Starting phenix.real_space_refine on Wed Feb 21 23:36:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6be1_7088/02_2024/6be1_7088_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6be1_7088/02_2024/6be1_7088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6be1_7088/02_2024/6be1_7088.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6be1_7088/02_2024/6be1_7088.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6be1_7088/02_2024/6be1_7088_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6be1_7088/02_2024/6be1_7088_updated.pdb" } resolution = 4.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 15500 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians P 5 5.49 5 S 50 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 11052 2.51 5 N 2701 2.21 5 O 3100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "B PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 428": "NH1" <-> "NH2" Residue "C TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 400": "NH1" <-> "NH2" Residue "C ARG 435": "NH1" <-> "NH2" Residue "D PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 400": "NH1" <-> "NH2" Residue "D ARG 435": "NH1" <-> "NH2" Residue "E PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 400": "NH1" <-> "NH2" Residue "E ARG 439": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16910 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3277 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 20, 'TRANS': 378} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3265 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 20, 'TRANS': 378} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 3272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3272 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 20, 'TRANS': 378} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 3266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3266 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 20, 'TRANS': 378} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 3269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3269 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 378} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {' NA': 1, 'NAG': 2, 'PX4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PX4:plan-2': 2} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 47 Unusual residues: {' CL': 1, 'NAG': 2, 'PX4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PX4:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'NAG': 1, 'PX4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PX4:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'BMA': 1, 'PX4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PX4:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 9.12, per 1000 atoms: 0.54 Number of scatterers: 16910 At special positions: 0 Unit cell: (106.4, 103.208, 177.688, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 50 16.00 P 5 15.00 Na 1 11.00 O 3100 8.00 N 2701 7.00 C 11052 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 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 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 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=4, symmetry=0 Links applied BETA1-3 " NAG H 1 " - " NAG H 2 " " NAG M 2 " - " BMA M 3 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " NAG-ASN " NAG A 501 " - " ASN A 82 " " NAG C 506 " - " ASN C 148 " " NAG D 504 " - " ASN D 82 " " NAG F 1 " - " ASN A 164 " " NAG G 1 " - " ASN A 148 " " NAG I 1 " - " ASN B 82 " " NAG J 1 " - " ASN B 148 " " NAG K 1 " - " ASN C 164 " " NAG L 1 " - " ASN C 82 " " NAG M 1 " - " ASN D 164 " " NAG N 1 " - " ASN D 148 " " NAG O 1 " - " ASN E 164 " " NAG P 1 " - " ASN E 82 " " NAG Q 1 " - " ASN E 148 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.50 Conformation dependent library (CDL) restraints added in 3.5 seconds 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3870 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 26 sheets defined 35.9% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.35 Creating SS restraints... Processing helix chain 'A' and resid 12 through 18 removed outlier: 3.828A pdb=" N LEU A 15 " --> pdb=" O LEU A 12 " (cutoff:3.500A) 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 175 Processing helix chain 'A' and resid 222 through 242 removed outlier: 5.788A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 250 through 269 Processing helix chain 'A' and resid 282 through 307 removed outlier: 4.238A pdb=" N TYR A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A 287 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N CYS A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 327 No H-bonds generated for 'chain 'A' and resid 324 through 327' Processing helix chain 'A' and resid 400 through 456 removed outlier: 3.796A pdb=" N GLN A 404 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 455 " --> pdb=" O THR A 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 19 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 175 Processing helix chain 'B' and resid 222 through 241 removed outlier: 5.744A pdb=" N LEU B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 251 through 270 removed outlier: 4.343A pdb=" N SER B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 307 removed outlier: 3.616A pdb=" N CYS B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 330 removed outlier: 3.752A pdb=" N ARG B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE B 329 " --> pdb=" O VAL B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 461 removed outlier: 4.597A pdb=" N ILE