Starting phenix.real_space_refine on Fri Feb 16 18:56:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6his_0228/02_2024/6his_0228_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6his_0228/02_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_0228/02_2024/6his_0228.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6his_0228/02_2024/6his_0228.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6his_0228/02_2024/6his_0228_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6his_0228/02_2024/6his_0228_updated.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 8.41, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 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: 6.00 Conformation dependent library (CDL) restraints added in 2.7 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... running ksdssp... Secondary structure from input PDB file: 55 helices and 20 sheets defined 40.3% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.96 Creating SS restraints... Processing helix chain 'A' and resid 12 through 20 removed outlier: 4.130A pdb=" N LEU A 19 " --> pdb=" O SER A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.601A pdb=" N ARG A 175 " --> pdb=" O PRO A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 225 No H-bonds generated for 'chain 'A' and resid 222 through 225' Processing helix chain 'A' and resid 228 through 243 removed outlier: 3.589A pdb=" N VAL A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N CYS A 243 " --> pdb=" O ILE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 271 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) removed outlier: 4.137A pdb=" N ASP A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 307 removed outlier: 3.887A pdb=" N VAL A 288 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N VAL A 289 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE A 296 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE A 302 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 304 " --> pdb=" O THR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 322 Processing helix chain 'A' and resid 327 through 333 Processing helix chain 'A' and resid 403 through 457 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 20 removed outlier: 4.130A pdb=" N LEU E 19 " --> pdb=" O SER E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 73 No H-bonds generated for 'chain 'E' and resid 71 through 73' Processing helix chain 'E' and resid 90 through 92 No H-bonds generated for 'chain 'E' and resid 90 through 92' Processing helix chain 'E' and resid 171 through 176 removed outlier: 3.601A pdb=" N ARG E 175 " --> pdb=" O PRO E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 225 No H-bonds generated for 'chain 'E' and resid 222 through 225' Processing helix chain 'E' and resid 228 through 243 removed outlier: 3.588A pdb=" N VAL E 240 " --> pdb=" O VAL E 236 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N CYS E 243 " --> pdb=" O ILE E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 271 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) removed outlier: 4.137A pdb=" N ASP E 271 " --> pdb=" O ILE E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 307 removed outlier: 3.888A pdb=" N VAL E 288 " --> pdb=" O VAL E 285 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N VAL E 289 " --> pdb=" O TYR E 286 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE E 296 " --> pdb=" O LEU E 293 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE E 302 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE E 304 " --> pdb=" O THR E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 322 Processing helix chain 'E' and resid 327 through 333 Processing helix chain 'E' and resid 403 through 457 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 20 removed outlier: 4.130A pdb=" N LEU B 19 " --> pdb=" O SER B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.602A pdb=" N ARG B 175 " --> pdb=" O PRO B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 225 No H-bonds generated for 'chain 'B' and resid 222 through 225' Processing helix chain 'B' and resid 228 through 243 removed outlier: 3.588A pdb=" N VAL B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N CYS B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 271 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) removed outlier: 4.138A pdb=" N ASP B 271 " --> pdb=" O ILE B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 307 removed outlier: 3.888A pdb=" N VAL B 288 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N VAL B 289 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE B 302 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B 304 " --> pdb=" O THR B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 322 Processing helix chain 'B' and resid 327 through 333 Processing helix chain 'B' and resid 403 through 457 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 20 removed outlier: 4.130A pdb=" N LEU C 19 " --> pdb=" O SER