Starting phenix.real_space_refine on Fri Sep 27 15:36:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6his_0228/09_2024/6his_0228.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6his_0228/09_2024/6his_0228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6his_0228/09_2024/6his_0228.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6his_0228/09_2024/6his_0228.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6his_0228/09_2024/6his_0228.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6his_0228/09_2024/6his_0228.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 45 5.16 5 C 10655 2.51 5 N 2595 2.21 5 O 2945 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16240 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3132 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 20, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "E" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3132 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 20, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3132 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 20, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3132 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 20, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3132 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 20, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 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: 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: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'TKT': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'TKT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'TKT': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'TKT': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'TKT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.53, per 1000 atoms: 0.71 Number of scatterers: 16240 At special positions: 0 Unit cell: (105.978, 104.939, 169.357, 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 45 16.00 O 2945 8.00 N 2595 7.00 C 10655 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG F 1 " - " ASN A 82 " " NAG G 1 " - " ASN A 164 " " NAG H 1 " - " ASN A 148 " " NAG I 1 " - " ASN E 82 " " NAG J 1 " - " ASN E 164 " " NAG K 1 " - " ASN E 148 " " NAG L 1 " - " ASN B 82 " " NAG M 1 " - " ASN B 164 " " NAG N 1 " - " ASN B 148 " " NAG O 1 " - " ASN C 82 " " NAG P 1 " - " ASN C 164 " " NAG Q 1 " - " ASN C 148 " " NAG R 1 " - " ASN D 82 " " NAG S 1 " - " ASN D 164 " " NAG T 1 " - " ASN D 148 " Time building additional restraints: 5.68 Conformation dependent library (CDL) restraints added in 2.3 seconds 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3760 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 10 sheets defined 45.0% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 Processing helix chain 'A' and resid 71 through 74 removed outlier: 4.042A pdb=" N GLN A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 71 through 74' Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 170 through 177 removed outlier: 3.968A pdb=" N VAL A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A 175 " --> pdb=" O PRO A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 226 removed outlier: 3.685A pdb=" N VAL A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 242 removed outlier: 3.544A pdb=" N SER A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 269 removed outlier: 4.603A pdb=" N SER A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS A 255 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 284 through 308 removed outlier: 4.939A pdb=" N CYS A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 295 " --> pdb=" O MET A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 325 removed outlier: 3.602A pdb=" N HIS A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 334 Processing helix chain 'A' and resid 402 through 458 removed outlier: 3.682A pdb=" N SER A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A 416 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 21 Processing helix chain 'E' and resid 71 through 74 removed outlier: 4.043A pdb=" N GLN E 74 " --> pdb=" O GLU E 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 71 through 74' Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 170 through 177 removed outlier: 3.967A pdb=" N VAL E 174 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG E 175 " --> pdb=" O PRO E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 226 removed outlier: 3.684A pdb=" N VAL E 225 " --> pdb=" O LEU E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 242 removed outlier: 3.544A pdb=" N SER E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL E 240 " --> pdb=" O VAL E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 269 removed outlier: 4.603A pdb=" N SER E 253 " --> pdb=" O GLY E 249 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS E 255 " --> pdb=" O ARG E 251 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR E 257 " --> pdb=" O SER E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 272 No H-bonds generated for 'chain 'E' and resid 270 through 272' Processing helix chain 'E' and resid 281 through 283 No H-bonds generated for 'chain 'E' and resid 