B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TRP B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 19 removed outlier: 3.562A pdb=" N LEU C 15 " --> pdb=" O LEU C 12 " (cutoff:3.500A) 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 175 Processing helix chain 'C' and resid 223 through 241 Proline residue: C 230 - end of helix Processing helix chain 'C' and resid 251 through 268 Processing helix chain 'C' and resid 282 through 307 removed outlier: 3.779A pdb=" N TYR C 286 " --> pdb=" O ILE C 283 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL C 289 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL C 305 " --> pdb=" O ILE C 302 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU C 307 " --> pdb=" O ILE C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 324 removed outlier: 3.744A pdb=" N HIS C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 404 Processing helix chain 'C' and resid 407 through 460 removed outlier: 3.883A pdb=" N TRP C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 18 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 175 Processing helix chain 'D' and resid 224 through 243 Proline residue: D 230 - end of helix removed outlier: 4.767A pdb=" N CYS D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 270 Processing helix chain 'D' and resid 282 through 307 removed outlier: 3.589A pdb=" N TYR D 286 " --> pdb=" O ILE D 283 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET D 291 " --> pdb=" O VAL D 288 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU D 294 " --> pdb=" O MET D 291 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU D 307 " --> pdb=" O ILE D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 325 removed outlier: 3.624A pdb=" N HIS D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU D 324 " --> pdb=" O TRP D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 332 Processing helix chain 'D' and resid 403 through 459 removed outlier: 3.751A pdb=" N PHE D 412 " --> pdb=" O SER D 408 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TRP D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 19 removed outlier: 3.729A pdb=" N LEU E 15 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP E 17 " --> pdb=" O ARG E 14 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU E 19 " --> pdb=" O SER E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 222 through 227 Processing helix chain 'E' and resid 229 through 241 Processing helix chain 'E' and resid 250 through 268 Processing helix chain 'E' and resid 283 through 307 Processing helix chain 'E' and resid 318 through 320 No H-bonds generated for 'chain 'E' and resid 318 through 320' Processing helix chain 'E' and resid 324 through 327 No H-bonds generated for 'chain 'E' and resid 324 through 327' Processing helix chain 'E' and resid 404 through 456 removed outlier: 3.892A pdb=" N PHE E 412 " --> pdb=" O SER E 408 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 163 through 167 removed outlier: 6.669A pdb=" N THR A 37 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR A 166 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL A 39 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP A 42 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 44 " --> pdb=" O TRP A 63 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N TYR A 61 " --> pdb=" O TYR A 46 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 50 through 52 removed outlier: 3.627A pdb=" N ASN A 50 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 57 " --> pdb=" O ASP A 52 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.746A pdb=" N THR A 154 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 147 through 149 removed outlier: 3.522A pdb=" N GLN A 147 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 216 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 199 through 202 removed outlier: 4.231A pdb=" N PHE A 199 " --> pdb=" O TYR A 207 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 201 " --> pdb=" O ASN A 205 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ASN A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 163 through 167 removed outlier: 6.958A pdb=" N THR B 37 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N THR B 166 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL B 39 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR B 38 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THR B 69 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP B 42 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE B 44 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N TYR B 61 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN B 125 " --> pdb=" O GLN B 66 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TRP B 68 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL B 123 " --> pdb=" O TRP B 68 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 50 through 52 Processing sheet with id= H, first strand: chain 'B' and resid 146 through 148 removed outlier: 3.745A pdb=" N GLN B 147 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE B 216 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 199 through 202 removed outlier: 4.176A pdb=" N PHE B 199 " --> pdb=" O TYR B 207 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE B 201 " --> pdb=" O ASN B 205 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ASN B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 163 through 167 removed outlier: 6.595A pdb=" N THR C 37 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR C 166 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL C 39 