C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'C' and resid 171 through 176 removed outlier: 3.601A pdb=" N ARG C 175 " --> pdb=" O PRO C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 225 No H-bonds generated for 'chain 'C' and resid 222 through 225' Processing helix chain 'C' and resid 228 through 243 removed outlier: 3.589A pdb=" N VAL C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N CYS C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 271 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) removed outlier: 4.137A pdb=" N ASP C 271 " --> pdb=" O ILE C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 307 removed outlier: 3.888A pdb=" N VAL C 288 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N VAL C 289 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE C 296 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE C 302 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE C 304 " --> pdb=" O THR C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 322 Processing helix chain 'C' and resid 327 through 333 Processing helix chain 'C' and resid 403 through 457 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 20 removed outlier: 4.130A pdb=" N LEU D 19 " --> pdb=" O SER D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 73 No H-bonds generated for 'chain 'D' and resid 71 through 73' Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 171 through 176 removed outlier: 3.601A pdb=" N ARG D 175 " --> pdb=" O PRO D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 225 No H-bonds generated for 'chain 'D' and resid 222 through 225' Processing helix chain 'D' and resid 228 through 243 removed outlier: 3.589A pdb=" N VAL D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N CYS D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 271 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) removed outlier: 4.137A pdb=" N ASP D 271 " --> pdb=" O ILE D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 307 removed outlier: 3.888A pdb=" N VAL D 288 " --> pdb=" O VAL D 285 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N VAL D 289 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D 296 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE D 302 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE D 304 " --> pdb=" O THR D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 322 Processing helix chain 'D' and resid 327 through 333 Processing helix chain 'D' and resid 403 through 457 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= A, first strand: chain 'A' and resid 163 through 167 removed outlier: 6.479A pdb=" N THR A 37 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR A 166 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL A 39 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR A 38 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR A 69 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP A 42 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR A 61 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ILE A 48 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N THR A 59 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 50 through 52 removed outlier: 3.587A pdb=" N ASN A 50 " --> pdb=" O THR A 59 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 85 through 89 Processing sheet with id= D, 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: 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= E, first strand: chain 'E' and resid 163 through 167 removed outlier: 6.479A pdb=" N THR E 37 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR E 166 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL E 39 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR E 38 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N THR E 69 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP E 42 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR E 61 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE E 48 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N THR E 59 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 50 through 52 removed outlier: 3.588A pdb=" N ASN E 50 " --> pdb=" O THR E 59 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 85 through 89 Processing sheet with id= H, 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: 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= I, first strand: chain 'B' and resid 163 through 167 removed outlier: 6.478A pdb=" N THR B 37 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR B 166 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL B 39 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR B 38 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N THR B 69 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP B 42 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR B 61 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ILE B 48 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N THR B 59 