Starting phenix.real_space_refine on Fri Feb 16 02:32:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm4_20386/02_2024/6pm4_20386.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm4_20386/02_2024/6pm4_20386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm4_20386/02_2024/6pm4_20386.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm4_20386/02_2024/6pm4_20386.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm4_20386/02_2024/6pm4_20386.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm4_20386/02_2024/6pm4_20386.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 90 5.16 5 C 9140 2.51 5 N 2265 2.21 5 O 2560 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-5238/modules/chem_data/mon_lib" Total number of atoms: 14055 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2767 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 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: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2767 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 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: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2767 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 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: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2767 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 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: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2767 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 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: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 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: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 7.82, per 1000 atoms: 0.56 Number of scatterers: 14055 At special positions: 0 Unit cell: (105.344, 105.344, 133.326, 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 90 16.00 O 2560 8.00 N 2265 7.00 C 9140 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=2.04 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=2.04 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=2.04 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=2.04 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=2.04 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 G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG F 1 " - " ASN A 54 " " NAG G 1 " - " ASN B 54 " " NAG H 1 " - " ASN C 54 " " NAG I 1 " - " ASN D 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 6.19 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: 50 helices and 25 sheets defined 42.7% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 25 through 34 Processing helix chain 'A' and resid 36 through 40 removed outlier: 4.398A pdb=" N TYR A 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 90 Processing helix chain 'A' and resid 102 through 109 removed outlier: 4.273A pdb=" N ASP A 107 " --> pdb=" O SER A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 236 through 243 Processing helix chain 'A' and resid 243 through 257 removed outlier: 3.732A pdb=" N ILE A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 287 removed outlier: 3.512A pdb=" N GLY A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 327 removed outlier: 4.339A pdb=" N ILE A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 428 removed outlier: 3.694A pdb=" N LEU A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 3.571A pdb=" N PHE A 414 " --> pdb=" O PHE A 410 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE A 423 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N THR A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR A 425 " --> pdb=" O TYR A 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 34 Processing helix chain 'B' and resid 36 through 40 removed outlier: 4.398A pdb=" N TYR B 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 102 through 109 removed outlier: 4.273A pdb=" N ASP B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 243 through 257 removed outlier: 3.732A pdb=" N ILE B 250 " --> pdb=" O PRO B 246 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 287 removed outlier: 3.512A pdb=" N GLY B 272 " --> pdb=" O ARG B 268 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 327 removed outlier: 4.338A pdb=" N ILE B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL B 305 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 428 removed outlier: 3.694A pdb=" N LEU B 394 " --> pdb=" O GLU B 390 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE B 395 " --> pdb=" O MET B 391 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) Proline residue: B 411 - end of helix removed outlier: 3.571A pdb=" N PHE B 414 " --> pdb=" O PHE B 410 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 419 " --> pdb=" O LEU B 415 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE B 423 " --> pdb=" O ILE B 419 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N THR B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR B 425 " --> pdb=" O TYR B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 34 Processing helix chain 'C' and resid 36 through 40 removed outlier: 4.397A pdb=" N TYR C 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 90 Processing helix chain 'C' and resid 102 through 109 removed outlier: 4.273A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 163 Processing helix chain 'C' and resid 236 through 243 Processing helix chain 'C' and resid 243 through 257 removed outlier: 3.732A pdb=" N ILE C 250 " --> pdb=" O PRO C 246 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 287 removed outlier: 3.511A pdb=" N GLY C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR C 278 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG C 287 " --> pdb=" O SER C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 327 removed outlier: 4.339A pdb=" N ILE C 301 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL C 305 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER C 312 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA C 313 " --> pdb=" O PHE C 309 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE C 323 " --> pdb=" O ALA C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 428 removed outlier: 3.694A pdb=" N LEU C 394 " --> pdb=" O GLU C 390 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE C 395 " --> pdb=" O MET C 391 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 3.571A pdb=" N PHE C 414 " --> pdb=" O PHE C 410 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C 419 " --> pdb=" O LEU C 415 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE C 423 " --> pdb=" O ILE C 419 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N THR C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR C 425 " --> pdb=" O TYR C 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 34 Processing helix chain 'D' and resid 36 through 40 removed outlier: 4.397A pdb=" N TYR D 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 90 Processing helix chain 'D' and resid 102 through 109 removed outlier: 4.273A pdb=" N ASP D 107 " --> pdb=" O SER D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 163 Processing helix chain 'D' and resid 236 through 243 Processing helix chain 'D' and resid 243 through 257 removed outlier: 3.732A pdb=" N ILE D 250 " --> pdb=" O PRO D 246 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 287 removed outlier: 3.511A pdb=" N GLY D 272 " --> pdb=" O ARG D 268 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR D 278 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG D 287 " --> pdb=" O SER D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 327 removed outlier: 4.339A pdb=" N ILE D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL D 305 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER D 312 " --> pdb=" O LEU D 308 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 428 removed outlier: 3.693A pdb=" N LEU D 394 " --> pdb=" O GLU D 390 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE D 395 " --> pdb=" O MET D 391 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL D 405 " --> pdb=" O ARG D 401 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER D 406 " --> pdb=" O ILE D 402 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) Proline residue: D 411 - end of helix removed outlier: 3.571A pdb=" N PHE D 414 " --> pdb=" O PHE D 410 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE D 419 " --> pdb=" O LEU D 415 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE D 423 " --> pdb=" O ILE D 419 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N THR D 424 " --> pdb=" O PHE D 420 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR D 425 " --> pdb=" O TYR D 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 34 Processing helix chain 'E' and resid 36 through 40 removed outlier: 4.397A pdb=" N TYR E 40 " --> pdb=" O VAL E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 90 Processing helix chain 'E' and resid 102 through 109 removed outlier: 4.273A pdb=" N ASP E 107 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 163 Processing helix chain 'E' and resid 236 through 243 Processing helix chain 'E' and resid 243 through 257 removed outlier: 3.732A pdb=" N ILE E 250 " --> pdb=" O PRO E 246 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE E 252 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER E 257 " --> pdb=" O LEU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 287 removed outlier: 3.512A pdb=" N GLY E 272 " --> pdb=" O ARG E 268 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR E 278 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG E 287 " --> pdb=" O SER E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 327 removed outlier: 4.339A pdb=" N ILE E 301 " --> pdb=" O LYS E 297 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL E 305 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER E 312 " --> pdb=" O LEU E 308 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA E 313 " --> pdb=" O PHE E 309 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 428 removed outlier: 3.694A pdb=" N LEU E 394 " --> pdb=" O GLU E 390 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE E 395 " --> pdb=" O MET E 391 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL E 405 " --> pdb=" O ARG E 401 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER E 406 " --> pdb=" O ILE E 402 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) Proline residue: E 411 - end of helix removed outlier: 3.571A pdb=" N PHE E 414 " --> pdb=" O PHE E 410 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE E 419 " --> pdb=" O LEU E 415 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE E 423 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N THR E 424 " --> pdb=" O PHE E 420 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR E 425 " --> pdb=" O TYR E 421 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 100 removed outlier: 6.620A pdb=" N PHE A 79 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ILE