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP C 42 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N TYR C 61 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ILE C 48 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR C 59 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE C 62 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU C 129 " --> pdb=" O ILE C 62 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 50 through 52 removed outlier: 4.026A pdb=" N ASN C 50 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR C 59 " --> pdb=" O ASN C 50 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 66 through 69 removed outlier: 3.673A pdb=" N TRP C 68 " --> pdb=" O VAL C 123 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 86 through 89 removed outlier: 3.520A pdb=" N LEU C 86 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.531A pdb=" N THR C 154 " --> pdb=" O LEU C 99 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 187 through 189 Processing sheet with id= P, first strand: chain 'C' and resid 192 through 196 removed outlier: 3.581A pdb=" N PHE C 193 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 199 through 202 removed outlier: 4.507A pdb=" N PHE C 199 " --> pdb=" O TYR C 207 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR C 207 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE C 201 " --> pdb=" O ASN C 205 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ASN C 205 " --> pdb=" O ILE C 201 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'D' and resid 37 through 39 Processing sheet with id= S, first strand: chain 'D' and resid 129 through 133 removed outlier: 3.821A pdb=" N LEU D 129 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE D 62 " --> pdb=" O LEU D 129 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA D 47 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TRP D 63 " --> pdb=" O MET D 45 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N MET D 45 " --> pdb=" O TRP D 63 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ARG D 65 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL D 43 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N TYR D 67 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE D 41 " --> pdb=" O TYR D 67 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 147 through 154 removed outlier: 3.774A pdb=" N GLN D 147 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE D 216 " --> pdb=" O GLN D 147 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N CYS D 149 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL D 214 " --> pdb=" O CYS D 149 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN D 205 " --> pdb=" O ASP D 202 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP D 202 " --> pdb=" O ASN D 205 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR D 207 " --> pdb=" O SER D 200 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N SER D 200 " --> pdb=" O TYR D 207 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLU D 209 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU D 198 " --> pdb=" O GLU D 209 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS D 211 " --> pdb=" O PHE D 196 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N PHE D 196 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TYR D 213 " --> pdb=" O PRO D 194 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 163 through 166 removed outlier: 6.421A pdb=" N THR E 37 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR E 166 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL E 39 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP E 42 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR E 61 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE E 48 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N THR E 59 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE E 62 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU E 129 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN E 125 " --> pdb=" O GLN E 66 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 50 through 52 Processing sheet with id= W, first strand: chain 'E' and resid 86 through 89 Processing sheet with id= X, first strand: chain 'E' and resid 187 through 189 Processing sheet with id= Y, first strand: chain 'E' and resid 192 through 196 removed outlier: 3.753A pdb=" N GLN E 195 " --> pdb=" O LYS E 211 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 199 through 202 removed outlier: 4.727A pdb=" N PHE E 199 " --> pdb=" O TYR E 207 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR E 207 " --> pdb=" O PHE E 199 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE E 201 " --> pdb=" O ASN E 205 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ASN E 205 " --> pdb=" O ILE E 201 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z 602 hydrogen bonds defined for protein. 1635 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: 4.66 Time building geometry restraints manager: 7.