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 50 through 52 removed outlier: 3.587A pdb=" N ASN B 50 " --> pdb=" O THR B 59 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 85 through 89 Processing sheet with id= L, 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: 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= M, first strand: chain 'C' and resid 163 through 167 removed outlier: 6.479A pdb=" N THR C 37 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR C 166 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL C 39 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N THR C 38 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR C 69 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP C 42 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR C 61 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE C 48 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N THR C 59 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 50 through 52 removed outlier: 3.588A pdb=" N ASN C 50 " --> pdb=" O THR C 59 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 85 through 89 Processing sheet with id= P, 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: 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= Q, first strand: chain 'D' and resid 163 through 167 removed outlier: 6.479A pdb=" N THR D 37 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR D 166 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL D 39 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR D 38 " --> pdb=" O THR D 69 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR D 69 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP D 42 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR D 61 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE D 48 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N THR D 59 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 50 through 52 removed outlier: 3.588A pdb=" N ASN D 50 " --> pdb=" O THR D 59 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 85 through 89 Processing sheet with id= T, 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: 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) 705 hydrogen bonds defined for protein. 1740 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: 4.53 Time building geometry restraints manager: 6.50 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: 97.93 - 105.70: 418 105.70 - 113.47: 9298 113.47 - 121.24: 8531 121.24 - 129.00: 4343 129.00 - 136.77: 200 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: 2380 2.76 - 3.30: 15755 3.30 - 3.83: 27625 3.83 - 4.37: 30470 4.37 - 4.90: 51637 Nonbonded interactions: 127867 Sorted by model distance: nonbonded pdb=" NZ LYS D 197 " pdb=" O7 NAG T 2 " model vdw 2.228 2.520 nonbonded pdb=" NZ LYS B 197 " pdb=" O7 NAG N 2 " model vdw 2.228 2.520 nonbonded pdb=" NZ LYS A 197 " pdb=" O7 NAG H 2 " model vdw 2.229 2.520 nonbonded pdb=" NZ LYS C 197 " pdb=" O7 NAG Q 2 " model vdw 2.229 2.520 nonbonded pdb=" NZ LYS E 197 " pdb=" O7 NAG K 2 " model vdw 2.229 2.520 ... (remaining 127862 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' 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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 3.820 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 42.220 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.940 ------------------------------------------------------------------------------- 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= 0.678 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 : 0.373 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: 0.1812 time to fit residues: 20.2927 Evaluate side-chains 57 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.331 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: 0.0032 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: 0.0040 chunk 79 optimal weight: 0.0970 chunk 49 optimal weight: 0.0020 chunk 97 optimal weight: 0.0670 chunk 76 optimal weight: 10.0000 chunk 148 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 overall best weight: 1.0338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 66 GLN E 119 HIS E 124 GLN E 205 ASN Total number of N/Q/H flips: 4 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: 0.7700 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16670 Z= 0.250 Angle : 0.868 10.161 22790 Z= 0.442 Chirality : 0.057 0.655 2755 Planarity : 0.008 0.127 2760 Dihedral : 11.069 78.228 2970 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.58 % Allowed : 5.54 % 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: -2.00 (0.18), residues: 1915 helix: -0.99 (0.16), residues: 730 sheet: -1.05 (0.22), residues: 445 loop : -1.65 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 63 HIS 0.007 0.002 HIS C 411 PHE 0.022 0.002 PHE B 222 TYR 0.015 0.002 TYR E 207 ARG 0.016 0.001 ARG C 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 74 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 