Starting phenix.real_space_refine on Sun Jul 21 11:16:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2o_26317/07_2024/7u2o_26317_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2o_26317/07_2024/7u2o_26317.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2o_26317/07_2024/7u2o_26317.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2o_26317/07_2024/7u2o_26317.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2o_26317/07_2024/7u2o_26317_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2o_26317/07_2024/7u2o_26317_trim.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 1.220 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9145 2.51 5 N 2265 2.21 5 O 2565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 268": "NH1" <-> "NH2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A ARG 407": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ARG 268": "NH1" <-> "NH2" Residue "B ARG 287": "NH1" <-> "NH2" Residue "B ARG 407": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 229": "NH1" <-> "NH2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C ARG 287": "NH1" <-> "NH2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D ARG 229": "NH1" <-> "NH2" Residue "D ARG 268": "NH1" <-> "NH2" Residue "D ARG 287": "NH1" <-> "NH2" Residue "D ARG 407": "NH1" <-> "NH2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 229": "NH1" <-> "NH2" Residue "E ARG 268": "NH1" <-> "NH2" Residue "E ARG 287": "NH1" <-> "NH2" Residue "E ARG 407": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 14075 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2770 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2770 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2770 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2770 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2770 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 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: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" 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: "R" 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: "V" 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: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'L2L': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'L2L': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'L2L': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'L2L': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'L2L': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.03, per 1000 atoms: 0.57 Number of scatterers: 14075 At special positions: 0 Unit cell: (105.537, 107.199, 132.129, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2565 8.00 N 2265 7.00 C 9145 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.02 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.02 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.02 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.03 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.02 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 168 " distance=2.03 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " NAG-ASN " NAG F 1 " - " ASN A 54 " " NAG J 1 " - " ASN B 54 " " NAG N 1 " - " ASN C 54 " " NAG R 1 " - " ASN D 54 " " NAG V 1 " - " ASN E 54 " Time building additional restraints: 5.80 Conformation dependent library (CDL) restraints added in 2.5 seconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 20 sheets defined 38.7% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 25 through 34 removed outlier: 3.842A pdb=" N LYS A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 90 Processing helix chain 'A' and resid 102 through 106 Processing helix chain 'A' and resid 236 through 243 Processing helix chain 'A' and resid 243 through 257 removed outlier: 3.603A pdb=" N ILE A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 287 removed outlier: 3.871A pdb=" N VAL A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE A 273 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 327 removed outlier: 4.214A pdb=" N ILE A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 307 " --> pdb=" O MET A 303 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N HIS A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 426 removed outlier: 4.139A pdb=" N SER A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Proline residue: A 411 - end of helix Processing helix chain 'B' and resid 25 through 34 removed outlier: 3.843A pdb=" N LYS B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 243 through 257 removed outlier: 3.602A pdb=" N ILE B 250 " --> pdb=" O PRO B 246 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 287 removed outlier: 3.871A pdb=" N VAL B 269 " --> pdb=" O ALA B 265 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE B 273 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 327 removed outlier: 4.213A pdb=" N ILE B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 307 " --> pdb=" O MET B 303 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N HIS B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 426 removed outlier: 4.139A pdb=" N SER B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG B 401 " --> pdb=" O SER B 397 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Proline residue: B 411 - end of helix Processing helix chain 'C' and resid 25 through 34 removed outlier: 3.841A pdb=" N LYS C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 90 Processing helix chain 'C' and resid 102 through 106 Processing helix chain 'C' and resid 236 through 243 Processing helix chain 'C' and resid 243 through 257 removed outlier: 3.602A pdb=" N ILE C 250 " --> pdb=" O PRO C 246 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 287 removed outlier: 3.872A pdb=" N VAL C 269 " --> pdb=" O ALA C 265 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE C 273 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG C 287 " --> pdb=" O SER C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 327 removed outlier: 4.213A pdb=" N ILE C 301 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 307 " --> pdb=" O MET C 303 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N HIS C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 426 removed outlier: 4.140A pdb=" N SER C 397 " --> pdb=" O LYS C 393 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG C 401 " --> pdb=" O SER C 397 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) Proline residue: C 411 - end of helix Processing helix chain 'D' and resid 25 through 34 removed outlier: 3.842A pdb=" N LYS D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 90 Processing helix chain 'D' and resid 102 through 106 Processing helix chain 'D' and resid 236 through 243 Processing helix chain 'D' and resid 243 through 257 removed outlier: 3.603A pdb=" N ILE D 250 " --> pdb=" O PRO D 246 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 287 removed outlier: 3.871A pdb=" N VAL D 269 " --> pdb=" O ALA D 265 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE D 273 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG D 287 " --> pdb=" O SER D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 327 removed outlier: 4.213A pdb=" N ILE D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 307 " --> pdb=" O MET D 303 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N HIS D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 426 removed outlier: 4.139A pdb=" N SER D 397 " --> pdb=" O LYS D 393 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG D 401 " --> pdb=" O SER D 397 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) Proline residue: D 411 - end of helix Processing helix chain 'E' and resid 25 through 34 removed outlier: 3.843A pdb=" N LYS E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 90 Processing helix chain 'E' and resid 102 through 106 Processing helix chain 'E' and resid 236 through 243 Processing helix chain 'E' and resid 243 through 257 removed outlier: 3.602A pdb=" N ILE E 250 " --> pdb=" O PRO E 246 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 287 removed outlier: 3.871A pdb=" N VAL E 269 " --> pdb=" O ALA E 265 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE E 273 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG E 287 " --> pdb=" O SER E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 327 removed outlier: 4.214A pdb=" N ILE E 301 " --> pdb=" O LYS E 297 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU E 307 " --> pdb=" O MET E 303 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N HIS E 327 " --> pdb=" O ILE E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 426 removed outlier: 4.138A pdb=" N SER E 397 " --> pdb=" O LYS E 393 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG E 401 " --> pdb=" O SER E 397 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) Proline residue: E 411 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 124 removed outlier: 7.205A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 132 through 136 removed outlier: 7.205A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N GLN A 193 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE A 59 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 116 removed outlier: 4.638A pdb=" N HIS A 231 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLU A 208 " --> pdb=" O HIS A 231 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N GLU A 233 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LYS A 206 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 216 through 217 Processing sheet with id=AA5, first strand: chain 'B' and resid 122 through 124 removed outlier: 7.205A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 132 through 136 removed outlier: 7.205A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N GLN B 193 " --> pdb=" O CYS B 57 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE B 59 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 114 through 116 removed outlier: 4.639A pdb=" N HIS B 231 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLU B 208 " --> pdb=" O HIS B 231 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N GLU B 233 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LYS B 206 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 216 through 217 Processing sheet with id=AA9, first strand: chain 'C' and resid 122 through 124 removed outlier: 7.205A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 132 through 136 removed outlier: 7.205A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N GLN C 193 " --> pdb=" O CYS C 57 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE C 59 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 114 through 116 removed outlier: 4.638A pdb=" N HIS C 231 " --> pdb=" O GLU C 208 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLU C 208 " --> pdb=" O HIS C 231 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N GLU C 233 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LYS C 206 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 216 through 217 Processing sheet with id=AB4, first strand: chain 'D' and resid 122 through 124 removed outlier: 7.206A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 132 through 136 removed outlier: 7.206A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N GLN D 193 " --> pdb=" O CYS D 57 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE D 59 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 114 through 116 removed outlier: 4.639A pdb=" N HIS D 231 " --> pdb=" O GLU D 208 