281 through 283' Processing helix chain 'E' and resid 284 through 308 removed outlier: 4.938A pdb=" N CYS E 290 " --> pdb=" O TYR E 286 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL E 295 " --> pdb=" O MET E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 325 removed outlier: 3.602A pdb=" N HIS E 323 " --> pdb=" O ASP E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 334 Processing helix chain 'E' and resid 402 through 458 removed outlier: 3.682A pdb=" N SER E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG E 410 " --> pdb=" O LEU E 406 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG E 416 " --> pdb=" O PHE E 412 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL E 432 " --> pdb=" O ARG E 428 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR E 441 " --> pdb=" O LEU E 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 21 Processing helix chain 'B' and resid 71 through 74 removed outlier: 4.043A pdb=" N GLN B 74 " --> pdb=" O GLU B 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 71 through 74' Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 170 through 177 removed outlier: 3.968A pdb=" N VAL B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG B 175 " --> pdb=" O PRO B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 removed outlier: 3.684A pdb=" N VAL B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 242 removed outlier: 3.545A pdb=" N SER B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 269 removed outlier: 4.603A pdb=" N SER B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS B 255 " --> pdb=" O ARG B 251 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 281 through 283 No H-bonds generated for 'chain 'B' and resid 281 through 283' Processing helix chain 'B' and resid 284 through 308 removed outlier: 4.939A pdb=" N CYS B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B 295 " --> pdb=" O MET B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 325 removed outlier: 3.602A pdb=" N HIS B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 334 Processing helix chain 'B' and resid 402 through 458 removed outlier: 3.682A pdb=" N SER B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 21 Processing helix chain 'C' and resid 71 through 74 removed outlier: 4.044A pdb=" N GLN C 74 " --> pdb=" O GLU C 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 71 through 74' Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 170 through 177 removed outlier: 3.967A pdb=" N VAL C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 175 " --> pdb=" O PRO C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 3.683A pdb=" N VAL C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 242 removed outlier: 3.544A pdb=" N SER C 231 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 269 removed outlier: 4.603A pdb=" N SER C 253 " --> pdb=" O GLY C 249 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS C 255 " --> pdb=" O ARG C 251 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR C 257 " --> pdb=" O SER C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 272 No H-bonds generated for 'chain 'C' and resid 270 through 272' Processing helix chain 'C' and resid 281 through 283 No H-bonds generated for 'chain 'C' and resid 281 through 283' Processing helix chain 'C' and resid 284 through 308 removed outlier: 4.939A pdb=" N CYS C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 295 " --> pdb=" O MET C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 325 removed outlier: 3.602A pdb=" N HIS C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 334 Processing helix chain 'C' and resid 402 through 458 removed outlier: 3.684A pdb=" N SER C 408 " --> pdb=" O GLN C 404 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG C 410 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG C 416 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 21 Processing helix chain 'D' and resid 71 through 74 removed outlier: 4.043A pdb=" N GLN D 74 " --> pdb=" O GLU D 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 71 through 74' Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 170 through 177 removed outlier: 3.966A pdb=" N VAL D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG D 175 " --> pdb=" O PRO D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 removed outlier: 3.684A pdb=" N VAL D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 242 removed outlier: 3.545A pdb=" N SER D 231 " --> pdb=" O LEU D 227 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 269 removed outlier: 4.604A pdb=" N SER D 253 " --> pdb=" O GLY D 249 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS D 255 " --> pdb=" O ARG D 251 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR D 257 " --> pdb=" O SER D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 272 No H-bonds generated for 'chain 'D' and resid 270 through 272' Processing helix chain 'D' and resid 281 through 283 No H-bonds generated for 'chain 'D' and resid 281 through 283' Processing helix chain 'D' and resid 284 through 308 removed outlier: 4.939A pdb=" N CYS D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 295 " --> pdb=" O MET D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 