152 THR cc_start: 0.8619 (m) cc_final: 0.8125 (m) REVERT: E 157 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.7853 (pp) REVERT: E 247 ASP cc_start: 0.7582 (t70) cc_final: 0.6900 (m-30) REVERT: E 286 TYR cc_start: 0.8264 (m-10) cc_final: 0.7718 (t80) REVERT: E 307 LEU cc_start: 0.8752 (tt) cc_final: 0.8082 (mm) REVERT: E 426 TRP cc_start: 0.8597 (m100) cc_final: 0.8200 (m-10) REVERT: E 428 ARG cc_start: 0.8278 (ttt-90) cc_final: 0.7920 (tpt170) REVERT: E 431 TYR cc_start: 0.8715 (m-80) cc_final: 0.8319 (m-80) outliers start: 2 outliers final: 1 residues processed: 73 average time/residue: 0.1787 time to fit residues: 15.4840 Evaluate side-chains 50 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.383 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: 0.0029 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- 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: 0.0980 chunk 53 optimal weight: 0.9980 chunk 143 optimal weight: 0.9980 chunk 117 optimal weight: 0.3980 chunk 47 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 186 optimal weight: 7.9990 chunk 153 optimal weight: 7.9990 chunk 171 optimal weight: 0.2980 chunk 58 optimal weight: 0.0370 chunk 138 optimal weight: 3.9990 overall best weight: 0.3658 ------------------------------------------------------------------------------- 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: 0.7679 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16670 Z= 0.200 Angle : 0.756 10.603 22790 Z= 0.373 Chirality : 0.057 0.655 2755 Planarity : 0.005 0.071 2760 Dihedral : 8.852 74.330 2970 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % 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: -1.90 (0.19), residues: 1915 helix: -0.74 (0.17), residues: 710 sheet: -1.43 (0.21), residues: 445 loop : -1.45 (0.25), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 456 HIS 0.012 0.002 HIS C 411 PHE 0.034 0.002 PHE C 103 TYR 0.015 0.002 TYR B 223 ARG 0.023 0.001 ARG E 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 74 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 101 ASN cc_start: 0.8312 (m110) cc_final: 0.8011 (m110) REVERT: B 152 THR cc_start: 0.8709 (m) cc_final: 0.8293 (m) REVERT: B 247 ASP cc_start: 0.7517 (t70) cc_final: 0.6889 (m-30) REVERT: B 286 TYR cc_start: 0.7959 (m-10) cc_final: 0.7439 (t80) REVERT: B 307 LEU cc_start: 0.8629 (tt) cc_final: 0.8137 (mm) REVERT: B 426 TRP cc_start: 0.8687 (m100) cc_final: 0.8115 (m100) REVERT: B 428 ARG cc_start: 0.8294 (ttt-90) cc_final: 0.7538 (ttt180) REVERT: B 431 TYR cc_start: 0.8713 (m-80) cc_final: 0.8210 (m-80) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1412 time to fit residues: 12.9629 Evaluate side-chains 50 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.406 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: 0.0031 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 1.9990 chunk 129 optimal weight: 0.0060 chunk 89 optimal weight: 9.9990 chunk 19 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 164 optimal weight: 8.9990 chunk 49 optimal weight: 0.1980 overall best weight: 1.4000 ------------------------------------------------------------------------------- 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: 0.7724 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16670 Z= 0.210 Angle : 0.667 7.595 22790 Z= 0.340 Chirality : 0.047 0.241 2755 Planarity : 0.005 0.045 2760 Dihedral : 7.479 74.437 2970 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % 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: -2.07 (0.19), residues: 1915 helix: -0.84 (0.18), residues: 720 sheet: -1.28 (0.22), residues: 455 loop : -1.80 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 68 HIS 0.006 0.001 HIS C 411 PHE 0.019 0.002 PHE E 103 TYR 0.020 0.002 TYR D 64 ARG 0.003 0.000 ARG A 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 67 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 101 ASN cc_start: 0.8225 (m110) cc_final: 0.7777 (m110) REVERT: B 207 TYR cc_start: 0.7548 (m-10) cc_final: 0.7336 (m-80) REVERT: B 247 ASP cc_start: 0.7550 (t70) cc_final: 0.6963 (m-30) REVERT: B 286 TYR cc_start: 0.7955 (m-10) cc_final: 0.7457 (t80) REVERT: B 307 LEU cc_start: 0.8666 (tt) cc_final: 0.8134 (mm) REVERT: B 426 TRP cc_start: 0.8674 (m100) cc_final: 0.8116 (m100) REVERT: B 428 ARG cc_start: 0.8116 (ttt-90) cc_final: 0.7371 (ttt180) REVERT: B 431 TYR cc_start: 0.8751 (m-80) cc_final: 0.8511 (m-80) REVERT: B 441 TYR cc_start: 0.8392 (t80) cc_final: 0.8185 (t80) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1359 time to fit residues: 11.5175 Evaluate side-chains 43 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.370 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: 0.0024 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: 0.0030 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 136 optimal weight: 0.0010 chunk 75 optimal weight: 8.9990 chunk 156 optimal weight: 0.0050 chunk 126 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 