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLU D 208 " --> pdb=" O HIS D 231 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N GLU D 233 " --> pdb=" O LYS D 206 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LYS D 206 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 216 through 217 Processing sheet with id=AB8, first strand: chain 'E' and resid 122 through 124 removed outlier: 7.205A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 132 through 136 removed outlier: 7.205A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N GLN E 193 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE E 59 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 114 through 116 removed outlier: 4.638A pdb=" N HIS E 231 " --> pdb=" O GLU E 208 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLU E 208 " --> pdb=" O HIS E 231 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N GLU E 233 " --> pdb=" O LYS E 206 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LYS E 206 " --> pdb=" O GLU E 233 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 216 through 217 750 hydrogen bonds defined for protein. 2190 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: 4.37 Time building geometry restraints manager: 6.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4340 1.34 - 1.47: 3687 1.47 - 1.60: 6223 1.60 - 1.72: 0 1.72 - 1.85: 165 Bond restraints: 14415 Sorted by residual: bond pdb=" C1 BMA J 3 " pdb=" C2 BMA J 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.53e+00 bond pdb=" C1 BMA N 3 " pdb=" C2 BMA N 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C1 BMA V 3 " pdb=" C2 BMA V 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.39e+00 bond pdb=" C1 BMA R 3 " pdb=" C2 BMA R 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.39e+00 ... (remaining 14410 not shown) Histogram of bond angle deviations from ideal: 98.65 - 105.72: 369 105.72 - 112.79: 7757 112.79 - 119.87: 4655 119.87 - 126.94: 6632 126.94 - 134.01: 172 Bond angle restraints: 19585 Sorted by residual: angle pdb=" O04 L2L C 600 " pdb=" S03 L2L C 600 " pdb=" O05 L2L C 600 " ideal model delta sigma weight residual 112.97 101.87 11.10 3.00e+00 1.11e-01 1.37e+01 angle pdb=" O04 L2L A 600 " pdb=" S03 L2L A 600 " pdb=" O05 L2L A 600 " ideal model delta sigma weight residual 112.97 101.89 11.08 3.00e+00 1.11e-01 1.36e+01 angle pdb=" O04 L2L B 600 " pdb=" S03 L2L B 600 " pdb=" O05 L2L B 600 " ideal model delta sigma weight residual 112.97 101.89 11.08 3.00e+00 1.11e-01 1.36e+01 angle pdb=" O04 L2L D 600 " pdb=" S03 L2L D 600 " pdb=" O05 L2L D 600 " ideal model delta sigma weight residual 112.97 101.90 11.07 3.00e+00 1.11e-01 1.36e+01 angle pdb=" O04 L2L E 600 " pdb=" S03 L2L E 600 " pdb=" O05 L2L E 600 " ideal model delta sigma weight residual 112.97 101.90 11.07 3.00e+00 1.11e-01 1.36e+01 ... (remaining 19580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.49: 8540 22.49 - 44.98: 200 44.98 - 67.47: 10 67.47 - 89.97: 40 89.97 - 112.46: 20 Dihedral angle restraints: 8810 sinusoidal: 3695 harmonic: 5115 Sorted by residual: dihedral pdb=" CB CYS D 154 " pdb=" SG CYS D 154 " pdb=" SG CYS D 168 " pdb=" CB CYS D 168 " ideal model delta sinusoidal sigma weight residual 93.00 42.18 50.82 1 1.00e+01 1.00e-02 3.53e+01 dihedral pdb=" CB CYS B 154 " pdb=" SG CYS B 154 " pdb=" SG CYS B 168 " pdb=" CB CYS B 168 " ideal model delta sinusoidal sigma weight residual 93.00 42.19 50.81 1 1.00e+01 1.00e-02 3.53e+01 dihedral pdb=" CB CYS A 154 " pdb=" SG CYS A 154 " pdb=" SG CYS A 168 " pdb=" CB CYS A 168 " ideal model delta sinusoidal sigma weight residual 93.00 42.20 50.80 1 1.00e+01 1.00e-02 3.53e+01 ... (remaining 8807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1853 0.054 - 0.107: 345 0.107 - 0.161: 52 0.161 - 0.215: 0 0.215 - 0.269: 10 Chirality restraints: 2260 Sorted by residual: chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C5 BMA R 3 " pdb=" C4 BMA R 3 " pdb=" C6 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C5 BMA V 3 " pdb=" C4 BMA V 3 " pdb=" C6 BMA V 3 " pdb=" O5 BMA V 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 2257 not shown) Planarity restraints: 2430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 151 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C VAL B 151 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL B 151 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU B 152 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 151 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.26e+00 pdb=" C VAL A 151 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL A 151 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU A 152 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 151 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.20e+00 pdb=" C VAL D 151 " -0.035 2.00e-02 2.50e+03 pdb=" O VAL D 151 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU D 152 " 0.012 2.00e-02 2.50e+03 ... (remaining 2427 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 287 2.66 - 3.22: 14540 3.22 - 3.78: 21205 3.78 - 4.34: 30758 4.34 - 4.90: 47876 Nonbonded interactions: 114666 Sorted by model distance: nonbonded pdb=" OG1 THR C 178 " pdb=" OD1 ASN C 180 " model vdw 2.101 2.440 nonbonded pdb=" OG1 THR B 178 " pdb=" OD1 ASN B 180 " model vdw 2.101 2.440 nonbonded pdb=" OG1 THR A 178 " pdb=" OD1 ASN A 180 " model vdw 2.102 2.440 nonbonded pdb=" OG1 THR E 178 " pdb=" OD1 ASN E 180 " model vdw 2.102 2.440 nonbonded pdb=" OG1 THR D 178 " pdb=" OD1 ASN D 180 " model vdw 2.102 2.440 ... (remaining 114661 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'N' selection = chain 'R' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 39.660 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 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 : 0.007 0.043 14415 Z= 0.417 Angle : 0.837 11.097 19585 Z= 0.455 Chirality : 0.048 0.269 2260 Planarity : 0.005 0.051 2425 Dihedral : 13.058 112.457 5460 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 37.