A 61 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG A 81 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE A 59 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLN A 83 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N CYS A 57 " --> pdb=" O GLN A 83 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N ASN A 85 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL A 55 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 123 removed outlier: 3.598A pdb=" N THR A 149 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE A 79 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ILE A 61 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG A 81 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE A 59 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLN A 83 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N CYS A 57 " --> pdb=" O GLN A 83 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N ASN A 85 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL A 55 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLN A 193 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 5.942A 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 Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 116 Processing sheet with id=AA5, first strand: chain 'A' and resid 216 through 217 Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 100 removed outlier: 6.621A pdb=" N PHE B 79 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE B 61 " --> pdb=" O PHE B 79 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG B 81 " --> pdb=" O ILE B 59 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE B 59 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLN B 83 " --> pdb=" O CYS B 57 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N CYS B 57 " --> pdb=" O GLN B 83 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N ASN B 85 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL B 55 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 122 through 123 removed outlier: 3.597A pdb=" N THR B 149 " --> pdb=" O ASN B 123 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N PHE B 79 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE B 61 " --> pdb=" O PHE B 79 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG B 81 " --> pdb=" O ILE B 59 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE B 59 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLN B 83 " --> pdb=" O CYS B 57 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N CYS B 57 " --> pdb=" O GLN B 83 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N ASN B 85 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL B 55 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLN B 193 " --> pdb=" O CYS B 57 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE B 59 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AA9, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AB1, first strand: chain 'B' and resid 216 through 217 Processing sheet with id=AB2, first strand: chain 'C' and resid 99 through 100 removed outlier: 6.620A pdb=" N PHE C 79 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE C 61 " --> pdb=" O PHE C 79 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG C 81 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ILE C 59 " --> pdb=" O ARG C 81 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLN C 83 " --> pdb=" O CYS C 57 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N CYS C 57 " --> pdb=" O GLN C 83 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N ASN C 85 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N VAL C 55 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 122 through 123 removed outlier: 3.598A pdb=" N THR C 149 " --> pdb=" O ASN C 123 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE C 79 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE C 61 " --> pdb=" O PHE C 79 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG C 81 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ILE C 59 " --> pdb=" O ARG C 81 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLN C 83 " --> pdb=" O CYS C 57 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N CYS C 57 " --> pdb=" O GLN C 83 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N ASN C 85 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N VAL C 55 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N GLN C 193 " --> pdb=" O CYS C 57 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ILE C 59 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AB5, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AB6, first strand: chain 'C' and resid 216 through 217 Processing sheet with id=AB7, first strand: chain 'D' and resid 99 through 100 removed outlier: 6.621A pdb=" N PHE D 79 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ILE D 61 " --> pdb=" O PHE D 79 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG D 81 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE D 59 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLN D 83 " --> pdb=" O CYS D 57 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N CYS D 57 " --> pdb=" O GLN D 83 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N ASN D 85 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL D 55 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 122 through 123 removed outlier: 3.598A pdb=" N THR D 149 " --> pdb=" O ASN D 123 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N PHE D 79 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ILE