93 optimal weight: 0.0980 chunk 164 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 overall best weight: 1.8204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 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: 0.7759 moved from start: 0.4133 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= 0.201 Angle : 0.627 6.445 22790 Z= 0.319 Chirality : 0.046 0.233 2755 Planarity : 0.005 0.056 2760 Dihedral : 6.860 74.558 2970 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % 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: -1.74 (0.19), residues: 1915 helix: -0.74 (0.18), residues: 720 sheet: -1.22 (0.23), residues: 425 loop : -1.32 (0.25), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 68 HIS 0.006 0.001 HIS A 411 PHE 0.013 0.002 PHE B 196 TYR 0.024 0.002 TYR C 441 ARG 0.003 0.000 ARG A 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 60 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 ASN cc_start: 0.8274 (m110) cc_final: 0.7875 (m110) REVERT: B 207 TYR cc_start: 0.7676 (m-10) cc_final: 0.7451 (m-80) REVERT: B 247 ASP cc_start: 0.7572 (t70) cc_final: 0.6927 (m-30) REVERT: B 286 TYR cc_start: 0.8019 (m-10) cc_final: 0.7446 (t80) REVERT: B 307 LEU cc_start: 0.8731 (tt) cc_final: 0.8176 (mm) REVERT: B 426 TRP cc_start: 0.8724 (m100) cc_final: 0.8153 (m100) REVERT: B 428 ARG cc_start: 0.8083 (ttt-90) cc_final: 0.7313 (ttt180) REVERT: B 431 TYR cc_start: 0.8822 (m-80) cc_final: 0.8584 (m-80) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1336 time to fit residues: 10.1952 Evaluate side-chains 45 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.383 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: 0.0028 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 ------------------------------------------------------------------------------- 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: 4.9990 chunk 165 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 60 optimal weight: 0.2980 chunk 96 optimal weight: 0.9980 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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: 0.7782 moved from start: 0.4365 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= 0.210 Angle : 0.628 6.611 22790 Z= 0.320 Chirality : 0.047 0.235 2755 Planarity : 0.005 0.044 2760 Dihedral : 6.724 76.216 2970 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % 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: -1.66 (0.19), residues: 1915 helix: -0.70 (0.18), residues: 725 sheet: -1.10 (0.23), residues: 425 loop : -1.30 (0.25), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 68 HIS 0.005 0.001 HIS A 411 PHE 0.012 0.002 PHE E 103 TYR 0.022 0.002 TYR A 441 ARG 0.002 0.000 ARG C 34 *********************** 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 62 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 TRP cc_start: 0.9198 (p90) cc_final: 0.8976 (p90) REVERT: B 101 ASN cc_start: 0.8297 (m110) cc_final: 0.7853 (m110) REVERT: B 207 TYR cc_start: 0.7533 (m-10) cc_final: 0.7263 (m-10) REVERT: B 247 ASP cc_start: 0.7625 (t70) cc_final: 0.6979 (m-30) REVERT: B 286 TYR cc_start: 0.8067 (m-10) cc_final: 0.7517 (t80) REVERT: B 307 LEU cc_start: 0.8763 (tt) cc_final: 0.8150 (mm) REVERT: B 426 TRP cc_start: 0.8736 (m100) cc_final: 0.8148 (m100) REVERT: B 428 ARG cc_start: 0.8236 (ttt-90) cc_final: 0.7437 (ttt180) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1406 time to fit residues: 10.9095 Evaluate side-chains 47 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.343 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: 0.0026 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 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 : 0.002 ------------------------------------------------------------------------------- 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: 6.9990 chunk 20 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 134 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 183 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 111 optimal weight: 0.4980 chunk 84 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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: 0.7821 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 16670 Z= 0.233 Angle : 0.665 10.232 22790 Z= 0.334 Chirality : 0.047 0.232 2755 Planarity : 0.005 0.042 2760 Dihedral : 6.682 77.535 2970 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % 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: -1.34 (0.20), residues: 1915 helix: -0.45 (0.19), residues: 695 sheet: -0.93 (0.24), residues: 425 loop : -1.08 (0.25), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 68 HIS 0.005 0.001 HIS A 411 PHE 0.015 0.002 PHE D 242 TYR 0.027 0.002 TYR D 441 ARG 0.003 0.000 ARG C 28 *********************** 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 65 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 68 TRP cc_start: 0.9221 (p90) cc_final: 0.8979 (p90) REVERT: B 101 