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2593 1.32 - 1.44: 4952 1.44 - 1.56: 9698 1.56 - 1.69: 15 1.69 - 1.81: 80 Bond restraints: 17338 Sorted by residual: bond pdb=" O2 PX4 E 508 " pdb=" P1 PX4 E 508 " ideal model delta sigma weight residual 1.497 1.691 -0.194 2.00e-02 2.50e+03 9.45e+01 bond pdb=" O2 PX4 A 509 " pdb=" P1 PX4 A 509 " ideal model delta sigma weight residual 1.497 1.691 -0.194 2.00e-02 2.50e+03 9.39e+01 bond pdb=" O3 PX4 E 508 " pdb=" P1 PX4 E 508 " ideal model delta sigma weight residual 1.649 1.465 0.184 2.00e-02 2.50e+03 8.44e+01 bond pdb=" O3 PX4 A 509 " pdb=" P1 PX4 A 509 " ideal model delta sigma weight residual 1.649 1.465 0.184 2.00e-02 2.50e+03 8.44e+01 bond pdb=" C9 PX4 A 509 " pdb=" O5 PX4 A 509 " ideal model delta sigma weight residual 1.327 1.431 -0.104 2.00e-02 2.50e+03 2.71e+01 ... (remaining 17333 not shown) Histogram of bond angle deviations from ideal: 89.19 - 99.13: 2 99.13 - 109.08: 1464 109.08 - 119.02: 12945 119.02 - 128.97: 9071 128.97 - 138.91: 193 Bond angle restraints: 23675 Sorted by residual: angle pdb=" C3 NAG G 1 " pdb=" C4 NAG G 1 " pdb=" O4 NAG G 1 " ideal model delta sigma weight residual 107.29 136.30 -29.01 3.00e+00 1.11e-01 9.35e+01 angle pdb=" C3 NAG K 2 " pdb=" C4 NAG K 2 " pdb=" O4 NAG K 2 " ideal model delta sigma weight residual 107.29 136.10 -28.81 3.00e+00 1.11e-01 9.22e+01 angle pdb=" C3 NAG F 1 " pdb=" C4 NAG F 1 " pdb=" O4 NAG F 1 " ideal model delta sigma weight residual 107.29 135.66 -28.37 3.00e+00 1.11e-01 8.94e+01 angle pdb=" C5 NAG P 1 " pdb=" C4 NAG P 1 " pdb=" O4 NAG P 1 " ideal model delta sigma weight residual 111.70 138.91 -27.21 3.00e+00 1.11e-01 8.23e+01 angle pdb=" C4 NAG M 2 " pdb=" C3 NAG M 2 " pdb=" O3 NAG M 2 " ideal model delta sigma weight residual 112.02 89.19 22.83 3.00e+00 1.11e-01 5.79e+01 ... (remaining 23670 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.68: 10310 32.68 - 65.36: 272 65.36 - 98.04: 61 98.04 - 130.72: 27 130.72 - 163.40: 4 Dihedral angle restraints: 10674 sinusoidal: 4729 harmonic: 5945 Sorted by residual: dihedral pdb=" CB CYS B 135 " pdb=" SG CYS B 135 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 147.42 -54.42 1 1.00e+01 1.00e-02 4.01e+01 dihedral pdb=" CB CYS A 135 " pdb=" SG CYS A 135 " pdb=" SG CYS A 149 " pdb=" CB CYS A 149 " ideal model delta sinusoidal sigma weight residual 93.00 144.31 -51.31 1 1.00e+01 1.00e-02 3.60e+01 dihedral pdb=" CB CYS D 135 " pdb=" SG CYS D 135 " pdb=" SG CYS D 149 " pdb=" CB CYS D 149 " ideal model delta sinusoidal sigma weight residual 93.00 143.56 -50.56 1 1.00e+01 1.00e-02 3.50e+01 ... (remaining 10671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.808: 2814 0.808 - 1.616: 0 1.616 - 2.424: 1 2.424 - 3.232: 3 3.232 - 4.039: 1 Chirality restraints: 2819 Sorted by residual: chirality pdb=" C4 NAG Q 1 " pdb=" C3 NAG Q 1 " pdb=" C5 NAG Q 1 " pdb=" O4 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.53 1.51 -4.04 2.00e-01 2.50e+01 4.08e+02 chirality pdb=" C4 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" C5 NAG F 1 " pdb=" O4 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.53 0.69 -3.22 2.00e-01 2.50e+01 2.60e+02 chirality pdb=" C4 NAG P 1 " pdb=" C3 NAG P 1 " pdb=" C5 NAG P 1 " pdb=" O4 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.53 0.69 -3.22 2.00e-01 2.50e+01 2.59e+02 ... (remaining 2816 not shown) Planarity restraints: 2886 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 213 " 0.016 2.00e-02 2.50e+03 2.42e-02 1.17e+01 pdb=" CG TYR E 213 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR E 213 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR E 213 " -0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR E 213 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR E 213 " 0.045 2.00e-02 2.50e+03 pdb=" CZ TYR E 213 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 213 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 280 " -0.044 5.00e-02 4.00e+02 6.71e-02 7.21e+00 pdb=" N PRO D 281 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO D 281 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 281 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 233 " 0.021 2.00e-02 2.50e+03 1.77e-02 5.51e+00 pdb=" CG PHE A 233 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 233 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 233 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 233 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 233 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE A 233 " -0.000 2.00e-02 2.50e+03 ... (remaining 2883 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4678 2.82 - 3.34: 14303 3.34 - 3.86: 27565 3.86 - 4.38: 27900 4.38 - 4.90: 48646 Nonbonded interactions: 123092 Sorted by model distance: nonbonded pdb=" O ALA D 47 " pdb=" OG1 THR D 60 " model vdw 2.301 2.440 nonbonded pdb=" O VAL C 39 " pdb=" OG1 THR C 166 " model vdw 2.334 2.440 nonbonded pdb=" OH TYR D 116 " pdb=" O LEU E 157 " model vdw 2.336 2.440 nonbonded pdb=" O ALA E 47 " pdb=" OG1 THR E 60 " model vdw 2.341 2.440 nonbonded pdb=" O PHE C 222 " pdb=" OG SER C 226 " model vdw 2.342 2.440 ... (remaining 123087 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 318 or (resid 319 and (name N or name CA or name \ C or name O or name CB )) or resid 320 through 322 or (resid 323 through 326 an \ d (name N or name CA or name C or name O or name CB )) or resid 327 through 332 \ or (resid 333 and (name N or name CA or name C or name O or name CB )) or resid \ 334 through 338 or (resid 397 through 399 and (name N or name CA or name C or na \ me O or name CB )) or resid 400 through 462)) selection = (chain 'B' and (resid 6 through 311 or (resid 312 and (name N or name CA or name \ C or name O or name CB )) or resid 313 through 398 or (resid 399 and (name N or \ name CA or name C or name O or name CB )) or resid 400 through 462)) selection = (chain 'C' and (resid 6 through 311 or (resid 312 and (name N or name CA or name \ C or name O or name CB )) or resid 313 through 318 or (resid 319 and (name N or \ name CA or name C or name O or name CB )) or resid 320 through 325 or (resid 32 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 327 through \ 338 or (resid 397 through 399 and (name N or name