224 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR A 228 " --> pdb=" O MET A 224 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N PHE A 229 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL A 252 " --> pdb=" O PHE A 229 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR A 231 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE A 250 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N HIS A 233 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ARG A 248 " --> pdb=" O HIS A 233 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLU A 235 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLU A 254 " --> pdb=" O MET A 267 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N MET A 267 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU A 256 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N LEU A 265 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 279 through 287 removed outlier: 5.575A pdb=" N HIS A 281 " --> pdb=" O ALA A 296 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA A 296 " --> pdb=" O HIS A 281 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 340 through 341 removed outlier: 3.536A pdb=" N LYS A 347 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 340 through 341 Processing sheet with id=AA8, first strand: chain 'A' and resid 442 through 447 removed outlier: 4.194A pdb=" N LYS A 465 " --> pdb=" O GLN A 455 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP A 468 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL A 476 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 512 through 515 removed outlier: 6.404A pdb=" N ILE A 520 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N GLN A 550 " --> pdb=" O PRO A 535 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N PHE A 537 " --> pdb=" O ARG A 548 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARG A 548 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL A 539 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 179 through 180 removed outlier: 4.828A pdb=" N LYS B 560 " --> pdb=" O GLU B 579 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU B 592 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 215 through 225 removed outlier: 6.420A pdb=" N SER B 232 " --> pdb=" O PRO B 220 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU B 222 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA B 230 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N MET B 224 " --> pdb=" O TYR B 228 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR B 228 " --> pdb=" O MET B 224 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN B 247 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE B 237 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N SER B 245 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU B 254 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N MET B 267 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU B 256 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N LEU B 265 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 279 through 287 removed outlier: 5.495A pdb=" N HIS B 281 " --> pdb=" O ALA B 296 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA B 296 " --> pdb=" O HIS B 281 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 340 through 341 removed outlier: 3.546A pdb=" N LYS B 347 " --> pdb=" O PHE B 369 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 340 through 341 Processing sheet with id=AB6, first strand: chain 'B' and resid 442 through 447 removed outlier: 4.220A pdb=" N LYS B 465 " --> pdb=" O GLN B 455 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP B 468 " --> pdb=" O ASN B 478 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL B 476 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 512 through 515 removed outlier: 6.558A pdb=" N ILE B 520 " --> pdb=" O ILE B 514 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLN B 550 " --> pdb=" O PRO B 535 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHE B 537 " --> pdb=" O ARG B 548 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG B 548 " --> pdb=" O PHE B 537 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL B 539 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB9, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.448A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TRP E 33 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N MET E 34 " --> pdb=" O GLU E 50 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLU E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.448A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N CYS E 98 " --> pdb=" O TRP E 109 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TRP E 109 " --> pdb=" O CYS E 98 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ARG E 100 " --> pdb=" O ALA E 107 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'F' and resid 10 through 14 removed outlier: 6.202A pdb=" N LEU F 11 " --> pdb=" O GLU F 109 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LYS F 111 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL F 13 " --> pdb=" O LYS F 111 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TRP F 39 " --> pdb=" O LEU F 51 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 10 through 14 removed outlier: 6.202A pdb=" N LEU F 11 " --> pdb=" O GLU F 109 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LYS F 111 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL F 13 " --> pdb=" O LYS F 111 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 30 through 31 Processing sheet with id=AC6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC7, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.205A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TRP