ASN cc_start: 0.8349 (m110) cc_final: 0.7819 (m110) REVERT: B 207 TYR cc_start: 0.7528 (m-80) cc_final: 0.6987 (m-10) REVERT: B 247 ASP cc_start: 0.7695 (t70) cc_final: 0.6969 (m-30) REVERT: B 286 TYR cc_start: 0.8144 (m-10) cc_final: 0.7596 (t80) REVERT: B 301 THR cc_start: 0.9394 (t) cc_final: 0.9187 (t) REVERT: B 307 LEU cc_start: 0.8808 (tt) cc_final: 0.8170 (mm) REVERT: B 426 TRP cc_start: 0.8713 (m100) cc_final: 0.8173 (m100) REVERT: B 428 ARG cc_start: 0.8273 (ttt-90) cc_final: 0.7791 (tpt170) REVERT: B 431 TYR cc_start: 0.8759 (m-80) cc_final: 0.8363 (m-80) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1285 time to fit residues: 10.6300 Evaluate side-chains 47 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.362 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 : 0.032 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 90 optimal weight: 0.0670 chunk 17 optimal weight: 8.9990 chunk 143 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 175 optimal weight: 9.9990 overall best weight: 2.1524 ------------------------------------------------------------------------------- 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: 0.7809 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16670 Z= 0.235 Angle : 0.688 7.127 22790 Z= 0.351 Chirality : 0.047 0.232 2755 Planarity : 0.005 0.039 2760 Dihedral : 6.749 78.770 2970 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % 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: -1.36 (0.20), residues: 1915 helix: -0.49 (0.19), residues: 695 sheet: -0.90 (0.24), residues: 425 loop : -1.10 (0.25), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 68 HIS 0.005 0.001 HIS B 158 PHE 0.014 0.002 PHE A 242 TYR 0.023 0.002 TYR E 441 ARG 0.002 0.000 ARG A 219 *********************** 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 66 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 68 TRP cc_start: 0.9212 (p90) cc_final: 0.8981 (p90) REVERT: B 101 ASN cc_start: 0.8318 (m110) cc_final: 0.7761 (m110) REVERT: B 108 LYS cc_start: 0.7719 (mtmt) cc_final: 0.6525 (pptt) REVERT: B 207 TYR cc_start: 0.7630 (m-80) cc_final: 0.7114 (m-10) REVERT: B 247 ASP cc_start: 0.7712 (t70) cc_final: 0.6969 (m-30) REVERT: B 286 TYR cc_start: 0.8153 (m-10) cc_final: 0.7637 (t80) REVERT: B 426 TRP cc_start: 0.8666 (m100) cc_final: 0.8209 (m100) REVERT: B 428 ARG cc_start: 0.8194 (ttt-90) cc_final: 0.7401 (ttt180) REVERT: B 431 TYR cc_start: 0.8857 (m-80) cc_final: 0.8305 (m-80) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1328 time to fit residues: 10.9501 Evaluate side-chains 46 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.371 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 : 0.002 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.0980 chunk 170 optimal weight: 4.9990 chunk 175 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 74 optimal weight: 0.0670 chunk 134 optimal weight: 0.5980 chunk 52 optimal weight: 0.4980 chunk 154 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 112 optimal weight: 0.0670 chunk 180 optimal weight: 4.9990 overall best weight: 0.2656 ------------------------------------------------------------------------------- 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: 0.7760 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 16670 Z= 0.228 Angle : 0.741 11.858 22790 Z= 0.375 Chirality : 0.049 0.237 2755 Planarity : 0.005 0.054 2760 Dihedral : 6.615 80.913 2970 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: -1.73 (0.19), residues: 1915 helix: -0.88 (0.18), residues: 725 sheet: -1.02 (0.24), residues: 425 loop : -1.27 (0.26), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 68 HIS 0.005 0.001 HIS A 411 PHE 0.017 0.002 PHE E 103 TYR 0.024 0.002 TYR C 61 ARG 0.008 0.000 ARG D 175 *********************** 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 71 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 100 ILE cc_start: 0.9102 (mp) cc_final: 0.8312 (mp) REVERT: B 101 ASN cc_start: 0.8279 (m110) cc_final: 0.7806 (m110) REVERT: B 102 GLU cc_start: 0.8830 (mp0) cc_final: 0.7858 (mp0) REVERT: B 108 LYS cc_start: 0.7635 (mtmt) cc_final: 0.6502 (pptt) REVERT: B 152 THR cc_start: 0.8945 (m) cc_final: 0.7945 (p) REVERT: B 207 TYR cc_start: 0.7575 (m-80) cc_final: 0.6761 (m-10) REVERT: B 242 PHE cc_start: 0.8727 (m-80) cc_final: 0.8206 (m-80) REVERT: B 247 ASP cc_start: 0.7597 (t70) cc_final: 0.6957 (m-30) REVERT: B 286 TYR cc_start: 0.8064 (m-10) cc_final: 0.7638 (t80) REVERT: B 307 LEU cc_start: 0.8810 (tt) cc_final: 0.8094 (mm) REVERT: B 410 ARG cc_start: 0.7709 (mmt180) cc_final: 0.7304 (tmt170) REVERT: B 426 TRP cc_start: 0.8649 (m100) cc_final: 0.8112 (m100) REVERT: B 428 ARG cc_start: 0.8107 (ttt-90) cc_final: 0.7490 (tpt170) REVERT: B 431 TYR cc_start: 0.8787 (m-80) cc_final: 0.8257 (m-80) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1990 time to fit residues: 18.0672 Evaluate side-chains 48 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.368 