CA or name C or name O or name \ CB )) or resid 400 through 462)) selection = (chain 'D' and (resid 6 through 311 or (resid 312 and (name N or name CA or name \ C or name O or name CB )) or resid 313 through 338 or (resid 397 through 399 an \ d (name N or name CA or name C or name O or name CB )) or resid 400 through 462) \ ) selection = (chain 'E' and (resid 6 through 311 or (resid 312 and (name N or name CA or name \ C or name O or name CB )) or resid 313 through 318 or (resid 319 and (name N or \ name CA or name C or name O or name CB )) or resid 320 through 338 or (resid 39 \ 7 through 399 and (name N or name CA or name C or name O or name CB )) or resid \ 400 through 462)) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.010 Extract box with map and model: 6.330 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 44.280 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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 : 0.006 0.194 17338 Z= 0.401 Angle : 1.278 29.009 23675 Z= 0.599 Chirality : 0.146 4.039 2819 Planarity : 0.007 0.067 2872 Dihedral : 16.375 163.399 6789 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 1.66 % Allowed : 8.45 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.36 (0.15), residues: 1975 helix: -2.07 (0.15), residues: 705 sheet: -2.56 (0.26), residues: 320 loop : -3.72 (0.15), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 68 HIS 0.005 0.001 HIS E 158 PHE 0.039 0.003 PHE A 233 TYR 0.045 0.002 TYR E 213 ARG 0.013 0.001 ARG B 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 353 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 THR cc_start: 0.8908 (m) cc_final: 0.8667 (p) REVERT: A 221 LEU cc_start: 0.7971 (mm) cc_final: 0.7759 (pp) REVERT: A 247 ASP cc_start: 0.8169 (m-30) cc_final: 0.7766 (t0) REVERT: A 254 PHE cc_start: 0.8674 (t80) cc_final: 0.8405 (t80) REVERT: A 434 ASP cc_start: 0.8539 (t0) cc_final: 0.8233 (t70) REVERT: A 436 LEU cc_start: 0.9137 (pp) cc_final: 0.8608 (mt) REVERT: B 42 ASP cc_start: 0.7693 (t70) cc_final: 0.7463 (t0) REVERT: B 165 ILE cc_start: 0.9447 (mp) cc_final: 0.9113 (pt) REVERT: B 247 ASP cc_start: 0.8028 (m-30) cc_final: 0.7795 (t0) REVERT: B 254 PHE cc_start: 0.9135 (t80) cc_final: 0.8895 (t80) REVERT: B 305 VAL cc_start: 0.9340 (t) cc_final: 0.9090 (m) REVERT: C 105 ASP cc_start: 0.7992 (t0) cc_final: 0.7781 (t0) REVERT: C 221 LEU cc_start: 0.8176 (mm) cc_final: 0.7639 (tp) REVERT: C 254 PHE cc_start: 0.8737 (t80) cc_final: 0.8428 (t80) REVERT: C 305 VAL cc_start: 0.9426 (t) cc_final: 0.9222 (m) REVERT: C 436 LEU cc_start: 0.9108 (pp) cc_final: 0.8490 (mt) REVERT: D 254 PHE cc_start: 0.8867 (t80) cc_final: 0.8234 (t80) REVERT: D 257 THR cc_start: 0.9205 (m) cc_final: 0.8913 (p) REVERT: D 305 VAL cc_start: 0.9326 (t) cc_final: 0.9112 (m) REVERT: D 411 HIS cc_start: 0.8314 (m90) cc_final: 0.8045 (m-70) REVERT: D 437 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8600 (pt) REVERT: E 247 ASP cc_start: 0.8222 (m-30) cc_final: 0.7772 (t0) REVERT: E 259 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9076 (tp) REVERT: E 305 VAL cc_start: 0.9288 (t) cc_final: 0.9077 (m) REVERT: E 436 LEU cc_start: 0.9181 (pp) cc_final: 0.8789 (mt) outliers start: 30 outliers final: 2 residues processed: 369 average time/residue: 0.2684 time to fit residues: 148.0778 Evaluate side-chains 181 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 177 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 152 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 177 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 HIS D 124 GLN E 9 GLN E 56 GLN ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 17338 Z= 0.307 Angle : 0.785 12.725 23675 Z= 0.387 Chirality : 0.051 0.307 2819 Planarity : 0.005 0.048 2872 Dihedral : 14.675 170.616 2958 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.94 % Allowed : 6.24 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.18), residues: 1975 helix: -0.32 (0.19), residues: 730 sheet: -2.44 (0.30), residues: 275 loop : -3.22 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 68 HIS 0.012 0.001 HIS B 118 PHE 0.017 0.002 PHE E 233 TYR 0.025 0.002 TYR C 262 ARG 0.011 0.001 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 243 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 THR cc_start: 0.9015 (m) cc_final: 0.8795 (p) REVERT: A 61 TYR cc_start: 0.8871 (t80) cc_final: 0.8629 (t80) REVERT: A 247 ASP cc_start: 0.8397 (m-30) cc_final: 0.7878 (t0) REVERT: A 254 PHE cc_start: 0.8827 (t80) cc_final: 0.8523 (t80) REVERT: B 42 ASP cc_start: 0.8259 (t70) cc_final: 0.7778 (t0) REVERT: B 254 PHE cc_start: 0.9216 (t80) cc_final: 0.8964 (t80) REVERT: C 210 MET cc_start: 0.8678 (ppp) cc_final: 0.8307 (ppp) REVERT: C 221 LEU cc_start: 0.8209 (mm) cc_final: 0.7546 (tp) REVERT: C 254 PHE cc_start: 0.8925 (t80) cc_final: 0.8646 (t80) REVERT: D 210 MET cc_start: 0.8548 (ppp) cc_final: 0.8178 (tmm) REVERT: D 254 PHE cc_start: 0.9072 (t80) cc_final: 0.8597 (t80) REVERT: D 433 LEU cc_start: 0.9528 (tt) cc_final: 0.9326 (pp) REVERT: E 247 ASP cc_start: 0.8305 (m-30) cc_final: 0.7885 (t0) REVERT: E 259 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.8974 (tp) REVERT: E 413 LEU cc_start: 0.9374 (mt) cc_final: 0.9009 (mt) REVERT: E 436 LEU cc_start: 0.9239 (pp) cc_final: 0.8811 (mt) outliers start: 17 outliers final: 1 residues processed: 249 average time/residue: 0.2531 time to fit residues: 99.5294 Evaluate side-chains 146 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 144 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 191 optimal weight: 6.9990 chunk 157 optimal weight: 0.6980 chunk 175 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 HIS ** C 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 ASN ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 460 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17338 Z= 0.293 Angle : 0.763 11.748 23675 Z= 0.375 Chirality : 0.049 0.331 2819 Planarity : 0.005 0.049 2872 Dihedral : 12.918 168.430 2958 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.50 % Allowed : 5.80 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.18), residues: 1975 helix: 0.08 (0.20), residues: 730 sheet: -2.36 (0.30), residues: 275 loop : -2.79 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 168 HIS 0.007 0.001 HIS B 119 PHE 0.016 0.002 PHE E 233 TYR 0.023 0.002 TYR C 262 ARG 0.008 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 203 time to evaluate : 2.