H 33 " --> pdb=" O VAL H 101 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.205A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N CYS H 98 " --> pdb=" O TRP H 109 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N TRP H 109 " --> pdb=" O CYS H 98 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ARG H 100 " --> pdb=" O ALA H 107 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.022A pdb=" N LEU L 11 " --> pdb=" O GLU L 109 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS L 111 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL L 13 " --> pdb=" O LYS L 111 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP L 39 " --> pdb=" O LEU L 51 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.022A pdb=" N LEU L 11 " --> pdb=" O GLU L 109 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS L 111 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL L 13 " --> pdb=" O LYS L 111 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 30 through 31 468 hydrogen bonds defined for protein. 1155 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: 4.09 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2864 1.33 - 1.46: 3177 1.46 - 1.59: 5433 1.59 - 1.72: 5 1.72 - 1.85: 98 Bond restraints: 11577 Sorted by residual: bond pdb=" CB ILE F 2 " pdb=" CG1 ILE F 2 " ideal model delta sigma weight residual 1.530 1.612 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" SD MET L 37 " pdb=" CE MET L 37 " ideal model delta sigma weight residual 1.791 1.698 0.093 2.50e-02 1.60e+03 1.37e+01 bond pdb=" N PRO A 441 " pdb=" CA PRO A 441 " ideal model delta sigma weight residual 1.468 1.424 0.044 1.20e-02 6.94e+03 1.32e+01 bond pdb=" N PRO A 365 " pdb=" CD PRO A 365 " ideal model delta sigma weight residual 1.473 1.423 0.050 1.40e-02 5.10e+03 1.28e+01 bond pdb=" CB TYR B 231 " pdb=" CG TYR B 231 " ideal model delta sigma weight residual 1.512 1.433 0.079 2.20e-02 2.07e+03 1.27e+01 ... (remaining 11572 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 12850 1.75 - 3.50: 2348 3.50 - 5.24: 441 5.24 - 6.99: 140 6.99 - 8.74: 14 Bond angle restraints: 15793 Sorted by residual: angle pdb=" C CYS A 493 " pdb=" N PRO A 494 " pdb=" CA PRO A 494 " ideal model delta sigma weight residual 120.21 127.93 -7.72 9.60e-01 1.09e+00 6.47e+01 angle pdb=" C ASP B 302 " pdb=" N PRO B 303 " pdb=" CA PRO B 303 " ideal model delta sigma weight residual 119.56 127.71 -8.15 1.02e+00 9.61e-01 6.39e+01 angle pdb=" C LYS A 391 " pdb=" N PRO A 392 " pdb=" CA PRO A 392 " ideal model delta sigma weight residual 119.56 127.37 -7.81 1.02e+00 9.61e-01 5.87e+01 angle pdb=" C THR B 272 " pdb=" N PRO B 273 " pdb=" CA PRO B 273 " ideal model delta sigma weight residual 119.66 125.13 -5.47 7.20e-01 1.93e+00 5.77e+01 angle pdb=" C LYS A 322 " pdb=" N PRO A 323 " pdb=" CA PRO A 323 " ideal model delta sigma weight residual 119.78 127.29 -7.51 1.03e+00 9.43e-01 5.32e+01 ... (remaining 15788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7012 17.95 - 35.89: 204 35.89 - 53.84: 51 53.84 - 71.79: 23 71.79 - 89.73: 7 Dihedral angle restraints: 7297 sinusoidal: 3055 harmonic: 4242 Sorted by residual: dihedral pdb=" CB CYS A 146 " pdb=" SG CYS A 146 " pdb=" SG CYS C 146 " pdb=" CB CYS C 146 " ideal model delta sinusoidal sigma weight residual 93.00 -177.27 -89.73 1 1.00e+01 1.00e-02 9.56e+01 dihedral pdb=" CB CYS A 382 " pdb=" SG CYS A 382 " pdb=" SG CYS A 395 " pdb=" CB CYS A 395 " ideal model delta sinusoidal sigma weight residual -86.00 -159.74 73.74 1 1.00e+01 1.00e-02 6.91e+01 dihedral pdb=" CB CYS B 387 " pdb=" SG CYS B 387 " pdb=" SG CYS B 499 " pdb=" CB CYS B 499 " ideal model delta sinusoidal sigma weight residual 93.00 155.17 -62.17 1 1.00e+01 1.00e-02 5.12e+01 ... (remaining 7294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1242 0.078 - 0.156: 445 0.156 - 0.234: 92 0.234 - 0.313: 41 0.313 - 0.391: 27 Chirality restraints: 1847 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.11e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.93e+01 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.90e+01 ... (remaining 1844 not shown) Planarity restraints: 2021 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 481 " 0.048 2.00e-02 2.50e+03 4.86e-02 2.96e+01 pdb=" CG ASN A 481 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A 481 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 481 " -0.074 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 481 " 0.040 2.00e-02 2.50e+03 4.07e-02 2.07e+01 pdb=" CG ASN B 481 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN B 481 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN B 481 " -0.062 2.00e-02 2.50e+03 pdb=" C1 NAG Q 1 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 159 " -0.030 2.00e-02 2.50e+03 3.05e-02 1.16e+01 pdb=" CG ASN A 159 " 0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A 159 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 159 " 0.047 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " -0.037 2.00e-02 2.50e+03 ... (remaining 2018 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 4396 2.90 - 3.40: 9695 3.40 - 3.90: 19242 3.90 - 4.40: 21941 4.40 - 4.90: 36750 Nonbonded interactions: 92024 Sorted by model distance: nonbonded pdb=" O ARG A 435 " pdb=" NZ LYS A 465 " model vdw 2.400 3.120 nonbonded pdb=" OD2 ASP A 420 " pdb=" NZ LYS A 425 " model vdw 2.421 3.120 nonbonded pdb=" N THR B 149 " pdb=" O THR B 149 " model vdw 2.476 2.496 nonbonded pdb=" N ASP B 360 " pdb=" OD1 ASP B 360 " model vdw 2.490 3.120 nonbonded pdb=" N ASP B 433 " pdb=" OD1 ASP B 433 " model vdw 2.509 3.120 ... (remaining 92019 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 132 through 144 and (name N or name CA or name C