325 removed outlier: 3.602A pdb=" N HIS D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 334 Processing helix chain 'D' and resid 402 through 458 removed outlier: 3.682A pdb=" N SER D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG D 410 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG D 416 " --> pdb=" O PHE D 412 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 89 removed outlier: 6.845A pdb=" N TYR A 114 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N TYR A 126 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL A 57 " --> pdb=" O ASN A 50 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASN A 50 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N THR A 59 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ILE A 48 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR A 61 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP A 42 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR A 69 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR A 38 " --> pdb=" O THR A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.987A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N LEU A 157 " --> pdb=" O SER A 206 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N SER A 206 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ASN A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE A 201 " --> pdb=" O ASN A 205 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE A 199 " --> pdb=" O TYR A 207 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 209 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU A 191 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 85 through 89 removed outlier: 6.846A pdb=" N TYR E 114 " --> pdb=" O TYR E 126 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N TYR E 126 " --> pdb=" O TYR E 114 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL E 57 " --> pdb=" O ASN E 50 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASN E 50 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N THR E 59 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE E 48 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR E 61 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP E 42 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N THR E 69 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR E 38 " --> pdb=" O THR E 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 98 through 100 removed outlier: 3.986A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N LEU E 157 " --> pdb=" O SER E 206 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N SER E 206 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ASN E 205 " --> pdb=" O ILE E 201 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE E 201 " --> pdb=" O ASN E 205 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE E 199 " --> pdb=" O TYR E 207 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU E 209 " --> pdb=" O LYS E 197 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU E 191 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ARG E 217 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LEU E 189 " --> pdb=" O ARG E 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 85 through 89 removed outlier: 6.845A pdb=" N TYR B 114 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N TYR B 126 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL B 57 " --> pdb=" O ASN B 50 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASN B 50 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N THR B 59 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ILE B 48 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR B 61 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP B 42 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N THR B 69 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR B 38 " --> pdb=" O THR B 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 100 removed outlier: 3.987A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N LEU B 157 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N SER B 206 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ASN B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE B 201 " --> pdb=" O ASN B 205 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B 199 " --> pdb=" O TYR B 207 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU B 209 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 85 through 89 removed outlier: 6.845A pdb=" N TYR C 114 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N TYR C 126 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL C 57 " --> pdb=" O ASN C 50 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASN C 50 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N THR C 59 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE C 48 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR C 61 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP C 42 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR C 69 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N THR C 38 " --> pdb=" O THR C 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.987A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N LEU C 157 " --> pdb=" O SER C 206 