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % 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: -4.77 (0.16), residues: 1710 helix: -3.68 (0.14), residues: 585 sheet: -3.06 (0.18), residues: 390 loop : -2.55 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 422 HIS 0.003 0.002 HIS C 217 PHE 0.017 0.002 PHE C 309 TYR 0.017 0.003 TYR C 144 ARG 0.007 0.001 ARG B 407 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 556 time to evaluate : 1.542 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 43 ARG cc_start: 0.9032 (mtm-85) cc_final: 0.8653 (mtm-85) REVERT: A 104 SER cc_start: 0.8212 (p) cc_final: 0.7601 (t) REVERT: A 127 VAL cc_start: 0.9007 (t) cc_final: 0.8648 (p) REVERT: A 206 LYS cc_start: 0.8711 (mtpt) cc_final: 0.8281 (mttp) REVERT: A 295 TYR cc_start: 0.8847 (p90) cc_final: 0.8646 (p90) REVERT: B 105 MET cc_start: 0.6200 (mmp) cc_final: 0.5754 (mmp) REVERT: B 127 VAL cc_start: 0.9003 (t) cc_final: 0.8655 (p) REVERT: B 206 LYS cc_start: 0.8611 (mtpt) cc_final: 0.8231 (mttp) REVERT: B 239 TYR cc_start: 0.8761 (m-80) cc_final: 0.8139 (m-80) REVERT: B 295 TYR cc_start: 0.8867 (p90) cc_final: 0.8567 (p90) REVERT: C 43 ARG cc_start: 0.9024 (mtm-85) cc_final: 0.8525 (mtm-85) REVERT: C 104 SER cc_start: 0.8295 (p) cc_final: 0.7557 (p) REVERT: C 105 MET cc_start: 0.6121 (mmp) cc_final: 0.5865 (mmp) REVERT: C 127 VAL cc_start: 0.9038 (t) cc_final: 0.8621 (p) REVERT: C 137 SER cc_start: 0.9171 (m) cc_final: 0.8472 (p) REVERT: C 206 LYS cc_start: 0.8647 (mtpt) cc_final: 0.8394 (mttm) REVERT: C 210 ASP cc_start: 0.8513 (m-30) cc_final: 0.8156 (m-30) REVERT: C 239 TYR cc_start: 0.8718 (m-80) cc_final: 0.8508 (m-80) REVERT: D 43 ARG cc_start: 0.9046 (mtm-85) cc_final: 0.8758 (mtm-85) REVERT: D 104 SER cc_start: 0.8210 (p) cc_final: 0.7547 (t) REVERT: D 105 MET cc_start: 0.6113 (mmp) cc_final: 0.5834 (mmp) REVERT: D 127 VAL cc_start: 0.9005 (t) cc_final: 0.8629 (p) REVERT: D 206 LYS cc_start: 0.8726 (mtpt) cc_final: 0.8359 (mttm) REVERT: D 299 ILE cc_start: 0.9091 (tp) cc_final: 0.8874 (tp) REVERT: E 43 ARG cc_start: 0.9019 (mtm-85) cc_final: 0.8689 (mtm-85) REVERT: E 104 SER cc_start: 0.8121 (p) cc_final: 0.7090 (p) REVERT: E 127 VAL cc_start: 0.8846 (t) cc_final: 0.8524 (p) REVERT: E 130 ASP cc_start: 0.8342 (m-30) cc_final: 0.8110 (m-30) REVERT: E 206 LYS cc_start: 0.8664 (mtpt) cc_final: 0.8368 (mttp) outliers start: 0 outliers final: 0 residues processed: 556 average time/residue: 0.2805 time to fit residues: 219.2466 Evaluate side-chains 386 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 386 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 154 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN B 77 ASN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN B 235 GLN C 77 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN C 171 GLN D 77 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN D 202 GLN E 77 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14415 Z= 0.308 Angle : 0.781 7.150 19585 Z= 0.408 Chirality : 0.049 0.208 2260 Planarity : 0.005 0.045 2425 Dihedral : 11.332 74.319 2195 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.64 % Allowed : 11.06 % Favored : 85.30 % 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: -2.98 (0.18), residues: 1710 helix: -1.59 (0.18), residues: 595 sheet: -1.98 (0.21), residues: 390 loop : -2.14 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 422 HIS 0.003 0.001 HIS C 125 PHE 0.025 0.002 PHE D 322 TYR 0.022 0.002 TYR A 421 ARG 0.004 0.001 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 458 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.7832 (tptt) REVERT: A 43 ARG cc_start: 0.8969 (mtm-85) cc_final: 0.8337 (mtm-85) REVERT: A 133 LEU cc_start: 0.8593 (tp) cc_final: 0.8271 (tt) REVERT: A 159 LYS cc_start: 0.8594 (mttt) cc_final: 0.8204 (mtmt) REVERT: A 206 LYS cc_start: 0.8750 (mtpt) cc_final: 0.8268 (mttp) REVERT: A 240 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8802 (mp) REVERT: B 32 LYS cc_start: 0.8563 (pttp) cc_final: 0.7950 (tptt) REVERT: B 130 ASP cc_start: 0.8477 (m-30) cc_final: 0.8226 (m-30) REVERT: B 133 LEU cc_start: 0.8626 (tp) cc_final: 0.8300 (tt) REVERT: B 159 LYS cc_start: 0.8687 (mttt) cc_final: 0.8411 (mtpt) REVERT: B 206 LYS cc_start: 0.8590 (mtpt) cc_final: 0.8238 (mttp) REVERT: B 239 TYR cc_start: 0.8670 (m-80) cc_final: 0.8383 (m-80) REVERT: B 295 TYR cc_start: 0.8952 (p90) cc_final: 0.8667 (p90) REVERT: C 32 LYS cc_start: 0.8441 (pttp) cc_final: 0.7696 (tptt) REVERT: C 133 LEU cc_start: 0.8630 (tp) cc_final: 0.8261 (tt) REVERT: C 137 SER cc_start: 0.9063 (m) cc_final: 0.8215 (p) REVERT: C 208 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7490 (tm-30) REVERT: C 210 ASP cc_start: 0.8457 (m-30) cc_final: 0.8155 (m-30) REVERT: C 239 TYR cc_start: 0.8713 (m-80) cc_final: 0.8500 (m-80) REVERT: C 282 GLN cc_start: 0.8864 (mm-40) cc_final: 0.8504 (mm-40) REVERT: D 43 ARG cc_start: 0.9118 (mtm-85) cc_final: 0.8570 (mtm-85) REVERT: D 133 LEU cc_start: 0.8609 (tp) cc_final: 0.8274 (tt) REVERT: D 159 LYS cc_start: 0.8680 (mttt) cc_final: 0.8383 (mtpt) REVERT: D 165 VAL cc_start: 0.9308 (t) cc_final: 0.9084 (p) REVERT: D 282 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8338 (mm-40) REVERT: E 32 LYS cc_start: 0.8459 (pttp) cc_final: 0.7814 (tptt) REVERT: E 43 ARG cc_start: 0.9112 (mtm-85) cc_final: 0.8667 (mtm-85) REVERT: E 133 LEU cc_start: 0.8469 (tp) cc_final: 0.8098 (tt) REVERT: E 156 MET cc_start: 0.9049 (tpp) cc_final: 0.8753 (mmt) REVERT: E 159 LYS cc_start: 0.8646 (mttt) cc_final: 0.8356 (mtpt) REVERT: E 206 LYS