or name \ O or name CB )) or resid 145 through 195 or (resid 196 and (name N or name CA or \ name C or name O or name CB )) or resid 197 through 203 or (resid 204 and (name \ N or name CA or name C or name O or name CB )) or resid 205 through 208 or (res \ id 209 through 210 and (name N or name CA or name C or name O or name CB )) or r \ esid 211 through 238 or (resid 239 and (name N or name CA or name C or name O or \ name CB )) or resid 240 through 263 or (resid 264 and (name N or name CA or nam \ e C or name O or name CB )) or resid 265 through 288 or (resid 289 and (name N o \ r name CA or name C or name O or name CB )) or resid 290 through 312 or (resid 3 \ 13 and (name N or name CA or name C or name O or name CB )) or resid 314 through \ 373 or (resid 374 and (name N or name CA or name C or name O or name CB )) or r \ esid 375 through 388 or (resid 389 and (name N or name CA or name C or name O or \ name CB )) or resid 390 through 410 or (resid 411 and (name N or name CA or nam \ e C or name O or name CB )) or resid 412 through 422 or (resid 423 and (name N o \ r name CA or name C or name O or name CB )) or resid 424 through 439 or (resid 4 \ 40 and (name N or name CA or name C or name O or name CB )) or resid 441 through \ 514 or (resid 515 and (name N or name CA or name C or name O or name CB )) or r \ esid 516 through 553 or (resid 554 through 555 and (name N or name CA or name C \ or name O or name CB )) or resid 556 through 581 or (resid 582 through 586 and ( \ name N or name CA or name C or name O or name CB )) or resid 587 through 602)) selection = (chain 'B' and (resid 132 through 160 or (resid 161 and (name N or name CA or na \ me C or name O or name CB )) or resid 162 through 163 or (resid 164 and (name N \ or name CA or name C or name O or name CB )) or resid 165 through 169 or (resid \ 170 and (name N or name CA or name C or name O or name CB )) or resid 171 throug \ h 173 or (resid 174 through 176 and (name N or name CA or name C or name O or na \ me CB )) or resid 177 through 209 or (resid 210 and (name N or name CA or name C \ or name O or name CB )) or resid 211 through 218 or (resid 219 and (name N or n \ ame CA or name C or name O or name CB )) or resid 220 through 225 or (resid 226 \ and (name N or name CA or name C or name O or name CB )) or resid 227 through 23 \ 4 or (resid 235 and (name N or name CA or name C or name O or name CB )) or resi \ d 236 through 241 or (resid 242 and (name N or name CA or name C or name O or na \ me CB )) or resid 243 through 245 or (resid 246 and (name N or name CA or name C \ or name O or name CB )) or resid 247 through 271 or (resid 272 and (name N or n \ ame CA or name C or name O or name CB )) or resid 273 through 287 or (resid 288 \ through 289 and (name N or name CA or name C or name O or name CB )) or resid 29 \ 0 through 298 or (resid 299 and (name N or name CA or name C or name O or name C \ B )) or resid 300 through 306 or (resid 307 through 308 and (name N or name CA o \ r name C or name O or name CB )) or resid 309 through 325 or (resid 326 and (nam \ e N or name CA or name C or name O or name CB )) or resid 327 through 337 or (re \ sid 338 through 339 and (name N or name CA or name C or name O or name CB )) or \ resid 340 through 345 or (resid 346 and (name N or name CA or name C or name O o \ r name CB )) or resid 347 through 359 or (resid 360 and (name N or name CA or na \ me C or name O or name CB )) or resid 361 through 375 or (resid 376 and (name N \ or name CA or name C or name O or name CB )) or resid 377 through 380 or (resid \ 381 and (name N or name CA or name C or name O or name CB )) or resid 382 throug \ h 383 or (resid 384 through 386 and (name N or name CA or name C or name O or na \ me CB )) or resid 387 through 390 or (resid 391 and (name N or name CA or name C \ or name O or name CB )) or resid 392 or (resid 393 and (name N or name CA or na \ me C or name O or name CB )) or resid 394 through 432 or (resid 433 and (name N \ or name CA or name C or name O or name CB )) or resid 434 through 470 or (resid \ 471 and (name N or name CA or name C or name O or name CB )) or resid 472 throug \ h 500 or (resid 501 and (name N or name CA or name C or name O or name CB )) or \ resid 502 through 504 or (resid 505 and (name N or name CA or name C or name O o \ r name CB )) or resid 506 through 526 or (resid 527 through 528 and (name N or n \ ame CA or name C or name O or name CB )) or resid 529 through 532 or (resid 533 \ and (name N or name CA or name C or name O or name CB )) or resid 534 through 58 \ 2 or resid 585 through 602)) } ncs_group { reference = (chain 'C' and (resid 132 through 152 or (resid 153 and (name N or name CA or na \ me C or name O or name CB )) or resid 154 through 165)) selection = (chain 'D' and ((resid 132 through 145 and (name N or name CA or name C or name \ O or name CB )) or resid 146 through 156 or (resid 157 and (name N or name CA or \ name C or name O or name CB )) or resid 158 through 165)) } ncs_group { reference = (chain 'E' and (resid 1 through 10 or (resid 11 through 13 and (name N or name C \ A or name C or name O or name CB )) or resid 14 through 20 or (resid 21 and (nam \ e N or name CA or name C or name O or name CB )) or resid 22 through 24 or (resi \ d 25 and (name N or name CA or name C or name O or name CB )) or resid 26 throug \ h 66 or (resid 67 and (name N or name CA or name C or name O or name CB )) or re \ sid 68 through 85 or (resid 86 through 87 and (name N or name CA or name C or na \ me O or name CB )) or resid 88 through 90 or (resid 91 and (name N or name CA or \ name C or name O or name CB )) or resid 92 or (resid 93 and (name N or name CA \ or name C or name O or name CB )) or