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N SER C 206 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ASN C 205 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE C 201 " --> pdb=" O ASN C 205 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE C 199 " --> pdb=" O TYR C 207 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU C 209 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU C 191 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 85 through 89 removed outlier: 6.844A pdb=" N TYR D 114 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N TYR D 126 " --> pdb=" O TYR D 114 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL D 57 " --> pdb=" O ASN D 50 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASN D 50 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N THR D 59 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE D 48 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR D 61 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP D 42 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR D 69 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR D 38 " --> pdb=" O THR D 69 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 98 through 100 removed outlier: 3.986A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N LEU D 157 " --> pdb=" O SER D 206 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N SER D 206 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ASN D 205 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE D 201 " --> pdb=" O ASN D 205 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE D 199 " --> pdb=" O TYR D 207 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU D 209 " --> pdb=" O LYS D 197 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU D 191 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) 775 hydrogen bonds defined for protein. 2325 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: 4.69 Time building geometry restraints manager: 6.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2510 1.31 - 1.44: 4734 1.44 - 1.57: 9336 1.57 - 1.70: 20 1.70 - 1.83: 70 Bond restraints: 16670 Sorted by residual: bond pdb=" C5 TKT C 501 " pdb=" N1 TKT C 501 " ideal model delta sigma weight residual 1.463 1.282 0.181 2.00e-02 2.50e+03 8.22e+01 bond pdb=" C5 TKT B 501 " pdb=" N1 TKT B 501 " ideal model delta sigma weight residual 1.463 1.282 0.181 2.00e-02 2.50e+03 8.19e+01 bond pdb=" C5 TKT E 501 " pdb=" N1 TKT E 501 " ideal model delta sigma weight residual 1.463 1.282 0.181 2.00e-02 2.50e+03 8.17e+01 bond pdb=" C5 TKT A 501 " pdb=" N1 TKT A 501 " ideal model delta sigma weight residual 1.463 1.282 0.181 2.00e-02 2.50e+03 8.17e+01 bond pdb=" C5 TKT D 501 " pdb=" N1 TKT D 501 " ideal model delta sigma weight residual 1.463 1.282 0.181 2.00e-02 2.50e+03 8.15e+01 ... (remaining 16665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.09: 22240 4.09 - 8.19: 460 8.19 - 12.28: 50 12.28 - 16.38: 35 16.38 - 20.47: 5 Bond angle restraints: 22790 Sorted by residual: angle pdb=" CA LEU C 73 " pdb=" CB LEU C 73 " pdb=" CG LEU C 73 " ideal model delta sigma weight residual 116.30 136.77 -20.47 3.50e+00 8.16e-02 3.42e+01 angle pdb=" CA LEU B 73 " pdb=" CB LEU B 73 " pdb=" CG LEU B 73 " ideal model delta sigma weight residual 116.30 136.77 -20.47 3.50e+00 8.16e-02 3.42e+01 angle pdb=" CA LEU A 73 " pdb=" CB LEU A 73 " pdb=" CG LEU A 73 " ideal model delta sigma weight residual 116.30 136.74 -20.44 3.50e+00 8.16e-02 3.41e+01 angle pdb=" CA LEU D 73 " pdb=" CB LEU D 73 " pdb=" CG LEU D 73 " ideal model delta sigma weight residual 116.30 136.73 -20.43 3.50e+00 8.16e-02 3.41e+01 angle pdb=" CA LEU E 73 " pdb=" CB LEU E 73 " pdb=" CG LEU E 73 " ideal model delta sigma weight residual 116.30 136.71 -20.41 3.50e+00 8.16e-02 3.40e+01 ... (remaining 22785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.02: 9742 21.02 - 42.05: 493 42.05 - 63.07: 75 63.07 - 84.09: 35 84.09 - 105.11: 25 Dihedral angle restraints: 10370 sinusoidal: 4600 harmonic: 5770 Sorted by residual: dihedral pdb=" CA SER C 179 " pdb=" C SER C 179 " pdb=" N ILE C 180 " pdb=" CA ILE C 180 " ideal model delta harmonic sigma weight residual -180.00 -115.57 -64.43 0 5.00e+00 4.00e-02 1.66e+02 dihedral pdb=" CA SER B 179 " pdb=" C SER B 179 " pdb=" N ILE B 180 " pdb=" CA ILE B 180 " ideal model delta harmonic sigma weight residual -180.00 -115.60 -64.40 0 5.00e+00 4.00e-02 1.66e+02 dihedral pdb=" CA SER D 179 " pdb=" C SER D 179 " pdb=" N ILE D 180 " pdb=" CA ILE D 180 " ideal model delta harmonic sigma weight residual -180.00 -115.67 -64.33 0 5.00e+00 4.00e-02 1.66e+02 ... (remaining 10367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1687 0.062 - 0.124: 760 0.124 - 0.186: 192 0.186 - 0.248: 71 0.248 - 0.310: 45 Chirality restraints: 2755 Sorted by residual: chirality pdb=" CB VAL C 252 " pdb=" CA VAL C 252 " pdb=" CG1 VAL C 252 " pdb=" CG2 VAL C 252 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CB VAL A 252 " pdb=" CA VAL A 252 " pdb=" CG1 VAL A 252 " pdb=" CG2 VAL A 252 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CB VAL E 252 " pdb=" CA VAL E 252 " pdb=" CG1 VAL E 252 " pdb=" CG2 VAL E 252 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 2752 not shown) Planarity