Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 23:56:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6his_0228/04_2023/6his_0228_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6his_0228/04_2023/6his_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_0228/04_2023/6his_0228.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6his_0228/04_2023/6his_0228.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6his_0228/04_2023/6his_0228_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6his_0228/04_2023/6his_0228_updated.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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: 8.85, per 1000 atoms: 0.54 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: 6.99 Conformation dependent library (CDL) restraints added in 2.4 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: 1.40 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: 4.64 Time building geometry restraints manager: 7.38 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 - 16.99: 8816 16.99 - 33.98: 594 33.98 - 50.97: 100 50.97 - 67.96: 10 67.96 - 84.95: 5 Dihedral angle restraints: 9525 sinusoidal: 3755 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 9522 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.390 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 42.110 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.140 ------------------------------------------------------------------------------- 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 : 11.988 84.950 5750 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 % 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 *********************** 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 : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 96 average time/residue: 0.1970 time to fit residues: 22.0698 Evaluate side-chains 52 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.414 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6086 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 : 0.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 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: 0.0034 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0015 ------------------------------------------------------------------------------- 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: 3.9990 chunk 110 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 66 GLN E 124 GLN E 205 ASN Total number of N/Q/H flips: 3 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: 0.7675 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 16670 Z= 0.243 Angle : 0.879 12.559 22790 Z= 0.444 Chirality : 0.061 0.835 2755 Planarity : 0.008 0.138 2760 Dihedral : 7.558 77.443 2125 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer Outliers : 0.29 % 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: -2.05 (0.18), residues: 1915 helix: -1.03 (0.16), residues: 730 sheet: -1.07 (0.22), residues: 445 loop : -1.69 (0.25), residues: 740 *********************** 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 71 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 70 average time/residue: 0.1863 time to fit residues: 15.4053 Evaluate side-chains 48 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.392 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0432 time to fit residues: 0.6483 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 : 0.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 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: 0.0033 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0013 ------------------------------------------------------------------------------- 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: 0.0670 chunk 53 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 47 optimal weight: 0.0270 chunk 172 optimal weight: 8.9990 chunk 186 optimal weight: 8.9990 chunk 153 optimal weight: 0.5980 chunk 171 optimal weight: 0.0010 chunk 58 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 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: 0.7667 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 16670 Z= 0.229 Angle : 0.773 11.086 22790 Z= 0.386 Chirality : 0.054 0.577 2755 Planarity : 0.006 0.081 2760 Dihedral : 7.269 75.557 2125 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer Outliers : 0.00 % 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: -1.95 (0.19), residues: 1915 helix: -0.72 (0.17), residues: 710 sheet: -1.59 (0.20), residues: 455 loop : -1.45 (0.26), residues: 750 *********************** REFINEMENT MACRO_CYCLE 3 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: 0 poor density : 74 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1649 time to fit residues: 14.9163 Evaluate side-chains 47 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.421 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5461 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 ------------------------------------------------------------------------------- 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: 4.9990 chunk 129 optimal weight: 0.0270 chunk 89 optimal weight: 5.9990 chunk 19 optimal weight: 0.0980 chunk 82 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 chunk 49 optimal weight: 0.3980 overall best weight: 1.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 16670 Z= 0.230 Angle : 0.699 9.913 22790 Z= 0.351 Chirality : 0.047 0.214 2755 Planarity : 0.005 0.055 2760 Dihedral : 7.261 85.087 2125 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer Outliers : 0.00 % 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: -2.09 (0.19), residues: 1915 helix: -0.75 (0.17), residues: 720 sheet: -1.46 (0.21), residues: 475 loop : -1.78 (0.26), residues: 720 *********************** 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 65 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1423 time to fit residues: 11.5776 Evaluate side-chains 43 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.390 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5140 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 : 0.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 ------------------------------------------------------------------------------- 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: 10.9990 chunk 104 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 136 optimal weight: 0.0170 chunk 75 optimal weight: 3.9990 chunk 156 optimal weight: 0.7980 chunk 126 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 overall best weight: 2.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 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: 0.7768 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 16670 Z= 0.265 Angle : 0.681 9.454 22790 Z= 0.345 Chirality : 0.046 0.206 2755 Planarity : 0.005 0.043 2760 Dihedral : 6.644 70.904 2125 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer Outliers : 0.00 % 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: -1.85 (0.19), residues: 1915 helix: -0.81 (0.17), residues: 685 sheet: -1.29 (0.22), residues: 410 loop : -1.39 (0.24), residues: 820 *********************** 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 56 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1281 time to fit residues: 9.2646 Evaluate side-chains 38 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.348 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4694 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0021 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 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: 0.0027 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0013 ------------------------------------------------------------------------------- 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: 0.5980 chunk 165 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 45 optimal weight: 0.6980 chunk 183 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 60 optimal weight: 0.0870 chunk 96 optimal weight: 8.9990 overall best weight: 1.8762 ------------------------------------------------------------------------------- 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: 0.7788 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 16670 Z= 0.202 Angle : 0.666 9.327 22790 Z= 0.332 Chirality : 0.047 0.224 2755 Planarity : 0.004 0.040 2760 Dihedral : 6.476 70.825 2125 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer Outliers : 0.00 % 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: -1.63 (0.19), residues: 1915 helix: -0.72 (0.18), residues: 695 sheet: -0.94 (0.23), residues: 410 loop : -1.33 (0.25), residues: 810 *********************** 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 59 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1363 time to fit residues: 10.2310 Evaluate side-chains 40 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.400 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5311 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 : 0.