resid 94 through 117)) selection = (chain 'H' and (resid 1 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 72 or (resid 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 or (resid 75 thro \ ugh 77 and (name N or name CA or name C or name O or name CB )) or resid 78 thro \ ugh 86 or (resid 87 and (name N or name CA or name C or name O or name CB )) or \ resid 88 through 117)) } ncs_group { reference = (chain 'F' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 or (resid 5 and (name N or name CA or name C or name O o \ r name CB )) or resid 6 or (resid 7 and (name N or name CA or name C or name O o \ r name CB )) or resid 8 through 13 or (resid 14 through 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 or (resid 17 and (name N or name \ CA or name C or name O or name CB )) or resid 18 through 19 or (resid 20 and (n \ ame N or name CA or name C or name O or name CB )) or resid 21 or (resid 22 and \ (name N or name CA or name C or name O or name CB )) or resid 23 through 25 or ( \ resid 26 through 28 and (name N or name CA or name C or name O or name CB )) or \ resid 29 through 66 or (resid 67 and (name N or name CA or name C or name O or n \ ame CB )) or resid 68 or (resid 69 and (name N or name CA or name C or name O or \ name CB )) or resid 70 or (resid 71 and (name N or name CA or name C or name O \ or name CB )) or resid 72 or (resid 73 through 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 or (resid 76 and (name N or name CA or na \ me C or name O or name CB )) or resid 77 through 83 or (resid 84 through 85 and \ (name N or name CA or name C or name O or name CB )) or resid 86 through 111)) selection = (chain 'L' and resid 2 through 111) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 68.390 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: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 29.810 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 102.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 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 : 0.017 0.105 11630 Z= 0.895 Angle : 1.525 8.757 15928 Z= 1.000 Chirality : 0.097 0.391 1847 Planarity : 0.006 0.068 2007 Dihedral : 9.784 86.530 4507 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 0.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.94 % Favored : 97.99 % Rotamer: Outliers : 0.19 % Allowed : 1.31 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.22), residues: 1446 helix: 0.62 (0.64), residues: 58 sheet: 0.97 (0.22), residues: 524 loop : 0.23 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.006 TRP B 310 HIS 0.005 0.001 HIS A 333 PHE 0.022 0.004 PHE B 466 TYR 0.038 0.005 TYR B 351 ARG 0.005 0.001 ARG E 69 Details of bonding type rmsd link_NAG-ASN : bond 0.06432 ( 14) link_NAG-ASN : angle 2.07240 ( 42) link_BETA1-4 : bond 0.06693 ( 13) link_BETA1-4 : angle 3.87381 ( 39) hydrogen bonds : bond 0.14734 ( 420) hydrogen bonds : angle 8.05977 ( 1155) link_BETA1-6 : bond 0.05424 ( 2) link_BETA1-6 : angle 2.02315 ( 6) SS BOND : bond 0.02740 ( 24) SS BOND : angle 3.62550 ( 48) covalent geometry : bond 0.01662 (11577) covalent geometry : angle 1.50150 (15793) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 238 time to evaluate : 1.322 Fit side-chains REVERT: B 224 MET cc_start: 0.8591 (mtt) cc_final: 0.8340 (mtt) REVERT: E 34 MET cc_start: 0.8000 (mmm) cc_final: 0.7266 (mmt) REVERT: D 155 ILE cc_start: 0.8215 (mt) cc_final: 0.8003 (mt) outliers start: 2 outliers final: 0 residues processed: 239 average time/residue: 0.3274 time to fit residues: 105.7978 Evaluate side-chains 154 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 2.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 ASN B 434 GLN B 478 ASN B 600 GLN F 46 GLN H 84 GLN L 58 GLN D 139 ASN C 156 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.152055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.120331 restraints weight = 14021.420| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.20 r_work: 0.3133 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11630 Z= 0.169 Angle : 0.681 11.007 15928 Z= 0.352 Chirality : 0.049 0.183 1847 Planarity : 0.005 0.043 2007 Dihedral : 5.255 29.275 2181 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.87 % Favored : 98.06 % Rotamer: Outliers : 2.07 % Allowed : 7.14 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.22), residues: 1446 helix: 1.92 (0.71), residues: 60 sheet: 0.74 (0.22), residues: 556 loop : 0.15 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 519 HIS 0.004 0.001 HIS C 156 PHE 0.015 0.002 PHE A 369 TYR 0.019 0.002 TYR B 351 ARG 0.006 0.001 ARG L 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 14) link_NAG-ASN : angle 1.69140 ( 42) link_BETA1-4 : bond 0.00633 ( 13) link_BETA1-4 : angle 1.97185 ( 39) hydrogen bonds : bond 0.04151 ( 420) hydrogen bonds : angle 5.90234 ( 1155) link_BETA1-6 : bond 0.00602 ( 2) link_BETA1-6 : angle 1.44951 ( 6) SS BOND : bond 0.00347 ( 24) SS BOND : angle 2.40698 ( 48) covalent geometry : bond 0.00387 (11577) covalent geometry : angle 0.65730 (15793) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 TYR cc_start: 0.8983 (OUTLIER) cc_final: 0.7513 (t80) REVERT: B 192 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.7980 (tttp) REVERT: E 31 TYR cc_start: 0.9087 (m-80) cc_final: 0.8715 (m-80) REVERT: E 52 ARG cc_start: 0.7754 (mmt180) cc_final: 0.7468 (mtt90) REVERT: F 24 ARG cc_start: 0.7239 (mmp-170) cc_final: 0.6995 (mmm160) REVERT: F 100 TYR cc_start: 0.8829 (m-80) cc_final: 0.8604 (m-10) REVERT: H 87 ASN cc_start: 0.7178 (t0) cc_final: 0.6947 (t0) outliers start: 22 outliers final: 10 residues processed: 188 average time/residue: 0.2640 time to fit residues: 68.8161 Evaluate side-chains 157 