restraints: 2775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 209 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" CD GLU D 209 " -0.045 2.00e-02 2.50e+03 pdb=" OE1 GLU D 209 " 0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU D 209 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 209 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" CD GLU A 209 " -0.045 2.00e-02 2.50e+03 pdb=" OE1 GLU A 209 " 0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU A 209 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 209 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.84e+00 pdb=" CD GLU B 209 " -0.045 2.00e-02 2.50e+03 pdb=" OE1 GLU B 209 " 0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU B 209 " 0.016 2.00e-02 2.50e+03 ... (remaining 2772 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2340 2.76 - 3.30: 15745 3.30 - 3.83: 27640 3.83 - 4.37: 30305 4.37 - 4.90: 51557 Nonbonded interactions: 127587 Sorted by model distance: nonbonded pdb=" NZ LYS D 197 " pdb=" O7 NAG T 2 " model vdw 2.228 3.120 nonbonded pdb=" NZ LYS B 197 " pdb=" O7 NAG N 2 " model vdw 2.228 3.120 nonbonded pdb=" NZ LYS A 197 " pdb=" O7 NAG H 2 " model vdw 2.229 3.120 nonbonded pdb=" NZ LYS C 197 " pdb=" O7 NAG Q 2 " model vdw 2.229 3.120 nonbonded pdb=" NZ LYS E 197 " pdb=" O7 NAG K 2 " model vdw 2.229 3.120 ... (remaining 127582 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' } Set up NCS constraints Number of NCS constrained groups: 3 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } pdb_interpretation.ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'T' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 41.420 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 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 : 0.011 0.181 16670 Z= 0.689 Angle : 1.573 20.472 22790 Z= 0.802 Chirality : 0.082 0.310 2755 Planarity : 0.007 0.031 2760 Dihedral : 14.279 105.113 6595 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.29 % Allowed : 11.08 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.17), residues: 1915 helix: -1.30 (0.16), residues: 715 sheet: -1.77 (0.20), residues: 475 loop : -1.90 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.005 TRP A 456 HIS 0.012 0.004 HIS A 411 PHE 0.025 0.004 PHE B 196 TYR 0.031 0.004 TYR A 207 ARG 0.006 0.001 ARG B 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8490 (mp0) cc_final: 0.8130 (mp0) REVERT: A 144 PHE cc_start: 0.6705 (m-10) cc_final: 0.6443 (m-80) REVERT: A 152 THR cc_start: 0.8350 (m) cc_final: 0.7959 (p) REVERT: A 156 TRP cc_start: 0.7710 (t-100) cc_final: 0.7032 (t60) REVERT: A 211 LYS cc_start: 0.8437 (mttm) cc_final: 0.7957 (ptpp) REVERT: A 247 ASP cc_start: 0.7438 (t70) cc_final: 0.6697 (m-30) REVERT: A 286 TYR cc_start: 0.8007 (m-10) cc_final: 0.7599 (t80) REVERT: A 422 VAL cc_start: 0.8794 (t) cc_final: 0.8509 (t) REVERT: A 426 TRP cc_start: 0.8388 (m100) cc_final: 0.8111 (m100) REVERT: A 428 ARG cc_start: 0.8503 (tmt90) cc_final: 0.7697 (tpt170) REVERT: A 441 TYR cc_start: 0.8472 (t80) cc_final: 0.7966 (t80) outliers start: 1 outliers final: 0 residues processed: 96 average time/residue: 0.1830 time to fit residues: 20.5554 Evaluate side-chains 57 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.347 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0020 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0032 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 6.9990 chunk 144 optimal weight: 0.0980 chunk 79 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 76 optimal weight: 9.9990 chunk 148 optimal weight: 0.5980 chunk 57 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 124 GLN E 205 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16670 Z= 0.295 Angle : 0.895 11.842 22790 Z= 0.462 Chirality : 0.063 0.873 2755 Planarity : 0.008 0.144 2760 Dihedral : 11.058 77.394 2970 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.87 % Allowed : 5.25 % Favored : 93.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.19), residues: 1915 helix: -0.62 (0.17), residues: 725 sheet: -0.96 (0.23), residues: 445 loop : -1.67 (0.25), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 63 HIS 0.008 0.002 HIS C 411 PHE 0.021 0.002 PHE E 222 TYR 0.015 0.002 TYR A 207 ARG 0.005 0.001 ARG B 410 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 152 THR cc_start: 0.8889 (m) cc_final: 0.8199 (m) REVERT: E 157 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.7809 (pp) REVERT: E 247 ASP cc_start: 0.7601 (t70) cc_final: 0.6897 (m-30) REVERT: E 286 TYR cc_start: 0.7927 (m-10) cc_final: 0.7530 (t80) REVERT: E 307 LEU cc_start: 0.8766 (tt) cc_final: 0.8175 (mm) REVERT: E 426 TRP cc_start: 0.8614 (m100) cc_final: 0.8219 (m-10) REVERT: E 428 ARG cc_start: 0.8301 (ttt-90) cc_final: 0.7950 (tpt170) REVERT: E 431 TYR cc_start: 0.8733 (m-80) cc_final: 0.8312 (m-80) outliers start: 3 outliers final: 1 residues processed: 77 average time/residue: 0.1605 time to fit residues: 15.0289 Evaluate side-chains 46 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.360 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0024 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0029 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 