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 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: 0.0034 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0013 ------------------------------------------------------------------------------- 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: 5.9990 chunk 20 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 134 optimal weight: 0.2980 chunk 154 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 183 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 111 optimal weight: 0.0010 chunk 84 optimal weight: 0.0050 chunk 113 optimal weight: 3.9990 overall best weight: 1.0604 ------------------------------------------------------------------------------- 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: 0.7753 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 16670 Z= 0.197 Angle : 0.677 9.484 22790 Z= 0.334 Chirality : 0.047 0.226 2755 Planarity : 0.004 0.039 2760 Dihedral : 6.455 68.816 2125 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer Outliers : 0.00 % 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: -1.76 (0.19), residues: 1915 helix: -0.72 (0.18), residues: 725 sheet: -0.89 (0.24), residues: 410 loop : -1.61 (0.25), residues: 780 *********************** 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 61 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1407 time to fit residues: 10.7623 Evaluate side-chains 44 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.421 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5532 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 : 0.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0013 ------------------------------------------------------------------------------- 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: 0.9990 chunk 109 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 90 optimal weight: 0.3980 chunk 17 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 166 optimal weight: 0.1980 chunk 175 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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: 0.7725 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 16670 Z= 0.191 Angle : 0.688 9.641 22790 Z= 0.342 Chirality : 0.047 0.224 2755 Planarity : 0.004 0.041 2760 Dihedral : 6.418 69.125 2125 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer Outliers : 0.00 % 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: -1.80 (0.19), residues: 1915 helix: -0.76 (0.18), residues: 725 sheet: -1.02 (0.24), residues: 415 loop : -1.55 (0.25), residues: 775 *********************** 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 58 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1211 time to fit residues: 9.1488 Evaluate side-chains 42 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.413 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5990 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0022 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0017 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0031 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0016 ------------------------------------------------------------------------------- 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: 7.9990 chunk 170 optimal weight: 2.9990 chunk 175 optimal weight: 9.9990 chunk 102 optimal weight: 0.0570 chunk 74 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 52 optimal weight: 0.0040 chunk 154 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 overall best weight: 1.0114 ------------------------------------------------------------------------------- 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: 0.7742 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 16670 Z= 0.177 Angle : 0.667 8.510 22790 Z= 0.333 Chirality : 0.047 0.226 2755 Planarity : 0.004 0.038 2760 Dihedral : 6.325 68.737 2125 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer Outliers : 0.00 % 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: -1.70 (0.19), residues: 1915 helix: -0.70 (0.19), residues: 725 sheet: -0.90 (0.24), residues: 415 loop : -1.51 (0.25), residues: 775 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1359 time to fit residues: 11.1780 Evaluate side-chains 41 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.402 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5349 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0022 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0014 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0015 ------------------------------------------------------------------------------- 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: 0.4980 chunk 85 optimal weight: 10.0000 chunk 125 optimal weight: 0.0370 chunk 189 optimal weight: 10.0000 chunk 174 optimal weight: 0.9980 chunk 150 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 92 optimal weight: 0.4980 chunk 119 optimal weight: 0.9980 chunk 160 optimal weight: 0.0040 overall best weight: 0.4070 ------------------------------------------------------------------------------- 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: 0.7731 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 16670 Z= 0.202 Angle : 0.735 10.322 22790 Z= 0.368 Chirality : 0.059 0.796 2755 Planarity : 0.007 0.137 2760 Dihedral : 6.459 69.161 2125 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer Outliers : 0.00 % 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: -1.69 (0.19), residues: 1915 helix: -0.87 (0.18), residues: 715 sheet: -0.72 (0.25), residues: 415 loop : -1.42 (0.24), residues: 785 ********************** 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 62 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1176 time to fit residues: 9.5078 Evaluate side-chains 37 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.375 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7249 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 : 0.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 ------------------------------------------------------------------------------- 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: 3.9990 chunk 22 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 155 optimal weight: 0.2980 chunk 19 optimal weight: 0.0060 chunk 27 optimal weight: 0.0270 chunk 132 optimal weight: 0.1980 chunk 8 optimal weight: 7.9990 overall best weight: 0.2454 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.098053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.085367 restraints weight = 12010.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.087214 restraints weight = 6911.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.088457 restraints weight = 4477.716| |-----------------------------------------------------------------------------| r_work (final): 0.3404 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2128 r_free = 0.2128 target = 0.036593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2128 r_free = 0.2128 target = 0.036583 restraints weight = 255.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2128 r_free = 0.2128 target = 0.036602 restraints weight = 3.343 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 4)-----------------| | r_work = 0.2128 r_free = 0.2128 target = 0.036595 restraints weight = 0.326 | |-----------------------------------------------------------------------------| r_work (final): 0.2123 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.048441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2391 r_free = 0.2391 target = 0.045307 restraints weight = 277.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2414 r_free = 0.2414 target = 0.046418 restraints weight = 152.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2430 r_free = 0.2430 target = 0.047146 restraints weight = 88.004| |-----------------------------------------------------------------------------| r_work (final): 0.2427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 16670 Z= 0.193 Angle : 0.707 8.123 22790 Z= 0.358 Chirality : 0.055 0.605 2755 Planarity : 0.005 0.049 2760 Dihedral : 6.484 69.476 2125 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer Outliers : 0.00 % 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: -0.77 (0.18), residues: 710 sheet: -0.78 (0.25), residues: 415 loop : -1.60 (0.24), residues: 790 =============================================================================== Job complete usr+sys time: 2638.29 seconds wall clock time: 49 minutes 49.20 seconds (2989.20 seconds total)