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 478 ASN Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain H residue 84 GLN Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 99 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 64 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 137 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 chunk 132 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 130 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 GLN B 186 ASN B 450 GLN B 509 ASN ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.151352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.120185 restraints weight = 14215.669| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.23 r_work: 0.3137 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11630 Z= 0.153 Angle : 0.619 12.236 15928 Z= 0.316 Chirality : 0.047 0.182 1847 Planarity : 0.004 0.050 2007 Dihedral : 5.077 57.254 2181 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.28 % Favored : 97.65 % Rotamer: Outliers : 1.88 % Allowed : 9.11 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.22), residues: 1446 helix: 2.17 (0.74), residues: 64 sheet: 0.63 (0.22), residues: 546 loop : 0.15 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 519 HIS 0.004 0.001 HIS B 233 PHE 0.009 0.001 PHE F 102 TYR 0.015 0.001 TYR A 291 ARG 0.004 0.000 ARG E 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 14) link_NAG-ASN : angle 1.43768 ( 42) link_BETA1-4 : bond 0.00617 ( 13) link_BETA1-4 : angle 1.88982 ( 39) hydrogen bonds : bond 0.03623 ( 420) hydrogen bonds : angle 5.58211 ( 1155) link_BETA1-6 : bond 0.00218 ( 2) link_BETA1-6 : angle 1.35417 ( 6) SS BOND : bond 0.00301 ( 24) SS BOND : angle 2.30140 ( 48) covalent geometry : bond 0.00358 (11577) covalent geometry : angle 0.59581 (15793) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 TYR cc_start: 0.8979 (OUTLIER) cc_final: 0.7562 (t80) REVERT: B 192 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8031 (tttp) REVERT: B 559 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7897 (mm-40) REVERT: E 31 TYR cc_start: 0.9087 (m-80) cc_final: 0.8657 (m-80) REVERT: D 141 ASN cc_start: 0.6385 (t0) cc_final: 0.6177 (t0) outliers start: 20 outliers final: 13 residues processed: 178 average time/residue: 0.2394 time to fit residues: 61.0987 Evaluate side-chains 166 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain L residue 13 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 51 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 73 optimal weight: 0.0170 chunk 14 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 HIS A 559 GLN B 186 ASN B 434 GLN F 58 GLN ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.150570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.119240 restraints weight = 14112.530| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.21 r_work: 0.3116 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11630 Z= 0.148 Angle : 0.584 9.869 15928 Z= 0.295 Chirality : 0.046 0.173 1847 Planarity : 0.004 0.051 2007 Dihedral : 4.786 54.564 2181 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.35 % Favored : 97.58 % Rotamer: Outliers : 2.35 % Allowed : 9.86 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.22), residues: 1446 helix: 2.51 (0.76), residues: 62 sheet: 0.56 (0.22), residues: 547 loop : 0.11 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 519 HIS 0.005 0.001 HIS B 233 PHE 0.009 0.001 PHE H 106 TYR 0.016 0.001 TYR A 291 ARG 0.005 0.000 ARG E 52 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 14) link_NAG-ASN : angle 1.31278 ( 42) link_BETA1-4 : bond 0.00520 ( 13) link_BETA1-4 : angle 1.64825 ( 39) hydrogen bonds : bond 0.03270 ( 420) hydrogen bonds : angle 5.31257 ( 1155) link_BETA1-6 : bond 0.00205 ( 2) link_BETA1-6 : angle 1.40390 ( 6) SS BOND : bond 0.00237 ( 24) SS BOND : angle 1.79560 ( 48) covalent geometry : bond 0.00348 (11577) covalent geometry : angle 0.56774 (15793) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 TYR cc_start: 0.8972 (OUTLIER) cc_final: 0.7678 (t80) REVERT: A 556 THR cc_start: 0.7490 (OUTLIER) cc_final: 0.7278 (p) REVERT: B 192 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8020 (tttp) REVERT: B 375 PHE cc_start: 0.8415 (t80) cc_final: 0.8138 (t80) REVERT: B 559 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7829 (mm-40) REVERT: E 31 TYR cc_start: 0.9104 (m-80) cc_final: 0.8674 (m-80) REVERT: L 78 ASN cc_start: 0.8221 (m-40) cc_final: 0.7887 (m-40) REVERT: D 141 ASN cc_start: 0.6465 (t0) cc_final: 0.6253 (t0) REVERT: D 157 GLU cc_start: 0.7833 (pt0) cc_final: 0.7628 (pt0) outliers start: 25 outliers final: 12 residues processed: 178 average time/residue: 0.2383 time to fit residues: 60.4880 Evaluate side-chains 159 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 56 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 50 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 126 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.0270 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 530 GLN A 559 GLN B 174 GLN B 186 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.150566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.119444 restraints weight = 14030.426| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.21 r_work: 0.3127 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11630 Z= 0.133 Angle : 0.565 11.491 15928 Z= 0.285 Chirality : 0.046 0.176 1847 Planarity : 0.004 0.051 2007 Dihedral : 4.615 49.560 2181 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.49 % Favored : 97.44 % Rotamer: Outliers : 2.54 % Allowed : 9.95 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.22), residues: 1446 helix: 2.00 (0.75), residues: 68 sheet: 0.61 (0.22), residues: 530 loop : 0.04 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 519 HIS 0.005 0.001 HIS B 233 PHE 0.008 0.001 PHE H 106 TYR 0.014 0.001 TYR A 291 ARG 0.005 0.000 ARG E 52 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 14) link_NAG-ASN : angle 1.26531 ( 42) link_BETA1-4 : bond 0.00507 ( 13) link_BETA1-4 : angle 1.60708 ( 39) hydrogen bonds : bond 0.03130 ( 420) hydrogen bonds : angle 5.20955 ( 1155) link_BETA1-6 : bond 0.00253 ( 2) link_BETA1-6 : angle 1.40589 ( 6) SS BOND : bond 0.00303 ( 24) SS BOND : angle 1.81062 ( 48) covalent geometry : bond 0.00315 (11577) covalent geometry : angle 0.54842 (15793) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 TYR cc_start: 0.8954 (OUTLIER) cc_final: 0.7726 (t80) REVERT: B 191 GLN cc_start: 0.8198 (mp10) cc_final: 0.7776 (mp10) REVERT: B 192 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.7966 (tttp) REVERT: B 242 ARG cc_start: 0.7925 (mtp180) cc_final: 0.7664 (mtp180) REVERT: B 291 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.8537 (t80) REVERT: B 351 TYR cc_start: 0.9171 (OUTLIER) cc_final: 0.8513 (t80) REVERT: B 375 PHE cc_start: 0.8393 (t80) cc_final: 0.8095 (t80) REVERT: B 559 GLN cc_start: 0.8043 (mm-40) cc_final: 0.7805 (mm-40) REVERT: E 31 TYR cc_start: 0.9090 (m-80) cc_final: 0.8686 (m-80) REVERT: L 78 ASN cc_start: 0.8307 (m-40) cc_final: 0.8060 (m-40) REVERT: D 157 GLU cc_start: 0.7799 (pt0) cc_final: 0.7585 (pt0) outliers start: 27 outliers final: 13 residues processed: 171 average time/residue: 0.2768 time to fit residues: 69.3381 Evaluate side-chains 160 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 56 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 91 optimal weight: 2.9990 chunk 131 optimal weight: 0.0770 chunk 132 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 559 GLN B 186 ASN ** B 191 GLN ** 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 = 0.3717 r_free = 0.3717 target = 0.150197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.118893 restraints weight = 14186.202| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.21 r_work: 0.3122 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11630 Z= 0.134 Angle : 0.560 10.453 15928 Z= 0.282 Chirality : 0.046 0.174 1847 Planarity : 0.004 0.052 2007 Dihedral : 4.494 42.920 2181 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.77 % Favored : 97.16 % Rotamer: Outliers : 2.35 % Allowed : 10.61 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.22), residues: 1446 helix: 1.94 (0.75), residues: 68 sheet: 0.60 (0.22), residues: 539 loop : 0.01 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 519 HIS 0.005 0.001 HIS B 233 PHE 0.009 0.001 PHE B 466 TYR 0.014 0.001 TYR A 291 ARG 0.004 0.000 ARG E 52 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 14) link_NAG-ASN : angle 1.21901 ( 42) link_BETA1-4 : bond 0.00486 ( 13) link_BETA1-4 : angle 1.57223 ( 39) hydrogen bonds : bond 0.03074 ( 420) hydrogen bonds : angle 5.17740 ( 1155) link_BETA1-6 : bond 0.00168 ( 2) link_BETA1-6 : angle 1.39859 ( 6) SS BOND : bond 0.00385 ( 24) SS BOND : angle 1.78649 ( 48) covalent geometry : bond 0.00315 (11577) covalent geometry : angle 0.54338 (15793) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 1.789 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.7677 (mptt) cc_final: 0.7349 (mmtp) REVERT: A 291 TYR cc_start: 0.8955 (OUTLIER) cc_final: 0.7757 (t80) REVERT: A 425 LYS cc_start: 0.7833 (pttp) cc_final: 0.7578 (pttp) REVERT: B 191 GLN cc_start: 0.8203 (mp10) cc_final: 0.7864 (mp10) REVERT: B 192 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.7984 (tttp) REVERT: B 291 TYR cc_start: 0.8818 (OUTLIER) cc_final: 0.8520 (t80) REVERT: B 351 TYR cc_start: 0.9170 (OUTLIER) cc_final: 0.8510 (t80) REVERT: B 375 PHE cc_start: 0.8385 (t80) cc_final: 0.8063 (t80) REVERT: B 559 GLN cc_start: 0.8048 (mm-40) cc_final: 0.7805 (mm-40) REVERT: E 31 TYR cc_start: 0.9060 (m-80) cc_final: 0.8655 (m-80) REVERT: L 37 MET cc_start: 0.8253 (tpt) cc_final: 0.8005 (tpt) REVERT: L 78 ASN cc_start: 0.8337 (m-40) cc_final: 0.8056 (m-40) outliers start: 25 outliers final: 16 residues processed: 170 average time/residue: 0.2703 time to fit residues: 67.7623 Evaluate side-chains 166 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 2.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 97 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 11 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 131 optimal weight: 0.0970 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 70 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 559 GLN B 186 ASN ** B 191 GLN ** 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 = 0.3719 r_free = 0.3719 target = 0.150288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.119025 restraints weight = 14275.105| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.22 r_work: 0.3124 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11630 Z= 0.131 Angle : 0.580 11.796 15928 Z= 0.290 Chirality : 0.046 0.223 1847 Planarity : 0.004 0.052 2007 Dihedral : 4.422 34.746 2181 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.04 % Favored : 96.89 % Rotamer: Outliers : 2.25 % Allowed : 10.61 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.22), residues: 1446 helix: 1.95 (0.75), residues: 67 sheet: 0.58 (0.22), residues: 538 loop : -0.04 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 519 HIS 0.005 0.001 HIS B 233 PHE 0.009 0.001 PHE B 466 TYR 0.013 0.001 TYR A 291 ARG 0.004 0.000 ARG E 52 Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 14) link_NAG-ASN : angle 1.18161 ( 42) link_BETA1-4 : bond 0.00468 ( 13) link_BETA1-4 : angle 1.54372 ( 39) hydrogen bonds : bond 0.03191 ( 420) hydrogen bonds : angle 5.07186 ( 1155) link_BETA1-6 : bond 0.00143 ( 2) link_BETA1-6 : angle 1.37456 ( 6) SS BOND : bond 0.00414 ( 24) SS BOND : angle 1.94046 ( 48) covalent geometry : bond 0.00312 (11577) covalent geometry : angle 0.56297 (15793) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 2.