0.0370 chunk 53 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 117 optimal weight: 6.9990 chunk 47 optimal weight: 0.0370 chunk 172 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 171 optimal weight: 0.0270 chunk 58 optimal weight: 6.9990 chunk 138 optimal weight: 0.6980 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16670 Z= 0.245 Angle : 0.816 11.239 22790 Z= 0.407 Chirality : 0.059 0.738 2755 Planarity : 0.005 0.036 2760 Dihedral : 9.252 75.346 2970 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.19), residues: 1915 helix: -0.43 (0.17), residues: 725 sheet: -1.10 (0.22), residues: 445 loop : -1.57 (0.25), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 456 HIS 0.011 0.002 HIS C 411 PHE 0.041 0.002 PHE C 103 TYR 0.017 0.002 TYR B 223 ARG 0.017 0.001 ARG D 410 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: B 64 TYR cc_start: 0.8779 (t80) cc_final: 0.8514 (t80) REVERT: B 68 TRP cc_start: 0.9103 (p90) cc_final: 0.8847 (p90) REVERT: B 212 PHE cc_start: 0.8027 (m-80) cc_final: 0.7616 (m-80) REVERT: B 247 ASP cc_start: 0.7632 (t70) cc_final: 0.6945 (m-30) REVERT: B 286 TYR cc_start: 0.7542 (m-10) cc_final: 0.7162 (t80) REVERT: B 307 LEU cc_start: 0.8770 (tt) cc_final: 0.8307 (mm) REVERT: B 426 TRP cc_start: 0.8706 (m100) cc_final: 0.8147 (m100) REVERT: B 428 ARG cc_start: 0.8292 (ttt-90) cc_final: 0.7861 (tpt170) REVERT: B 431 TYR cc_start: 0.8734 (m-80) cc_final: 0.8236 (m-80) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1321 time to fit residues: 11.5457 Evaluate side-chains 48 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.379 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0024 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0030 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 6.9990 chunk 129 optimal weight: 0.0010 chunk 89 optimal weight: 0.0970 chunk 19 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 chunk 49 optimal weight: 0.0040 overall best weight: 1.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 16670 Z= 0.294 Angle : 0.783 14.271 22790 Z= 0.396 Chirality : 0.055 0.577 2755 Planarity : 0.009 0.169 2760 Dihedral : 7.989 75.216 2970 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.18), residues: 1915 helix: -0.77 (0.17), residues: 725 sheet: -0.99 (0.23), residues: 420 loop : -1.86 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 68 HIS 0.013 0.002 HIS C 411 PHE 0.019 0.002 PHE C 103 TYR 0.017 0.002 TYR A 223 ARG 0.014 0.001 ARG D 410 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 68 TRP cc_start: 0.9133 (p90) cc_final: 0.8921 (p90) REVERT: B 247 ASP cc_start: 0.7572 (t70) cc_final: 0.6963 (m-30) REVERT: B 286 TYR cc_start: 0.7497 (m-10) cc_final: 0.7095 (t80) REVERT: B 301 THR cc_start: 0.8960 (m) cc_final: 0.8746 (m) REVERT: B 307 LEU cc_start: 0.8787 (tt) cc_final: 0.8310 (mm) REVERT: B 410 ARG cc_start: 0.7213 (tpt170) cc_final: 0.6910 (tmt170) REVERT: B 426 TRP cc_start: 0.8631 (m100) cc_final: 0.8097 (m100) REVERT: B 428 ARG cc_start: 0.8040 (ttt-90) cc_final: 0.7613 (tpt170) REVERT: B 431 TYR cc_start: 0.8781 (m-80) cc_final: 0.8531 (m-80) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1232 time to fit residues: 9.7137 Evaluate side-chains 43 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.410 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0024 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0038 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 136 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 156 optimal weight: 0.2980 chunk 126 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16670 Z= 0.239 Angle : 0.683 8.622 22790 Z= 0.349 Chirality : 0.049 0.261 2755 Planarity : 0.005 0.047 2760 Dihedral : 7.054 75.562 2970 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.19), residues: 1915 helix: -0.40 (0.17), residues: 730 sheet: -0.88 (0.24), residues: 420 loop : -1.53 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 68 HIS 0.005 0.001 HIS C 411 PHE 0.019 0.002 PHE E 196 TYR 0.013 0.002 TYR A 64 ARG 0.007 0.001 ARG D 410 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: B 68 TRP cc_start: 0.9159 (p90) cc_final: 0.8926 (p90) REVERT: B 247 ASP cc_start: 0.7619 (t70) cc_final: 0.6955 (m-30) REVERT: B 286 TYR cc_start: 0.7564 (m-10) cc_final: 0.7104 (t80) REVERT: B 301 THR cc_start: 0.8976 (m) cc_final: 0.8763 (m) REVERT: B 307 LEU cc_start: 0.8821 (tt) cc_final: 0.8303 (mm) REVERT: B 426 TRP cc_start: 0.8644 (m100) cc_final: 0.8056 (m100) REVERT: B 428 ARG cc_start: 0.8133 (ttt-90) cc_final: 0.7659 (tpt170) REVERT: B 431 TYR cc_start: 0.8839 (m-80) cc_final: 0.8637 (m-80) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1143 time to fit residues: 9.6351 Evaluate side-chains 45 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.350 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0025 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0031 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 1.9990 chunk 165 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 183 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 60 optimal weight: 0.0870 chunk 96 optimal weight: 0.5980 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16670 Z= 0.207 Angle : 0.665 