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 THR cc_start: 0.9108 (m) cc_final: 0.8858 (p) REVERT: A 247 ASP cc_start: 0.8566 (m-30) cc_final: 0.8011 (t0) REVERT: A 254 PHE cc_start: 0.8989 (t80) cc_final: 0.8690 (t80) REVERT: B 210 MET cc_start: 0.8606 (tmm) cc_final: 0.8315 (tmm) REVERT: C 210 MET cc_start: 0.8736 (ppp) cc_final: 0.8454 (ppp) REVERT: C 221 LEU cc_start: 0.8407 (mm) cc_final: 0.7696 (tp) REVERT: C 254 PHE cc_start: 0.9063 (t80) cc_final: 0.8509 (t80) REVERT: C 257 THR cc_start: 0.9218 (m) cc_final: 0.8999 (p) REVERT: C 417 ASP cc_start: 0.8362 (m-30) cc_final: 0.8016 (m-30) REVERT: D 197 LYS cc_start: 0.9352 (tmmt) cc_final: 0.9105 (tmtt) REVERT: D 254 PHE cc_start: 0.9004 (t80) cc_final: 0.8671 (t80) REVERT: D 288 VAL cc_start: 0.8821 (p) cc_final: 0.8564 (m) REVERT: D 433 LEU cc_start: 0.9550 (tt) cc_final: 0.9323 (pp) REVERT: E 210 MET cc_start: 0.8541 (ptm) cc_final: 0.8314 (ptp) REVERT: E 247 ASP cc_start: 0.8509 (m-30) cc_final: 0.8017 (t0) REVERT: E 259 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.8973 (tp) REVERT: E 289 VAL cc_start: 0.8608 (p) cc_final: 0.8288 (p) REVERT: E 413 LEU cc_start: 0.9284 (mt) cc_final: 0.8816 (mt) REVERT: E 436 LEU cc_start: 0.9255 (pp) cc_final: 0.8885 (mt) outliers start: 9 outliers final: 0 residues processed: 205 average time/residue: 0.2600 time to fit residues: 84.4334 Evaluate side-chains 133 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 119 optimal weight: 0.4980 chunk 178 optimal weight: 3.9990 chunk 188 optimal weight: 0.1980 chunk 93 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 HIS E 101 ASN ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17338 Z= 0.169 Angle : 0.725 10.755 23675 Z= 0.342 Chirality : 0.047 0.315 2819 Planarity : 0.004 0.045 2872 Dihedral : 11.937 169.073 2958 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.22 % Allowed : 4.80 % Favored : 94.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.19), residues: 1975 helix: 0.38 (0.20), residues: 730 sheet: -1.98 (0.31), residues: 275 loop : -2.65 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 68 HIS 0.013 0.001 HIS D 411 PHE 0.016 0.001 PHE D 233 TYR 0.029 0.001 TYR A 262 ARG 0.008 0.000 ARG C 410 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 200 time to evaluate : 2.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 THR cc_start: 0.9085 (m) cc_final: 0.8830 (p) REVERT: A 42 ASP cc_start: 0.7584 (m-30) cc_final: 0.7023 (t0) REVERT: A 247 ASP cc_start: 0.8637 (m-30) cc_final: 0.8026 (t0) REVERT: A 254 PHE cc_start: 0.8895 (t80) cc_final: 0.8556 (t80) REVERT: A 302 ILE cc_start: 0.9774 (mt) cc_final: 0.9490 (tp) REVERT: C 221 LEU cc_start: 0.8353 (mm) cc_final: 0.7611 (tp) REVERT: C 254 PHE cc_start: 0.8966 (t80) cc_final: 0.8367 (t80) REVERT: C 266 LEU cc_start: 0.9022 (mt) cc_final: 0.8398 (pp) REVERT: C 302 ILE cc_start: 0.9425 (tp) cc_final: 0.9179 (tp) REVERT: C 417 ASP cc_start: 0.8369 (m-30) cc_final: 0.8161 (m-30) REVERT: D 254 PHE cc_start: 0.8911 (t80) cc_final: 0.8495 (t80) REVERT: D 288 VAL cc_start: 0.8777 (p) cc_final: 0.8573 (m) REVERT: D 433 LEU cc_start: 0.9547 (tt) cc_final: 0.9323 (pp) REVERT: E 42 ASP cc_start: 0.8862 (t0) cc_final: 0.8525 (t0) REVERT: E 247 ASP cc_start: 0.8482 (m-30) cc_final: 0.7994 (t0) REVERT: E 259 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.8980 (tp) REVERT: E 305 VAL cc_start: 0.9394 (t) cc_final: 0.9181 (m) REVERT: E 413 LEU cc_start: 0.9306 (mt) cc_final: 0.8768 (mt) REVERT: E 436 LEU cc_start: 0.9303 (pp) cc_final: 0.8811 (mt) outliers start: 4 outliers final: 0 residues processed: 201 average time/residue: 0.2542 time to fit residues: 81.7493 Evaluate side-chains 137 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 160 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 169 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17338 Z= 0.232 Angle : 0.723 10.341 23675 Z= 0.353 Chirality : 0.047 0.321 2819 Planarity : 0.004 0.045 2872 Dihedral : 11.016 164.979 2958 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.19), residues: 1975 helix: 0.53 (0.20), residues: 730 sheet: -1.79 (0.32), residues: 275 loop : -2.48 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 168 HIS 0.005 0.001 HIS C 158 PHE 0.016 0.002 PHE C 103 TYR 0.026 0.001 TYR A 262 ARG 0.006 0.000 ARG C 410 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 THR cc_start: 0.9160 (m) cc_final: 0.8923 (p) REVERT: A 42 ASP cc_start: 0.7727 (m-30) cc_final: 0.7305 (t0) REVERT: A 254 PHE cc_start: 0.8890 (t80) cc_final: 0.8552 (t80) REVERT: A 302 ILE cc_start: 0.9795 (mt) cc_final: 0.9532 (tp) REVERT: B 210 MET cc_start: 0.8608 (tmm) cc_final: 0.8353 (tmm) REVERT: C 221 LEU cc_start: 0.8296 (mm) cc_final: 0.7505 (tp) REVERT: C 254 PHE cc_start: 0.8847 (t80) cc_final: 