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 TYR cc_start: 0.8957 (OUTLIER) cc_final: 0.7770 (t80) REVERT: A 425 LYS cc_start: 0.7922 (pttp) cc_final: 0.7568 (pttp) REVERT: B 190 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7353 (pt) REVERT: B 291 TYR cc_start: 0.8823 (OUTLIER) cc_final: 0.8531 (t80) REVERT: B 351 TYR cc_start: 0.9156 (OUTLIER) cc_final: 0.8505 (t80) REVERT: B 375 PHE cc_start: 0.8386 (t80) cc_final: 0.8029 (t80) REVERT: B 559 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7756 (mm-40) REVERT: E 31 TYR cc_start: 0.9066 (m-80) cc_final: 0.8687 (m-80) REVERT: F 93 GLN cc_start: 0.8081 (tt0) cc_final: 0.7772 (tt0) REVERT: L 37 MET cc_start: 0.8278 (tpt) cc_final: 0.8017 (tpt) REVERT: L 78 ASN cc_start: 0.8330 (m-40) cc_final: 0.8052 (m-40) outliers start: 24 outliers final: 16 residues processed: 162 average time/residue: 0.2589 time to fit residues: 61.5052 Evaluate side-chains 163 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 89 MET Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 97 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 85 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 126 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 39 optimal weight: 0.4980 chunk 116 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 GLN B 186 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.150216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.119062 restraints weight = 14158.108| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.20 r_work: 0.3122 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11630 Z= 0.131 Angle : 0.563 10.430 15928 Z= 0.282 Chirality : 0.046 0.172 1847 Planarity : 0.004 0.052 2007 Dihedral : 4.305 28.161 2181 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.84 % Favored : 97.10 % Rotamer: Outliers : 2.07 % Allowed : 11.17 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.22), residues: 1446 helix: 1.91 (0.74), residues: 67 sheet: 0.55 (0.22), residues: 538 loop : -0.07 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 519 HIS 0.005 0.001 HIS B 233 PHE 0.008 0.001 PHE B 466 TYR 0.013 0.001 TYR A 291 ARG 0.004 0.000 ARG B 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00212 ( 14) link_NAG-ASN : angle 1.15725 ( 42) link_BETA1-4 : bond 0.00464 ( 13) link_BETA1-4 : angle 1.52219 ( 39) hydrogen bonds : bond 0.03075 ( 420) hydrogen bonds : angle 5.05716 ( 1155) link_BETA1-6 : bond 0.00176 ( 2) link_BETA1-6 : angle 1.39504 ( 6) SS BOND : bond 0.00400 ( 24) SS BOND : angle 1.65773 ( 48) covalent geometry : bond 0.00313 (11577) covalent geometry : angle 0.54895 (15793) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 GLU cc_start: 0.8601 (mp0) cc_final: 0.8337 (mp0) REVERT: A 291 TYR cc_start: 0.8983 (OUTLIER) cc_final: 0.7847 (t80) REVERT: A 322 LYS cc_start: 0.8632 (mmtt) cc_final: 0.8318 (mmmt) REVERT: B 191 GLN cc_start: 0.8199 (mp10) cc_final: 0.7729 (mp10) REVERT: B 291 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.8584 (t80) REVERT: B 351 TYR cc_start: 0.9187 (OUTLIER) cc_final: 0.8560 (t80) REVERT: B 375 PHE cc_start: 0.8401 (t80) cc_final: 0.7967 (t80) REVERT: B 559 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7998 (mm-40) REVERT: B 600 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7150 (mm-40) REVERT: E 31 TYR cc_start: 0.9089 (m-80) cc_final: 0.8722 (m-80) REVERT: E 84 GLN cc_start: 0.7344 (tp40) cc_final: 0.6795 (tt0) REVERT: L 37 MET cc_start: 0.8516 (tpt) cc_final: 0.8278 (tpt) REVERT: L 78 ASN cc_start: 0.8443 (m-40) cc_final: 0.8172 (m-40) outliers start: 22 outliers final: 16 residues processed: 163 average time/residue: 0.2619 time to fit residues: 61.9168 Evaluate side-chains 163 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 89 MET Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 97 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 105 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 109 optimal weight: 0.1980 chunk 1 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.149896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.118388 restraints weight = 14034.435| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.15 r_work: 0.3137 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11630 Z= 0.135 Angle : 0.567 12.167 15928 Z= 0.283 Chirality : 0.046 0.170 1847 Planarity : 0.004 0.052 2007 Dihedral : 4.205 27.491 2181 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.04 % Favored : 96.89 % Rotamer: Outliers : 2.25 % Allowed : 11.55 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.22), residues: 1446 helix: 1.86 (0.74), residues: 67 sheet: 0.51 (0.22), residues: 540 loop : -0.10 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 519 HIS 0.005 0.001 HIS B 233 PHE 0.009 0.001 PHE B 466 TYR 0.014 0.001 TYR A 291 ARG 0.005 0.000 ARG B 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00231 ( 14) link_NAG-ASN : angle 1.13630 ( 42) link_BETA1-4 : bond 0.00462 ( 13) link_BETA1-4 : angle 1.49983 ( 39) hydrogen bonds : bond 0.03054 ( 420) hydrogen bonds : angle 5.06016 ( 1155) link_BETA1-6 : bond 0.00143 ( 2) link_BETA1-6 : angle 1.40269 ( 6) SS BOND : bond 0.00369 ( 24) SS BOND : angle 1.47066 ( 48) covalent geometry : bond 0.00321 (11577) covalent geometry : angle 0.55533 (15793) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 GLU cc_start: 0.8541 (mp0) cc_final: 0.8221 (mp0) REVERT: A 291 TYR cc_start: 0.9025 (OUTLIER) cc_final: 0.7786 (t80) REVERT: A 315 MET cc_start: 0.8487 (ptm) cc_final: 0.8216 (ptt) REVERT: A 322 LYS cc_start: 0.8656 (mmtt) cc_final: 0.8312 (mmmt) REVERT: B 191 GLN cc_start: 0.8181 (mp10) cc_final: 0.7649 (mp10) REVERT: B 242 ARG cc_start: 0.7986 (mtm110) cc_final: 0.7610 (mtp180) REVERT: B 291 TYR cc_start: 0.9009 (OUTLIER) cc_final: 0.8727 (t80) REVERT: B 351 TYR cc_start: 0.9213 (OUTLIER) cc_final: 0.8555 (t80) REVERT: B 375 PHE cc_start: 0.8326 (t80) cc_final: 0.7920 (t80) REVERT: B 559 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7843 (mm-40) REVERT: B 600 GLN cc_start: 0.7638 (mm-40) cc_final: 0.7108 (mm-40) REVERT: E 31 TYR cc_start: 0.9026 (m-80) cc_final: 0.8641 (m-80) REVERT: E 84 GLN cc_start: 0.7360 (tp40) cc_final: 0.6855 (tt0) REVERT: L 37 MET cc_start: 0.8411 (tpt) cc_final: 0.8099 (tpt) REVERT: L 78 ASN cc_start: 0.8301 (m-40) cc_final: 0.7963 (m-40) REVERT: D 157 GLU cc_start: 0.8028 (pt0) cc_final: 0.7665 (pt0) outliers start: 24 outliers final: 17 residues processed: 170 average time/residue: 0.2286 time to fit residues: 56.7753 Evaluate side-chains 166 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 89 MET Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 97 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 18 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 133 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 113 optimal weight: 0.0970 chunk 119 optimal weight: 0.7980 chunk 31 optimal weight: 0.0980 chunk 50 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 ASN B 187 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.149832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.118424 restraints weight = 14167.811| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.21 r_work: 0.3104 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11630 Z= 0.125 Angle : 0.561 10.582 15928 Z= 0.281 Chirality : 0.046 0.173 1847 Planarity : 0.004 0.052 2007 Dihedral : 4.177 26.928 2181 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.97 % Favored : 96.96 % Rotamer: Outliers : 1.97 % Allowed : 12.30 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.22), residues: 1446 helix: 1.89 (0.74), residues: 67 sheet: 0.54 (0.22), residues: 540 loop : -0.08 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 47 HIS 0.005 0.001 HIS B 233 PHE 0.007 0.001 PHE A 466 TYR 0.014 0.001 TYR F 53 ARG 0.004 0.000 ARG B 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00197 ( 14) link_NAG-ASN : angle 1.11215 ( 42) link_BETA1-4 : bond 0.00448 ( 13) link_BETA1-4 : angle 1.48827 ( 39) hydrogen bonds : bond 0.02994 ( 420) hydrogen bonds : angle 5.05046 ( 1155) link_BETA1-6 : bond 0.00179 ( 2) link_BETA1-6 : angle 1.38716 ( 6) SS BOND : bond 0.00334 ( 24) SS BOND : angle 1.42242 ( 48) covalent geometry : bond 0.00297 (11577) covalent geometry : angle 0.54974 (15793) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 GLU cc_start: 0.8378 (mp0) cc_final: 0.8098 (mp0) REVERT: A 291 TYR cc_start: 0.8961 (OUTLIER) cc_final: 0.7784 (t80) REVERT: A 315 MET cc_start: 0.8198 (ptm) cc_final: 0.7962 (ptt) REVERT: A 322 LYS cc_start: 0.8510 (mmtt) cc_final: 0.8230 (mmmt) REVERT: B 191 GLN cc_start: 0.8027 (mp10) cc_final: 0.7629 (mp10) REVERT: B 225 ASP cc_start: 0.8157 (t70) cc_final: 0.7889 (t0) REVERT: B 291 TYR cc_start: 0.8838 (OUTLIER) cc_final: 0.8571 (t80) REVERT: B 351 TYR cc_start: 0.9145 (OUTLIER) cc_final: 0.8501 (t80) REVERT: B 375 PHE cc_start: 0.8301 (t80) cc_final: 0.7922 (t80) REVERT: B 559 GLN cc_start: 0.8026 (mm-40) cc_final: 0.7761 (mm-40) REVERT: B 600 GLN cc_start: 0.7520 (mm-40) cc_final: 0.7118 (mm-40) REVERT: E 31 TYR cc_start: 0.9037 (m-80) cc_final: 0.8654 (m-80) REVERT: L 37 MET cc_start: 0.8246 (tpt) cc_final: 0.7936 (tpt) REVERT: L 78 ASN cc_start: 0.8336 (m-40) cc_final: 0.8008 (m-40) outliers start: 21 outliers final: 17 residues processed: 162 average time/residue: 0.2201 time to fit residues: 52.1423 Evaluate side-chains 166 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 89 MET Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 97 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 6 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 141 optimal weight: 0.4980 chunk 91 optimal weight: 0.6980 chunk 135 optimal weight: 6.9990 chunk 39 optimal weight: 0.0980 chunk 65 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.150253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.118471 restraints weight = 14137.798| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.23 r_work: 0.3112 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11630 Z= 0.119 Angle : 0.556 11.204 15928 Z= 0.278 Chirality : 0.046 0.169 1847 Planarity : 0.004 0.052 2007 Dihedral : 4.145 26.746 2181 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.84 % Favored : 97.10 % Rotamer: Outliers : 1.97 % Allowed : 12.49 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.22), residues: 1446 helix: 2.57 (0.76), residues: 61 sheet: 0.55 (0.22), residues: 540 loop : -0.06 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 271 HIS 0.005 0.001 HIS B 233 PHE 0.007 0.001 PHE A 466 TYR 0.013 0.001 TYR F 53 ARG 0.006 0.000 ARG B 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 14) link_NAG-ASN : angle 1.09635 ( 42) link_BETA1-4 : bond 0.00443 ( 13) link_BETA1-4 : angle 1.48056 ( 39) hydrogen bonds : bond 0.02958 ( 420) hydrogen bonds : angle 5.03017 ( 1155) link_BETA1-6 : bond 0.00191 ( 2) link_BETA1-6 : angle 1.37738 ( 6) SS BOND : bond 0.00372 ( 24) SS BOND : angle 1.53844 ( 48) covalent geometry : bond 0.00284 (11577) covalent geometry : angle 0.54367 (15793) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6696.95 seconds wall clock time: 119 minutes 43.54 seconds (7183.54 seconds total)