cc_start: 0.8677 (mtpt) cc_final: 0.8471 (mttp) REVERT: E 248 LEU cc_start: 0.8508 (tt) cc_final: 0.8290 (tp) outliers start: 55 outliers final: 35 residues processed: 484 average time/residue: 0.2461 time to fit residues: 174.0765 Evaluate side-chains 418 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 381 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 301 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 154 optimal weight: 0.0050 chunk 167 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 chunk 153 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS C 47 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN D 141 ASN D 202 GLN D 231 HIS E 47 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14415 Z= 0.260 Angle : 0.717 8.195 19585 Z= 0.369 Chirality : 0.048 0.230 2260 Planarity : 0.005 0.046 2425 Dihedral : 8.662 52.623 2195 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.10 % Allowed : 12.78 % Favored : 82.12 % 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: -1.98 (0.19), residues: 1710 helix: -0.49 (0.20), residues: 600 sheet: -1.24 (0.24), residues: 345 loop : -1.97 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 422 HIS 0.003 0.001 HIS C 125 PHE 0.024 0.002 PHE A 322 TYR 0.020 0.002 TYR A 421 ARG 0.005 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 395 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8539 (pttp) cc_final: 0.7814 (tptt) REVERT: A 133 LEU cc_start: 0.8594 (tp) cc_final: 0.8316 (tt) REVERT: A 141 ASN cc_start: 0.8482 (m110) cc_final: 0.8255 (m110) REVERT: A 206 LYS cc_start: 0.8722 (mtpt) cc_final: 0.8217 (mttp) REVERT: A 240 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8774 (mp) REVERT: B 32 LYS cc_start: 0.8519 (pttp) cc_final: 0.7907 (tptt) REVERT: B 133 LEU cc_start: 0.8628 (tp) cc_final: 0.8391 (tt) REVERT: B 159 LYS cc_start: 0.8700 (mttt) cc_final: 0.8433 (mtpt) REVERT: B 206 LYS cc_start: 0.8632 (mtpt) cc_final: 0.8277 (mttp) REVERT: B 239 TYR cc_start: 0.8634 (m-80) cc_final: 0.8260 (m-80) REVERT: B 295 TYR cc_start: 0.8960 (p90) cc_final: 0.8758 (p90) REVERT: C 133 LEU cc_start: 0.8717 (tp) cc_final: 0.8456 (tt) REVERT: C 159 LYS cc_start: 0.8622 (mttt) cc_final: 0.8391 (mtpt) REVERT: C 210 ASP cc_start: 0.8424 (m-30) cc_final: 0.8180 (m-30) REVERT: C 239 TYR cc_start: 0.8666 (m-80) cc_final: 0.8320 (m-80) REVERT: D 43 ARG cc_start: 0.9029 (mtm-85) cc_final: 0.8524 (mtm-85) REVERT: D 54 ASN cc_start: 0.8040 (m-40) cc_final: 0.7589 (p0) REVERT: D 159 LYS cc_start: 0.8695 (mttt) cc_final: 0.8429 (mtpt) REVERT: E 43 ARG cc_start: 0.8973 (mtm-85) cc_final: 0.8309 (mtm-85) REVERT: E 83 GLN cc_start: 0.7940 (mt0) cc_final: 0.7710 (mt0) REVERT: E 156 MET cc_start: 0.9035 (tpp) cc_final: 0.8809 (mmt) REVERT: E 159 LYS cc_start: 0.8622 (mttt) cc_final: 0.8362 (mtpt) outliers start: 77 outliers final: 57 residues processed: 430 average time/residue: 0.2277 time to fit residues: 146.4775 Evaluate side-chains 429 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 371 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 415 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.4980 chunk 116 optimal weight: 0.0870 chunk 80 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 141 ASN A 171 GLN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN C 141 ASN ** D 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 ASN E 141 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14415 Z= 0.232 Angle : 0.721 7.653 19585 Z= 0.374 Chirality : 0.051 0.443 2260 Planarity : 0.004 0.045 2425 Dihedral : 7.107 48.890 2195 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 5.10 % Allowed : 14.24 % Favored : 80.66 % Cbeta Deviations : 0.06 % 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: -1.39 (0.19), residues: 1710 helix: 0.20 (0.21), residues: 590 sheet: -0.75 (0.25), residues: 335 loop : -1.88 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 422 HIS 0.002 0.001 HIS C 125 PHE 0.026 0.002 PHE A 322 TYR 0.018 0.002 TYR A 421 ARG 0.003 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 388 time to evaluate : 1.542 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 133 LEU cc_start: 0.8567 (tp) cc_final: 0.8320 (tt) REVERT: A 206 LYS cc_start: 0.8705 (mtpt) cc_final: 0.8217 (mttp) REVERT: A 240 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8753 (mp) REVERT: A 428 ILE cc_start: 0.7148 (mp) cc_final: 0.6727 (mt) REVERT: B 32 LYS cc_start: 0.8547 (pttp) cc_final: 0.7913 (tptt) REVERT: B 133 LEU cc_start: 0.8558 (tp) cc_final: 0.8349 (tt) REVERT: B 141 ASN cc_start: 0.8555 (m110) cc_final: 0.8333 (m110) REVERT: B 159 LYS cc_start: 0.8694 (mttt) cc_final: 0.8413 (mtpt) REVERT: B 206 LYS cc_start: 0.8638 (mtpt) cc_final: 0.8287 (mttp) REVERT: B 227 GLU cc_start: 0.8303 (pt0) cc_final: 0.8021 (pt0) REVERT: B 239 TYR cc_start: 0.8603 (m-80) cc_final: 0.8039 (m-80) REVERT: B 240 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8711 (mp) REVERT: B 243 MET cc_start: 0.8614 (mtt) cc_final: 0.8362 (mtt) REVERT: B 282 GLN cc_start: 0.8862 (mm-40) cc_final: 0.8467 (mm-40) REVERT: C 133 LEU cc_start: 0.8638 (tp) cc_final: 0.8395 (tt) REVERT: C 159 LYS cc_start: 0.8635 (mttt) cc_final: 0.8378 (mtpt) REVERT: C 240 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8706 (mp) REVERT: D 159 LYS cc_start: 0.8698 (mttt) cc_final: 0.8423 (mtpt) REVERT: E 156 MET cc_start: 0.9033 (tpp) cc_final: 0.8781 (mmt) REVERT: E 159 LYS cc_start: 0.8618 (mttt) cc_final: 0.8340 (mtpt) outliers start: 77 outliers final: 65 residues processed: 426 average time/residue: 0.2276 time to fit residues: 146.6640 Evaluate side-chains 434 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 366 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 415 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 140 