7.318 22790 Z= 0.332 Chirality : 0.047 0.243 2755 Planarity : 0.005 0.045 2760 Dihedral : 6.649 76.471 2970 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.19), residues: 1915 helix: -0.28 (0.17), residues: 730 sheet: -0.81 (0.24), residues: 420 loop : -1.47 (0.25), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 68 HIS 0.005 0.001 HIS B 411 PHE 0.019 0.002 PHE E 103 TYR 0.019 0.002 TYR C 441 ARG 0.004 0.000 ARG B 315 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 GLN cc_start: 0.7453 (mm110) cc_final: 0.7031 (mm110) REVERT: B 247 ASP cc_start: 0.7544 (t70) cc_final: 0.6899 (m-30) REVERT: B 286 TYR cc_start: 0.7554 (m-10) cc_final: 0.6985 (t80) REVERT: B 301 THR cc_start: 0.8997 (m) cc_final: 0.8791 (m) REVERT: B 307 LEU cc_start: 0.8839 (tt) cc_final: 0.8370 (mm) REVERT: B 426 TRP cc_start: 0.8654 (m100) cc_final: 0.8035 (m100) REVERT: B 428 ARG cc_start: 0.8177 (ttt-90) cc_final: 0.7702 (tpt170) REVERT: B 431 TYR cc_start: 0.8908 (m-80) cc_final: 0.8681 (m-80) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1167 time to fit residues: 9.8149 Evaluate side-chains 45 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.346 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0021 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0031 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 183 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 111 optimal weight: 0.5980 chunk 84 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16670 Z= 0.265 Angle : 0.686 6.718 22790 Z= 0.348 Chirality : 0.048 0.229 2755 Planarity : 0.005 0.043 2760 Dihedral : 6.581 75.459 2970 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.19), residues: 1915 helix: -0.08 (0.18), residues: 730 sheet: -0.73 (0.24), residues: 420 loop : -1.43 (0.25), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 68 HIS 0.006 0.002 HIS A 411 PHE 0.012 0.002 PHE E 233 TYR 0.019 0.002 TYR E 441 ARG 0.004 0.001 ARG E 315 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 GLN cc_start: 0.7440 (mm110) cc_final: 0.6862 (mm-40) REVERT: B 247 ASP cc_start: 0.7744 (t70) cc_final: 0.6929 (m-30) REVERT: B 286 TYR cc_start: 0.7634 (m-10) cc_final: 0.7077 (t80) REVERT: B 287 PHE cc_start: 0.8586 (m-80) cc_final: 0.8309 (m-80) REVERT: B 301 THR cc_start: 0.9042 (m) cc_final: 0.8798 (m) REVERT: B 307 LEU cc_start: 0.8885 (tt) cc_final: 0.8417 (mm) REVERT: B 426 TRP cc_start: 0.8653 (m100) cc_final: 0.8018 (m100) REVERT: B 428 ARG cc_start: 0.8259 (ttt-90) cc_final: 0.7783 (tpt170) REVERT: B 431 TYR cc_start: 0.8965 (m-80) cc_final: 0.8739 (m-80) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1105 time to fit residues: 9.1016 Evaluate side-chains 48 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.370 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0022 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0030 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 124 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16670 Z= 0.179 Angle : 0.664 6.655 22790 Z= 0.328 Chirality : 0.048 0.239 2755 Planarity : 0.004 0.040 2760 Dihedral : 6.453 76.951 2970 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.19), residues: 1915 helix: -0.10 (0.18), residues: 730 sheet: -0.70 (0.24), residues: 420 loop : -1.25 (0.25), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 68 HIS 0.004 0.001 HIS A 411 PHE 0.014 0.002 PHE C 103 TYR 0.014 0.002 TYR D 64 ARG 0.003 0.000 ARG E 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 GLN cc_start: 0.7423 (mm110) cc_final: 0.7130 (mm110) REVERT: B 207 TYR cc_start: 0.7634 (m-80) cc_final: 0.7422 (m-10) REVERT: B 210 MET cc_start: 0.8633 (tpp) cc_final: 0.8334 (tpp) REVERT: B 212 PHE cc_start: 0.8417 (m-80) cc_final: 0.8164 (m-80) REVERT: B 247 ASP cc_start: 0.7499 (t70) cc_final: 0.6842 (m-30) REVERT: B 286 TYR cc_start: 0.7623 (m-10) cc_final: 0.6940 (t80) REVERT: B 287 PHE cc_start: 0.8494 (m-80) cc_final: 0.8244 (m-80) REVERT: B 307 LEU cc_start: 0.8828 (tt) cc_final: 0.8388 (mm) REVERT: B 426 TRP cc_start: 0.8658 (m100) cc_final: 0.7982 (m100) REVERT: B 428 ARG cc_start: 0.8232 (ttt-90) cc_final: 0.7772 (tpt170) REVERT: B 431 TYR cc_start: 0.8927 (m-80) cc_final: 0.8721 (m-80) REVERT: B 452 LEU cc_start: 0.7705 (mt) cc_final: 0.7462 (mt) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1130 time to fit residues: 9.6836 Evaluate side-chains 46 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.376 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0022 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.024 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0031 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 102 optimal weight: 0.3980 chunk 74 optimal weight: 0.0040 chunk 134 optimal weight: 0.7980 chunk 52 optimal weight: 0.0040 chunk 154 optimal weight: 0.0010 chunk 161 optimal weight: 3.9990 chunk 112 optimal weight: 0.0040 chunk 180 optimal weight: 4.9990 overall best weight: 0.0822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16670 Z= 0.174 Angle : 0.672 7.192 22790 Z= 0.331 Chirality : 0.048 0.233 2755 Planarity : 0.004 0.040 2760 Dihedral : 6.324 77.870 2970 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.19), residues: 1915 helix: -0.15 (0.18), residues: 