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: 0.0025 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 ------------------------------------------------------------------------------- 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: 0.3980 chunk 85 optimal weight: 0.9990 chunk 125 optimal weight: 0.0270 chunk 189 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 150 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 116 optimal weight: 0.0370 chunk 92 optimal weight: 0.0470 chunk 119 optimal weight: 3.9990 chunk 160 optimal weight: 0.0670 overall best weight: 0.1152 ------------------------------------------------------------------------------- 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: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16670 Z= 0.195 Angle : 0.703 8.933 22790 Z= 0.359 Chirality : 0.049 0.232 2755 Planarity : 0.006 0.085 2760 Dihedral : 6.410 81.050 2970 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.95 (0.18), residues: 725 sheet: -0.75 (0.24), residues: 425 loop : -1.42 (0.25), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 68 HIS 0.001 0.000 HIS E 158 PHE 0.044 0.003 PHE C 103 TYR 0.016 0.002 TYR A 61 ARG 0.015 0.001 ARG D 410 ********************** 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 73 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 ASN cc_start: 0.8048 (m110) cc_final: 0.7639 (m110) REVERT: B 108 LYS cc_start: 0.7665 (mtmt) cc_final: 0.6610 (tmmt) REVERT: B 152 THR cc_start: 0.8947 (m) cc_final: 0.8136 (m) REVERT: B 207 TYR cc_start: 0.7640 (m-80) cc_final: 0.6849 (m-10) REVERT: B 242 PHE cc_start: 0.8344 (m-80) cc_final: 0.8062 (m-80) REVERT: B 247 ASP cc_start: 0.7556 (t70) cc_final: 0.6922 (m-30) REVERT: B 286 TYR cc_start: 0.8034 (m-10) cc_final: 0.7360 (t80) REVERT: B 307 LEU cc_start: 0.8797 (tt) cc_final: 0.8094 (mm) REVERT: B 410 ARG cc_start: 0.7403 (mmt180) cc_final: 0.7123 (tmt170) REVERT: B 426 TRP cc_start: 0.8657 (m100) cc_final: 0.8101 (m100) REVERT: B 428 ARG cc_start: 0.8091 (ttt-90) cc_final: 0.7498 (tpt170) REVERT: B 431 TYR cc_start: 0.8769 (m-80) cc_final: 0.8335 (m-80) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1316 time to fit residues: 12.0864 Evaluate side-chains 46 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.384 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: 0.0021 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 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: 0.0026 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=1.00 ------------------------------------------------------------------------------- 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: 0.1980 chunk 41 optimal weight: 0.0470 chunk 150 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 155 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.096559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.083250 restraints weight = 12558.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.085136 restraints weight = 7174.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.086367 restraints weight = 4608.047| |-----------------------------------------------------------------------------| r_work (final): 0.3339 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2207 r_free = 0.2207 target = 0.035641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2208 r_free = 0.2208 target = 0.035500 restraints weight = 200.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2209 r_free = 0.2209 target = 0.035612 restraints weight = 15.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2209 r_free = 0.2209 target = 0.035640 restraints weight = 2.238 | |-----------------------------------------------------------------------------| r_work (final): 0.2215 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.049265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2415 r_free = 0.2415 target = 0.045443 restraints weight = 268.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.046467 restraints weight = 131.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2452 r_free = 0.2452 target = 0.047096 restraints weight = 83.708| |-----------------------------------------------------------------------------| r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.5304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16670 Z= 0.195 Angle : 0.664 7.607 22790 Z= 0.340 Chirality : 0.048 0.227 2755 Planarity : 0.006 0.085 2760 Dihedral : 6.319 79.866 2970 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % 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: -1.41 (0.20), residues: 1915 helix: -0.60 (0.19), residues: 685 sheet: -0.74 (0.25), residues: 415 loop : -1.19 (0.24), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 68 HIS 0.001 0.000 HIS B 158 PHE 0.036 0.002 PHE B 103 TYR 0.014 0.002 TYR A 64 ARG 0.014 0.001 ARG A 410 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2876.07 seconds wall clock time: 53 minutes 55.98 seconds (3235.98 seconds total)