optimal weight: 4.9990 chunk 113 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 ASN B 141 ASN C 231 HIS ** D 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14415 Z= 0.212 Angle : 0.688 7.813 19585 Z= 0.357 Chirality : 0.050 0.611 2260 Planarity : 0.004 0.042 2425 Dihedral : 6.499 55.455 2195 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 5.30 % Allowed : 16.03 % Favored : 78.68 % 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: -0.92 (0.19), residues: 1710 helix: 0.53 (0.21), residues: 595 sheet: -0.17 (0.26), residues: 320 loop : -1.70 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 186 HIS 0.002 0.001 HIS A 125 PHE 0.026 0.001 PHE A 322 TYR 0.018 0.001 TYR A 421 ARG 0.003 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 388 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.8552 (tp) cc_final: 0.8337 (tt) REVERT: A 206 LYS cc_start: 0.8720 (mtpt) cc_final: 0.8219 (mttp) REVERT: A 240 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8745 (mp) REVERT: B 139 ASN cc_start: 0.8885 (p0) cc_final: 0.8344 (p0) REVERT: B 141 ASN cc_start: 0.8389 (m-40) cc_final: 0.8062 (m-40) REVERT: B 159 LYS cc_start: 0.8674 (mttt) cc_final: 0.8377 (mtpt) REVERT: B 206 LYS cc_start: 0.8628 (mtpt) cc_final: 0.8292 (mttp) REVERT: B 227 GLU cc_start: 0.8281 (pt0) cc_final: 0.8042 (pt0) REVERT: B 239 TYR cc_start: 0.8572 (m-80) cc_final: 0.7984 (m-80) REVERT: B 240 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8678 (mp) REVERT: B 243 MET cc_start: 0.8595 (mtt) cc_final: 0.8358 (mtt) REVERT: B 250 ILE cc_start: 0.8420 (mm) cc_final: 0.8036 (mt) REVERT: B 282 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8393 (mm-40) REVERT: C 133 LEU cc_start: 0.8666 (tp) cc_final: 0.8411 (tt) REVERT: C 159 LYS cc_start: 0.8644 (mttt) cc_final: 0.8379 (mtpt) REVERT: C 240 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8648 (mp) REVERT: C 250 ILE cc_start: 0.8482 (mm) cc_final: 0.8147 (mt) REVERT: C 282 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8515 (mm-40) REVERT: D 141 ASN cc_start: 0.8307 (m-40) cc_final: 0.8084 (m-40) REVERT: D 159 LYS cc_start: 0.8686 (mttt) cc_final: 0.8411 (mtpt) REVERT: D 229 ARG cc_start: 0.8528 (mtp180) cc_final: 0.8224 (mtp180) REVERT: D 250 ILE cc_start: 0.8406 (mm) cc_final: 0.8098 (mt) REVERT: D 282 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8421 (mm-40) REVERT: E 159 LYS cc_start: 0.8604 (mttt) cc_final: 0.8331 (mtpt) REVERT: E 240 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8691 (mp) outliers start: 80 outliers final: 66 residues processed: 423 average time/residue: 0.2250 time to fit residues: 145.8928 Evaluate side-chains 432 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 362 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 415 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 136 optimal weight: 7.9990 chunk 76 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 171 GLN C 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14415 Z= 0.215 Angle : 0.691 8.431 19585 Z= 0.358 Chirality : 0.049 0.429 2260 Planarity : 0.004 0.040 2425 Dihedral : 6.383 57.183 2195 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 5.56 % Allowed : 16.03 % Favored : 78.41 % 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: -0.68 (0.20), residues: 1710 helix: 0.76 (0.22), residues: 595 sheet: 0.08 (0.26), residues: 320 loop : -1.65 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 186 HIS 0.002 0.001 HIS B 125 PHE 0.028 0.001 PHE B 414 TYR 0.017 0.002 TYR A 421 ARG 0.002 0.000 ARG C 229 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 382 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ASN cc_start: 0.8274 (m-40) cc_final: 0.7963 (m-40) REVERT: A 206 LYS cc_start: 0.8727 (mtpt) cc_final: 0.8214 (mttp) REVERT: A 240 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8760 (mp) REVERT: A 282 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8475 (mm-40) REVERT: B 139 ASN cc_start: 0.8865 (p0) cc_final: 0.8284 (p0) REVERT: B 141 ASN cc_start: 0.8402 (m-40) cc_final: 0.7913 (m-40) REVERT: B 159 LYS cc_start: 0.8662 (mttt) cc_final: 0.8354 (mtpt) REVERT: B 206 LYS cc_start: 0.8634 (mtpt) cc_final: 0.8281 (mttp) REVERT: B 227 GLU cc_start: 0.8283 (pt0) cc_final: 0.8005 (pt0) REVERT: B 239 TYR cc_start: 0.8527 (m-80) cc_final: 0.7944 (m-80) REVERT: B 240 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8638 (mp) REVERT: B 243 MET cc_start: 0.8631 (mtt) cc_final: 0.8401 (mtt) REVERT: B 282 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8429 (mm-40) REVERT: C 133 LEU cc_start: 0.8680 (tp) cc_final: 0.8447 (tt) REVERT: C 159 LYS cc_start: 0.8655 (mttt) cc_final: 0.8377 (mtpt) REVERT: C 240 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8593 (mp) REVERT: C 250 ILE cc_start: 0.8511 (mm) cc_final: 0.8188 (mt) REVERT: C 282 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8550 (mm-40) REVERT: D 105 MET cc_start: 0.8247 (ppp) cc_final: 0.7483 (ppp) REVERT: D 113 ASP cc_start: 0.9029 (p0) cc_final: 0.8808 (p0) REVERT: D 139 ASN cc_start: 0.8851 (p0) cc_final: 0.8276 (p0) REVERT: D 141 ASN cc_start: 0.8241 (m-40) cc_final: 0.8015 (m-40) REVERT: D 159 LYS cc_start: 0.8649 (mttt) cc_final: 0.8386 (mtpt) REVERT: D 212 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7611 (ptt90) REVERT: D 250 ILE cc_start: 0.8470 (mm) cc_final: 0.8158 (mt) REVERT: D 282 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8352 (mm-40) REVERT: E 159 LYS cc_start: 0.8628 (mttt) cc_final: 0.8331 (mtpt) REVERT: E 240 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8659 (mp) REVERT: E 250 ILE cc_start: 0.8356 (mm) cc_final: 0.8054 (mt) REVERT: E 282 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8495 (mm-40) outliers start: 84 outliers final: 69 residues processed: 420 average