0.8558 (t80) REVERT: C 262 TYR cc_start: 0.8163 (t80) cc_final: 0.7936 (t80) REVERT: C 417 ASP cc_start: 0.8427 (m-30) cc_final: 0.8206 (m-30) REVERT: C 436 LEU cc_start: 0.9181 (pp) cc_final: 0.8669 (mt) REVERT: D 197 LYS cc_start: 0.9176 (tmmt) cc_final: 0.8858 (tmtt) REVERT: D 288 VAL cc_start: 0.8732 (p) cc_final: 0.8477 (m) REVERT: D 433 LEU cc_start: 0.9545 (tt) cc_final: 0.9334 (pp) REVERT: E 42 ASP cc_start: 0.8869 (t0) cc_final: 0.8447 (t0) REVERT: E 247 ASP cc_start: 0.8548 (m-30) cc_final: 0.8001 (t0) REVERT: E 259 LEU cc_start: 0.9409 (pt) cc_final: 0.8929 (tp) REVERT: E 413 LEU cc_start: 0.9319 (mt) cc_final: 0.8799 (mt) REVERT: E 436 LEU cc_start: 0.9325 (pp) cc_final: 0.8840 (mt) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.2442 time to fit residues: 74.0463 Evaluate side-chains 130 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 7.9990 chunk 169 optimal weight: 0.2980 chunk 37 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 188 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 HIS ** C 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 HIS ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17338 Z= 0.243 Angle : 0.743 10.940 23675 Z= 0.359 Chirality : 0.047 0.316 2819 Planarity : 0.004 0.043 2872 Dihedral : 10.520 162.489 2958 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.06 % Allowed : 3.42 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.19), residues: 1975 helix: 0.63 (0.20), residues: 730 sheet: -1.73 (0.32), residues: 275 loop : -2.41 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 94 HIS 0.008 0.001 HIS D 411 PHE 0.016 0.002 PHE E 233 TYR 0.030 0.001 TYR A 262 ARG 0.005 0.000 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 178 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 THR cc_start: 0.9217 (m) cc_final: 0.8977 (p) REVERT: A 42 ASP cc_start: 0.7809 (m-30) cc_final: 0.7438 (t0) REVERT: A 302 ILE cc_start: 0.9802 (mt) cc_final: 0.9565 (tp) REVERT: B 210 MET cc_start: 0.8632 (tmm) cc_final: 0.8400 (tmm) REVERT: B 433 LEU cc_start: 0.9519 (mt) cc_final: 0.9284 (mt) REVERT: B 436 LEU cc_start: 0.9251 (pp) cc_final: 0.8844 (mm) REVERT: C 254 PHE cc_start: 0.8804 (t80) cc_final: 0.8515 (t80) REVERT: C 436 LEU cc_start: 0.9198 (pp) cc_final: 0.8678 (mt) REVERT: D 288 VAL cc_start: 0.8783 (p) cc_final: 0.8520 (m) REVERT: E 42 ASP cc_start: 0.8963 (t0) cc_final: 0.8586 (t0) REVERT: E 247 ASP cc_start: 0.8592 (m-30) cc_final: 0.8013 (t0) REVERT: E 413 LEU cc_start: 0.9331 (mt) cc_final: 0.8785 (mt) REVERT: E 436 LEU cc_start: 0.9346 (pp) cc_final: 0.8851 (mt) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.2333 time to fit residues: 68.1572 Evaluate side-chains 120 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 137 optimal weight: 5.9990 chunk 106 optimal weight: 0.0980 chunk 158 optimal weight: 0.6980 chunk 105 optimal weight: 7.9990 chunk 187 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17338 Z= 0.169 Angle : 0.742 12.544 23675 Z= 0.348 Chirality : 0.047 0.308 2819 Planarity : 0.004 0.045 2872 Dihedral : 9.973 161.657 2958 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.19), residues: 1975 helix: 0.65 (0.20), residues: 740 sheet: -1.50 (0.32), residues: 275 loop : -2.30 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 68 HIS 0.002 0.001 HIS C 158 PHE 0.016 0.001 PHE B 103 TYR 0.031 0.001 TYR A 262 ARG 0.006 0.000 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 THR cc_start: 0.9158 (m) cc_final: 0.8923 (p) REVERT: A 42 ASP cc_start: 0.7846 (m-30) cc_final: 0.7413 (t0) REVERT: A 302 ILE cc_start: 0.9797 (mt) cc_final: 0.9547 (tp) REVERT: B 210 MET cc_start: 0.8615 (tmm) cc_final: 0.8312 (tmm) REVERT: B 436 LEU cc_start: 0.9246 (pp) cc_final: 0.8855 (mm) REVERT: C 254 PHE cc_start: 0.8726 (t80) cc_final: 0.8453 (t80) REVERT: C 262 TYR cc_start: 0.8339 (t80) cc_final: 0.7760 (t80) REVERT: C 436 LEU cc_start: 0.9183 (pp) cc_final: 0.8667 (mt) REVERT: E 42 ASP cc_start: 0.8945 (t0) cc_final: 0.8498 (t0) REVERT: E 247 ASP cc_start: 0.8554 (m-30) cc_final: 0.7968 (t0) REVERT: E 259 LEU cc_start: 0.9387 (pt) cc_final: 0.9033 (tp) REVERT: E 413 LEU cc_start: 0.9322 (mt) cc_final: 0.8789 (mt) REVERT: E 436 LEU cc_start: 0.9358 (pp) cc_final: 0.8871 (mt) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2280 time to fit residues: 68.4244 Evaluate side-chains 124 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17338 Z= 0.194 Angle : 0.739 11.832 23675 Z= 0.349 Chirality : 0.046 0.306 2819 Planarity : 0.004 0.042 2872 Dihedral : 9.429 161.577 2958 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.20), residues: 1975 helix: 0.65 (0.20), residues: 740 sheet: -1.38 (0.32), residues: 275 loop : -2.25 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 68 HIS 0.008 0.001 HIS D 411 PHE 0.016 0.001 PHE C 103 TYR 0.040 0.001 TYR A 262 ARG 0.005 0.000 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 THR cc_start: 0.9167 (m) cc_final: 0.8934 (p) REVERT: A 42 ASP cc_start: 0.7877 (m-30) cc_final: 0.7448 (t0) REVERT: A 242 PHE cc_start: 0.8534 (t80) cc_final: 0.8294 (t80) REVERT: A 302 ILE cc_start: 0.9796 (mt) cc_final: 0.9570 (tp) REVERT: B 210 MET cc_start: 0.8643 (tmm) cc_final: 0.8324 (tmm) REVERT: B 433 LEU cc_start: 0.9513 (mt) cc_final: 0.9286 (mt) REVERT: B 436 LEU cc_start: 0.9251 (pp) cc_final: 0.8867 (mm) REVERT: C 254 PHE cc_start: 0.8690 (t80) cc_final: 0.8444 (t80) REVERT: C 436 LEU cc_start: 0.9176 (pp) cc_final: 0.8687 (mt) REVERT: D 197 LYS cc_start: 0.9091 (tmmt) cc_final: 0.8859 (tmtt) REVERT: E 42 ASP cc_start: 0.8933 (t0) cc_final: 0.8486 (t0) REVERT: E 247 ASP cc_start: 0.8570 (m-30) cc_final: 0.7968 (t0) REVERT: E 259 LEU cc_start: 0.9332 (pt) cc_final: 0.8971 (tp) REVERT: E 413 LEU cc_start: 0.9331 (mt) cc_final: 0.8804 (mt) REVERT: E 436 LEU cc_start: 0.9361 (pp) cc_final: 0.8870 (mt) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2406 time to fit residues: 70.7642 Evaluate side-chains 126 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 0.0000 chunk 164 optimal weight: 0.0970 chunk 175 optimal weight: 3.9990 chunk 105 optimal weight: 0.0060 chunk 76 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 165 optimal weight: 0.3980 chunk 174 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN ** C 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17338 Z= 0.159 Angle : 0.758 13.649 23675 Z= 0.349 Chirality : 0.046 0.299 2819 Planarity : 0.004 0.083 2872 Dihedral : 9.058 161.359 2958 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.47 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.20), residues: 1975 helix: 0.69 (0.21), residues: 740 sheet: -1.14 (0.33), residues: 275 loop : -2.24 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 456 HIS 0.010 0.001 HIS D 411 PHE 0.014 0.002 PHE D 153 TYR 0.035 0.001 TYR A 262 ARG 0.005 0.000 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 THR cc_start: 0.9130 (m) cc_final: 0.8896 (p) REVERT: A 42 ASP cc_start: 0.7860 (m-30) cc_final: 0.7362 (t0) REVERT: A 296 ILE cc_start: 0.9440 (pt) cc_final: 0.9176 (tt) REVERT: A 302 ILE cc_start: 0.9785 (mt) cc_final: 0.9521 (tp) REVERT: B 210 MET cc_start: 0.8583 (tmm) cc_final: 0.8271 (tmm) REVERT: B 436 LEU cc_start: 0.9250 (pp) cc_final: 0.8880 (mm) REVERT: C 247 ASP cc_start: 0.8761 (m-30) cc_final: 0.7782 (t0) REVERT: C 254 PHE cc_start: 0.8546 (t80) cc_final: 0.8287 (t80) REVERT: C 258 LEU cc_start: 0.9502 (pt) cc_final: 0.9273 (pt) REVERT: C 436 LEU cc_start: 0.9151 (pp) cc_final: 0.8677 (mt) REVERT: D 197 LYS cc_start: 0.9067 (tmmt) cc_final: 0.8806 (tmtt) REVERT: E 42 ASP cc_start: 0.8858 (t0) cc_final: 0.8368 (t0) REVERT: E 247 ASP cc_start: 0.8534 (m-30) cc_final: 0.7935 (t0) REVERT: E 259 LEU cc_start: 0.9326 (pt) cc_final: 0.9034 (tp) REVERT: E 413 LEU cc_start: 0.9288 (mt) cc_final: 0.8744 (mt) REVERT: E 436 LEU cc_start: 0.9333 (pp) cc_final: 0.8863 (mt) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.2373 time to fit residues: 73.9169 Evaluate side-chains 130 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 87 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 154 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 94 optimal weight: 0.4980 chunk 122 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17338 Z= 0.215 Angle : 0.749 12.197 23675 Z= 0.356 Chirality : 0.046 0.300 2819 Planarity : 0.004 0.075 2872 Dihedral : 8.790 161.153 2958 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.20), residues: 1975 helix: 0.67 (0.20), residues: 740 sheet: -1.16 (0.33), residues: 275 loop : -2.16 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 94 HIS 0.003 0.001 HIS B 158 PHE 0.015 0.002 PHE E 233 TYR 0.040 0.001 TYR A 262 ARG 0.004 0.000 ARG B 120 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 2.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 THR cc_start: 0.9159 (m) cc_final: 0.8946 (p) REVERT: A 42 ASP cc_start: 0.7892 (m-30) cc_final: 0.7487 (t0) REVERT: A 254 PHE cc_start: 0.8872 (t80) cc_final: 0.8577 (t80) REVERT: A 296 ILE cc_start: 0.9426 (pt) cc_final: 0.9197 (tt) REVERT: A 302 ILE cc_start: 0.9798 (mt) cc_final: 0.9575 (tp) REVERT: B 210 MET cc_start: 0.8626 (tmm) cc_final: 0.8260 (tmm) REVERT: B 433 LEU cc_start: 0.9515 (mt) cc_final: 0.9295 (mt) REVERT: B 436 LEU cc_start: 0.9264 (pp) cc_final: 0.8897 (mm) REVERT: C 247 ASP cc_start: 0.8791 (m-30) cc_final: 0.7828 (t0) REVERT: C 254 PHE cc_start: 0.8648 (t80) cc_final: 0.8417 (t80) REVERT: C 436 LEU cc_start: 0.9222 (pp) cc_final: 0.8739 (mt) REVERT: D 102 GLU cc_start: 0.8589 (mp0) cc_final: 0.8299 (mp0) REVERT: D 197 LYS cc_start: 0.9167 (tmmt) cc_final: 0.8881 (tmtt) REVERT: E 42 ASP cc_start: 0.8917 (t0) cc_final: 0.8487 (t0) REVERT: E 247 ASP cc_start: 0.8588 (m-30) cc_final: 0.7985 (t0) REVERT: E 259 LEU cc_start: 0.9361 (pt) cc_final: 0.9027 (tp) REVERT: E 413 LEU cc_start: 0.9325 (mt) cc_final: 0.8818 (mt) REVERT: E 436 LEU cc_start: 0.9351 (pp) cc_final: 0.8885 (mt) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2451 time to fit residues: 71.7006 Evaluate side-chains 127 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.0270 chunk 47 optimal weight: 0.6980 chunk 142 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 154 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 136 optimal weight: 7.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.080147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.060037 restraints weight = 63960.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.061860 restraints weight = 38101.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.062315 restraints weight = 25093.478| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17338 Z= 0.166 Angle : 0.761 14.181 23675 Z= 0.351 Chirality : 0.046 0.297 2819 Planarity : 0.004 0.070 2872 Dihedral : 8.490 160.809 2958 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.20), residues: 1975 helix: 0.69 (0.20), residues: 740 sheet: -1.11 (0.30), residues: 325 loop : -2.19 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 456 HIS 0.002 0.000 HIS B 460 PHE 0.027 0.001 PHE B 233 TYR 0.038 0.001 TYR A 262 ARG 0.004 0.000 ARG B 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2902.61 seconds wall clock time: 54 minutes 9.66 seconds (3249.66 seconds total)