725 sheet: -0.73 (0.24), residues: 420 loop : -1.51 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 68 HIS 0.004 0.001 HIS E 411 PHE 0.023 0.002 PHE E 103 TYR 0.022 0.002 TYR C 61 ARG 0.004 0.000 ARG D 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 GLN cc_start: 0.7429 (mm110) cc_final: 0.7090 (mm110) REVERT: B 152 THR cc_start: 0.8984 (m) cc_final: 0.8630 (m) REVERT: B 207 TYR cc_start: 0.7695 (m-80) cc_final: 0.7454 (m-10) REVERT: B 210 MET cc_start: 0.8536 (tpp) cc_final: 0.8173 (tpp) REVERT: B 247 ASP cc_start: 0.7493 (t70) cc_final: 0.6904 (m-30) REVERT: B 286 TYR cc_start: 0.7552 (m-10) cc_final: 0.6975 (t80) REVERT: B 307 LEU cc_start: 0.8805 (tt) cc_final: 0.8408 (mm) REVERT: B 426 TRP cc_start: 0.8684 (m100) cc_final: 0.8039 (m100) REVERT: B 428 ARG cc_start: 0.8165 (ttt-90) cc_final: 0.7721 (tpt170) REVERT: B 452 LEU cc_start: 0.7726 (mt) cc_final: 0.7459 (mt) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1167 time to fit residues: 9.9400 Evaluate side-chains 47 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.368 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0023 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0031 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 2.9990 chunk 85 optimal weight: 0.0370 chunk 125 optimal weight: 0.7980 chunk 189 optimal weight: 0.8980 chunk 174 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 116 optimal weight: 0.0470 chunk 92 optimal weight: 0.0010 chunk 119 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 overall best weight: 0.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16670 Z= 0.167 Angle : 0.670 8.504 22790 Z= 0.328 Chirality : 0.047 0.222 2755 Planarity : 0.004 0.040 2760 Dihedral : 6.155 77.701 2970 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.19), residues: 1915 helix: -0.01 (0.19), residues: 730 sheet: -0.84 (0.23), residues: 450 loop : -1.45 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 68 HIS 0.002 0.001 HIS D 411 PHE 0.013 0.001 PHE A 103 TYR 0.014 0.002 TYR C 64 ARG 0.003 0.000 ARG E 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 GLN cc_start: 0.7517 (mm110) cc_final: 0.7086 (mm-40) REVERT: B 152 THR cc_start: 0.9043 (m) cc_final: 0.7171 (m) REVERT: B 247 ASP cc_start: 0.7412 (t70) cc_final: 0.6907 (m-30) REVERT: B 286 TYR cc_start: 0.7497 (m-10) cc_final: 0.6989 (t80) REVERT: B 307 LEU cc_start: 0.8783 (tt) cc_final: 0.8461 (mm) REVERT: B 320 TRP cc_start: 0.7519 (m-90) cc_final: 0.7185 (m100) REVERT: B 426 TRP cc_start: 0.8662 (m100) cc_final: 0.8141 (m100) REVERT: B 428 ARG cc_start: 0.8148 (ttt-90) cc_final: 0.7697 (tpt170) REVERT: B 431 TYR cc_start: 0.8869 (m-80) cc_final: 0.8425 (m-80) REVERT: B 452 LEU cc_start: 0.7756 (mt) cc_final: 0.7451 (mt) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1135 time to fit residues: 9.7114 Evaluate side-chains 52 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.338 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0022 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0028 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 0.0870 chunk 132 optimal weight: 0.6980 chunk 8 optimal weight: 7.9990 overall best weight: 1.0560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.100071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.088216 restraints weight = 13344.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.089796 restraints weight = 8209.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.090697 restraints weight = 5522.326| |-----------------------------------------------------------------------------| r_work (final): 0.3358 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2160 r_free = 0.2160 target = 0.036142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2166 r_free = 0.2166 target = 0.036083 restraints weight = 216.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2163 r_free = 0.2163 target = 0.036093 restraints weight = 15.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2162 r_free = 0.2162 target = 0.036121 restraints weight = 2.687 | |-----------------------------------------------------------------------------| r_work (final): 0.2166 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.048646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2469 r_free = 0.2469 target = 0.045934 restraints weight = 263.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.046880 restraints weight = 134.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.047629 restraints weight = 80.990| |-----------------------------------------------------------------------------| r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16670 Z= 0.189 Angle : 0.662 7.336 22790 Z= 0.328 Chirality : 0.048 0.217 2755 Planarity : 0.004 0.039 2760 Dihedral : 6.125 77.238 2970 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.19), residues: 1915 helix: 0.10 (0.19), residues: 730 sheet: -0.81 (0.23), residues: 435 loop : -1.55 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 68 HIS 0.002 0.001 HIS D 158 PHE 0.016 0.001 PHE E 103 TYR 0.015 0.002 TYR B 64 ARG 0.003 0.000 ARG E 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2781.70 seconds wall clock time: 51 minutes 4.19 seconds (3064.19 seconds total)