D 61 " --> pdb=" O PHE D 79 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG D 81 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE D 59 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLN D 83 " --> pdb=" O CYS D 57 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N CYS D 57 " --> pdb=" O GLN D 83 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N ASN D 85 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL D 55 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N GLN D 193 " --> pdb=" O CYS D 57 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE D 59 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AC1, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AC2, first strand: chain 'D' and resid 216 through 217 Processing sheet with id=AC3, first strand: chain 'E' and resid 99 through 100 removed outlier: 6.620A pdb=" N PHE E 79 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE E 61 " --> pdb=" O PHE E 79 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG E 81 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ILE E 59 " --> pdb=" O ARG E 81 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLN E 83 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N CYS E 57 " --> pdb=" O GLN E 83 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N ASN E 85 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL E 55 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 122 through 123 removed outlier: 3.597A pdb=" N THR E 149 " --> pdb=" O ASN E 123 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE E 79 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE E 61 " --> pdb=" O PHE E 79 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG E 81 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ILE E 59 " --> pdb=" O ARG E 81 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLN E 83 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N CYS E 57 " --> pdb=" O GLN E 83 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N ASN E 85 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL E 55 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLN E 193 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ILE E 59 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 114 through 116 Processing sheet with id=AC6, first strand: chain 'E' and resid 114 through 116 Processing sheet with id=AC7, first strand: chain 'E' and resid 216 through 217 740 hydrogen bonds defined for protein. 2085 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: 5.27 Time building geometry restraints manager: 6.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4340 1.35 - 1.47: 3697 1.47 - 1.59: 6208 1.59 - 1.71: 0 1.71 - 1.84: 150 Bond restraints: 14395 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 2.57e+00 bond pdb=" CB ARG B 234 " pdb=" CG ARG B 234 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.57e+00 bond pdb=" C1 BMA H 3 " pdb=" C2 BMA H 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.56e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.56e+00 bond pdb=" CB ARG D 234 " pdb=" CG ARG D 234 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.53e+00 ... (remaining 14390 not shown) Histogram of bond angle deviations from ideal: 99.38 - 106.30: 436 106.30 - 113.22: 7937 113.22 - 120.14: 4991 120.14 - 127.06: 6003 127.06 - 133.98: 188 Bond angle restraints: 19555 Sorted by residual: angle pdb=" C VAL D 127 " pdb=" N THR D 128 " pdb=" CA THR D 128 " ideal model delta sigma weight residual 121.54 131.23 -9.69 1.91e+00 2.74e-01 2.58e+01 angle pdb=" C VAL C 127 " pdb=" N THR C 128 " pdb=" CA THR C 128 " ideal model delta sigma weight residual 121.54 131.22 -9.68 1.91e+00 2.74e-01 2.57e+01 angle pdb=" C VAL E 127 " pdb=" N THR E 128 " pdb=" CA THR E 128 " ideal model delta sigma weight residual 121.54 131.21 -9.67 1.91e+00 2.74e-01 2.56e+01 angle pdb=" C VAL B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 121.54 131.21 -9.67 1.91e+00 2.74e-01 2.56e+01 angle pdb=" C VAL A 127 " pdb=" N THR A 128 " pdb=" CA THR A 128 " ideal model delta sigma weight residual 121.54 131.20 -9.66 1.91e+00 2.74e-01 2.56e+01 ... (remaining 19550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.21: 8495 22.21 - 44.43: 210 44.43 - 66.64: 20 66.64 - 88.85: 40 88.85 - 111.06: 20 Dihedral angle restraints: 8785 sinusoidal: 3670 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 52.72 40.28 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" CB CYS C 154 " pdb=" SG CYS C 154 " pdb=" SG CYS C 168 " pdb=" CB CYS C 168 " ideal model delta sinusoidal sigma weight residual 93.00 52.74 40.26 1 1.00e+01 1.00e-02 2.27e+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 52.75 40.25 1 1.00e+01 1.00e-02 2.27e+01 ... (remaining 8782 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1722 0.057 - 0.114: 447 0.114 - 0.170: 76 0.170 - 0.227: 5 0.227 - 0.284: 10 Chirality restraints: 2260 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 2257 not shown) Planarity restraints: 2435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 127 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.60e+00 pdb=" C VAL E 127 " 0.037 2.00e-02 2.50e+03 pdb=" O VAL E 127 " -0.014 2.00e-02 2.50e+03 pdb=" N THR E 128 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 127 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.57e+00 pdb=" C VAL D 127 " -0.037 2.00e-02 2.50e+03 pdb=" O VAL D 127 " 0.014 2.00e-02 2.50e+03 pdb=" N THR D 128 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 