time/residue: 0.2349 time to fit residues: 152.1486 Evaluate side-chains 455 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 381 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 415 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 0.1980 chunk 18 optimal weight: 0.1980 chunk 93 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 163 optimal weight: 0.7980 chunk 102 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14415 Z= 0.238 Angle : 0.694 8.292 19585 Z= 0.360 Chirality : 0.049 0.459 2260 Planarity : 0.004 0.038 2425 Dihedral : 6.351 55.521 2195 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 5.56 % Allowed : 16.03 % Favored : 78.41 % 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: -0.58 (0.20), residues: 1710 helix: 0.84 (0.22), residues: 595 sheet: 0.15 (0.27), residues: 320 loop : -1.60 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 186 HIS 0.003 0.001 HIS B 125 PHE 0.027 0.001 PHE A 322 TYR 0.017 0.002 TYR A 421 ARG 0.002 0.000 ARG C 229 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 375 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8330 (ppp) cc_final: 0.7237 (ptt) REVERT: A 206 LYS cc_start: 0.8712 (mtpt) cc_final: 0.8197 (mttp) REVERT: A 240 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8751 (mp) REVERT: A 282 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8459 (mm-40) REVERT: B 141 ASN cc_start: 0.8363 (m-40) cc_final: 0.7905 (m-40) REVERT: B 159 LYS cc_start: 0.8659 (mttt) cc_final: 0.8350 (mtpt) REVERT: B 206 LYS cc_start: 0.8640 (mtpt) cc_final: 0.8239 (mttp) REVERT: B 227 GLU cc_start: 0.8289 (pt0) cc_final: 0.8009 (pt0) REVERT: B 239 TYR cc_start: 0.8518 (m-80) cc_final: 0.7947 (m-80) REVERT: B 243 MET cc_start: 0.8644 (mtt) cc_final: 0.8432 (mtt) REVERT: B 250 ILE cc_start: 0.8504 (mm) cc_final: 0.8151 (mt) REVERT: B 282 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8448 (mm-40) REVERT: C 133 LEU cc_start: 0.8689 (tp) cc_final: 0.8459 (tt) REVERT: C 159 LYS cc_start: 0.8646 (mttt) cc_final: 0.8367 (mtpt) REVERT: C 240 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8625 (mp) REVERT: C 244 TYR cc_start: 0.8834 (m-80) cc_final: 0.8530 (m-80) REVERT: C 250 ILE cc_start: 0.8531 (mm) cc_final: 0.8209 (mt) REVERT: C 282 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8539 (mm-40) REVERT: D 113 ASP cc_start: 0.9032 (p0) cc_final: 0.8802 (p0) REVERT: D 133 LEU cc_start: 0.8634 (tp) cc_final: 0.8387 (tt) REVERT: D 141 ASN cc_start: 0.8255 (m-40) cc_final: 0.8051 (m-40) REVERT: D 159 LYS cc_start: 0.8696 (mttt) cc_final: 0.8434 (mtpt) REVERT: D 212 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7535 (ptt90) REVERT: E 159 LYS cc_start: 0.8636 (mttt) cc_final: 0.8332 (mtpt) REVERT: E 240 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8653 (mp) REVERT: E 250 ILE cc_start: 0.8357 (mm) cc_final: 0.8054 (mt) REVERT: E 282 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8522 (mm-40) outliers start: 84 outliers final: 68 residues processed: 408 average time/residue: 0.2253 time to fit residues: 140.3134 Evaluate side-chains 446 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 374 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 415 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 6.9990 chunk 104 optimal weight: 0.4980 chunk 111 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 128 optimal weight: 0.0870 chunk 149 optimal weight: 2.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN C 171 GLN D 47 ASN E 171 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14415 Z= 0.201 Angle : 0.707 13.045 19585 Z= 0.364 Chirality : 0.049 0.445 2260 Planarity : 0.004 0.035 2425 Dihedral : 6.365 52.869 2195 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.57 % Allowed : 17.88 % Favored : 77.55 % 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: -0.51 (0.20), residues: 1710 helix: 0.96 (0.22), residues: 590 sheet: 0.28 (0.27), residues: 320 loop : -1.65 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 186 HIS 0.002 0.001 HIS D 217 PHE 0.029 0.001 PHE B 414 TYR 0.017 0.001 TYR A 421 ARG 0.002 0.000 ARG D 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 408 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8234 (ppp) cc_final: 0.7453 (ptt) REVERT: A 141 ASN cc_start: 0.8184 (m-40) cc_final: 0.7803 (m-40) REVERT: A 206 LYS cc_start: 0.8720 (mtpt) cc_final: 0.8176 (mttp) REVERT: A 240 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8734 (mp) REVERT: A 250 ILE cc_start: 0.8255 (mm) cc_final: 0.7949 (mt) REVERT: A 282 GLN cc_start: 0.8688 (mm-40) cc_final: 0.8481 (mm-40) REVERT: B 141 ASN cc_start: 0.8285 (m-40) cc_final: 0.7938 (m-40) REVERT: B 159 LYS cc_start: 0.8624 (mttt) cc_final: 0.8309 (mtpt) REVERT: B 206 LYS cc_start: 0.8650 (mtpt) cc_final: 0.8314 (mttp) REVERT: B 227 GLU cc_start: 0.8240 (pt0) cc_final: 0.7974 (pt0) REVERT: B 239 TYR cc_start: 0.8480 (m-80) cc_final: 0.7970 (m-80) REVERT: B 243 MET cc_start: 0.8634 (mtt) cc_final: 0.8418 (mtt) REVERT: B 250 ILE cc_start: 0.8517 (mm) cc_final: 0.8198 (mt) REVERT: B 282 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8415 (mm-40) REVERT: C 141 ASN cc_start: 0.8225 (m-40) cc_final: 0.7921 (m-40) REVERT: C 159 LYS cc_start: 0.8595 (mttt) cc_final: 0.8315 (mtpt) REVERT: C 244 TYR cc_start: 0.8801 (m-80) cc_final: 0.8455 (m-80) REVERT: C 250 ILE cc_start: 0.8539 (mm) cc_final: 0.8224 (mt) REVERT: D 113 ASP cc_start: 0.8994 (p0) cc_final: 0.8783 (p0) REVERT: D 133 LEU cc_start: 0.8600 (tp) cc_final: 0.8364 (tt) REVERT: D 159 LYS cc_start: 0.8646 (mttt) cc_final: 0.8363 (mtpt) REVERT: D 212 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7451 (ptt90) REVERT: E 159 LYS cc_start: 0.8603 (mttt) cc_final: 0.8308 (mtpt) REVERT: E 240 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8610 (mp) REVERT: E 250 ILE cc_start: 0.8297 (mm) cc_final: 0.8012 (mt) REVERT: E 282 GLN cc_start: 0.8707 (mm-40) cc_final: 0.8484 (mm-40) outliers start: 69 outliers final: 60 residues processed: 440 average time/residue: 0.2474 time to fit residues: 166.7386 Evaluate side-chains 453 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 390 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 415 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 152 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 137 optimal weight: 0.6980 chunk 144 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 161 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN C 171 GLN E 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14415 Z= 0.224 Angle : 0.717 9.708 19585 Z= 0.368 Chirality : 0.050 0.458 2260 Planarity : 0.004 0.033 2425 Dihedral : 6.319 49.907 2195 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.70 % Allowed : 18.01 % Favored : 77.28 % 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: -0.54 (0.20), residues: 1710 helix: 0.94 (0.22), residues: 590 sheet: 0.22 (0.27), residues: 325 loop : -1.66 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 186 HIS 0.002 0.001 HIS B 125 PHE 0.048 0.001 PHE E 48 TYR 0.019 0.002 TYR B 238 ARG 0.002 0.000 ARG C 229 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 392 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8268 (ppp) cc_final: 0.7588 (ptt) REVERT: A 206 LYS cc_start: 0.8691 (mtpt) cc_final: 0.8156 (mttp) REVERT: A 240 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8749 (mp) REVERT: A 250 ILE cc_start: 0.8286 (mm) cc_final: 0.7993 (mt) REVERT: A 282 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8499 (mm-40) REVERT: B 34 MET cc_start: 0.6846 (pmm) cc_final: 0.6259 (ptp) REVERT: B 141 ASN cc_start: 0.8291 (m-40) cc_final: 0.7974 (m-40) REVERT: B 159 LYS cc_start: 0.8598 (mttt) cc_final: 0.8311 (mtpt) REVERT: B 206 LYS cc_start: 0.8639 (mtpt) cc_final: 0.8308 (mttp) REVERT: B 227 GLU cc_start: 0.8261 (pt0) cc_final: 0.7986 (pt0) REVERT: B 239 TYR cc_start: 0.8531 (m-80) cc_final: 0.8028 (m-80) REVERT: B 243 MET cc_start: 0.8628 (mtt) cc_final: 0.8421 (mtt) REVERT: B 250 ILE cc_start: 0.8538 (mm) cc_final: 0.8219 (mt) REVERT: B 282 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8408 (mm-40) REVERT: C 34 MET cc_start: 0.6485 (pmm) cc_final: 0.5806 (pmm) REVERT: C 123 ASN cc_start: 0.8926 (p0) cc_final: 0.8724 (p0) REVERT: C 141 ASN cc_start: 0.8249 (m-40) cc_final: 0.7967 (m-40) REVERT: C 159 LYS cc_start: 0.8642 (mttt) cc_final: 0.8354 (mtpt) REVERT: C 240 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8581 (mp) REVERT: C 244 TYR cc_start: 0.8782 (m-80) cc_final: 0.8499 (m-80) REVERT: D 133 LEU cc_start: 0.8604 (tp) cc_final: 0.8369 (tt) REVERT: D 159 LYS cc_start: 0.8680 (mttt) cc_final: 0.8419 (mtpt) REVERT: D 212 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7628 (ptt90) REVERT: E 139 ASN cc_start: 0.8910 (p0) cc_final: 0.8535 (p0) REVERT: E 159 LYS cc_start: 0.8608 (mttt) cc_final: 0.8308 (mtpt) REVERT: E 240 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8618 (mp) REVERT: E 250 ILE cc_start: 0.8298 (mm) cc_final: 0.8010 (mt) REVERT: E 282 GLN cc_start: 0.8708 (mm-40) cc_final: 0.8475 (mm-40) outliers start: 71 outliers final: 64 residues processed: 422 average time/residue: 0.2354 time to fit residues: 151.3751 Evaluate side-chains 449 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 381 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 415 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.9566 > 50: distance: 29 - 39: 7.368 distance: 39 - 40: 8.880 distance: 40 - 41: 13.046 distance: 40 - 43: 11.139 distance: 41 - 42: 22.556 distance: 41 - 45: 8.869 distance: 43 - 44: 22.719 distance: 45 - 46: 13.796 distance: 46 - 47: 13.457 distance: 46 - 49: 16.013 distance: 47 - 48: 21.310 distance: 47 - 54: 15.778 distance: 49 - 50: 9.857 distance: 50 - 51: 13.881 distance: 51 - 52: 14.771 distance: 51 - 53: 18.373 distance: 54 - 55: 15.776 distance: 55 - 56: 30.458 distance: 55 - 58: 27.992 distance: 56 - 57: 45.546 distance: 56 - 66: 13.217 distance: 58 - 59: 21.732 distance: 59 - 60: 10.614 distance: 59 - 61: 3.126 distance: 60 - 62: 15.598 distance: 61 - 63: 5.108 distance: 62 - 64: 11.455 distance: 63 - 64: 10.888 distance: 64 - 65: 17.944 distance: 66 - 67: 20.122 distance: 66 - 72: 41.468 distance: 67 - 68: 20.867 distance: 67 - 70: 6.711 distance: 68 - 69: 34.655 distance: 68 - 73: 19.617 distance: 70 - 71: 14.000 distance: 71 - 72: 14.199 distance: 73 - 74: 20.406 distance: 74 - 75: 15.676 distance: 74 - 77: 3.950 distance: 75 - 76: 15.702 distance: 75 - 81: 37.122 distance: 77 - 78: 21.492 distance: 78 - 79: 18.300 distance: 78 - 80: 28.780 distance: 81 - 82: 35.467 distance: 82 - 83: 26.479 distance: 82 - 85: 32.827 distance: 83 - 84: 39.756 distance: 83 - 89: 26.599 distance: 85 - 86: 39.363 distance: 86 - 87: 33.664 distance: 86 - 88: 52.676 distance: 89 - 90: 46.879 distance: 90 - 91: 17.293 distance: 90 - 93: 36.643 distance: 91 - 92: 32.002 distance: 91 - 95: 15.679 distance: 93 - 94: 18.387 distance: 95 - 96: 43.375 distance: 96 - 97: 25.007 distance: 96 - 99: 20.730 distance: 97 - 98: 29.228 distance: 97 - 103: 12.482 distance: 99 - 100: 16.459 distance: 100 - 101: 21.268 distance: 100 - 102: 34.457 distance: 103 - 104: 15.880 distance: 104 - 105: 16.405 distance: 104 - 107: 28.201 distance: 105 - 106: 15.435 distance: 105 - 111: 3.408 distance: 107 - 108: 19.830 distance: 108 - 109: 12.240 distance: 108 - 110: 14.722 distance: 111 - 112: 11.522 distance: 112 - 113: 6.000 distance: 112 - 115: 17.294 distance: 113 - 114: 27.135 distance: 113 - 119: 8.082 distance: 115 - 116: 9.386 distance: 116 - 117: 29.323 distance: 116 - 118: 7.552