127 " -0.010 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C VAL A 127 " 0.037 2.00e-02 2.50e+03 pdb=" O VAL A 127 " -0.014 2.00e-02 2.50e+03 pdb=" N THR A 128 " -0.012 2.00e-02 2.50e+03 ... (remaining 2432 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3038 2.77 - 3.30: 13550 3.30 - 3.83: 24608 3.83 - 4.37: 29001 4.37 - 4.90: 47194 Nonbonded interactions: 117391 Sorted by model distance: nonbonded pdb=" OG1 THR E 178 " pdb=" OD1 ASN E 180 " model vdw 2.236 2.440 nonbonded pdb=" OG1 THR D 178 " pdb=" OD1 ASN D 180 " model vdw 2.237 2.440 nonbonded pdb=" OG1 THR A 178 " pdb=" OD1 ASN A 180 " model vdw 2.237 2.440 nonbonded pdb=" OG1 THR B 178 " pdb=" OD1 ASN B 180 " model vdw 2.237 2.440 nonbonded pdb=" OG1 THR C 178 " pdb=" OD1 ASN C 180 " model vdw 2.237 2.440 ... (remaining 117386 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 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 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: 7.490 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 41.090 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 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 0.049 14395 Z= 0.435 Angle : 0.959 9.693 19555 Z= 0.503 Chirality : 0.053 0.284 2260 Planarity : 0.006 0.051 2430 Dihedral : 13.638 111.065 5435 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % 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: -4.33 (0.16), residues: 1710 helix: -3.47 (0.13), residues: 560 sheet: -2.49 (0.24), residues: 345 loop : -2.47 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP B 110 HIS 0.004 0.002 HIS B 125 PHE 0.014 0.003 PHE C 115 TYR 0.013 0.003 TYR E 425 ARG 0.013 0.001 ARG A 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 291 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ARG cc_start: 0.9587 (ttm-80) cc_final: 0.9386 (ttp80) REVERT: A 130 ASP cc_start: 0.9306 (m-30) cc_final: 0.8893 (m-30) REVERT: A 134 LEU cc_start: 0.9647 (tp) cc_final: 0.9431 (tt) REVERT: A 202 GLN cc_start: 0.9453 (mt0) cc_final: 0.8978 (tm-30) REVERT: A 262 MET cc_start: 0.8785 (tpt) cc_final: 0.8519 (tpt) REVERT: A 282 GLN cc_start: 0.9587 (mm-40) cc_final: 0.9347 (mt0) REVERT: A 311 PHE cc_start: 0.9593 (m-80) cc_final: 0.9380 (m-10) REVERT: A 391 MET cc_start: 0.8291 (mmm) cc_final: 0.7973 (ttp) REVERT: A 417 PHE cc_start: 0.9658 (t80) cc_final: 0.9390 (t80) REVERT: B 80 LEU cc_start: 0.9674 (tp) cc_final: 0.9398 (tp) REVERT: B 82 GLN cc_start: 0.9581 (mt0) cc_final: 0.9219 (mp10) REVERT: B 130 ASP cc_start: 0.9271 (m-30) cc_final: 0.8861 (m-30) REVERT: B 134 LEU cc_start: 0.9628 (tp) cc_final: 0.9401 (tt) REVERT: B 163 MET cc_start: 0.9252 (mpp) cc_final: 0.8660 (mpp) REVERT: B 202 GLN cc_start: 0.9518 (mt0) cc_final: 0.9010 (tm-30) REVERT: B 244 TYR cc_start: 0.9531 (m-10) cc_final: 0.8756 (m-80) REVERT: B 262 MET cc_start: 0.8846 (tpt) cc_final: 0.8533 (tpt) REVERT: B 282 GLN cc_start: 0.9585 (mm-40) cc_final: 0.9234 (mt0) REVERT: B 311 PHE cc_start: 0.9624 (m-80) cc_final: 0.9393 (m-10) REVERT: B 391 MET cc_start: 0.8322 (mmm) cc_final: 0.8075 (ttp) REVERT: B 417 PHE cc_start: 0.9616 (t80) cc_final: 0.9364 (t80) REVERT: C 130 ASP cc_start: 0.9276 (m-30) cc_final: 0.8826 (m-30) REVERT: C 134 LEU cc_start: 0.9585 (tp) cc_final: 0.9382 (tt) REVERT: C 202 GLN cc_start: 0.9495 (mt0) cc_final: 0.9014 (tm-30) REVERT: C 242 GLN cc_start: 0.9470 (tt0) cc_final: 0.9209 (tp-100) REVERT: C 244 TYR cc_start: 0.9484 (m-10) cc_final: 0.8763 (m-80) REVERT: C 262 MET cc_start: 0.8832 (tpt) cc_final: 0.8539 (tpt) REVERT: C 282 GLN cc_start: 0.9563 (mm-40) cc_final: 0.9299 (mt0) REVERT: C 391 MET cc_start: 0.8258 (mmm) cc_final: 0.7969 (ttp) REVERT: C 417 PHE cc_start: 0.9619 (t80) cc_final: 0.9373 (t80) REVERT: D 130 ASP cc_start: 0.9264 (m-30) cc_final: 0.8826 (m-30) REVERT: D 163 MET cc_start: 0.9281 (mpp) cc_final: 0.8784 (mpp) REVERT: D 202 GLN cc_start: 0.9513 (mt0) cc_final: 0.9060 (tm-30) REVERT: D 244 TYR cc_start: 0.9499 (m-10) cc_final: 0.8696 (m-80) REVERT: D 262 MET cc_start: 0.8764 (tpt) cc_final: 0.8486 (tpt) REVERT: D 391 MET cc_start: 0.8370 (mmm) cc_final: 0.8096 (ttp) REVERT: D 417 PHE cc_start: 0.9611 (t80) cc_final: 0.9409 (t80) REVERT: E 80 LEU cc_start: 0.9690 (tp) cc_final: 0.9476 (tp) REVERT: E 82 GLN cc_start: 0.9632 (mt0) cc_final: 0.9233 (mp10) REVERT: E 130 ASP cc_start: 0.9220 (m-30) cc_final: 0.8880 (m-30) REVERT: E 163 MET cc_start: 0.9256 (mpp) cc_final: 0.8705 (mpp) REVERT: E 202 GLN cc_start: 0.9521 (mt0) cc_final: 0.9071 (tm-30) REVERT: E 262 MET cc_start: 0.8885 (tpt) cc_final: 0.8606 (tpt) REVERT: E 282 GLN cc_start: 0.9632 (mm-40) cc_final: 0.9351 (mt0) REVERT: E 391 MET cc_start: 0.8240 (mmm) cc_final: 0.7999 (ttp) REVERT: E 417 PHE cc_start: 0.9669 (t80) cc_final: 0.9402 (t80) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.2644 time to fit residues: 111.2742 Evaluate side-chains 161 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.536 ------------------------------------------------------------------------------- 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: 5.9990 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 44 optimal weight: 0.0000 chunk 86 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 133 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 overall best weight: 2.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 GLN A 83 GLN A 141 ASN A 202 GLN A 231 HIS B 62 ASN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN B 202 GLN B 231 HIS C 62 ASN C 82 GLN C 83 GLN C 141 ASN C 231 HIS D 62 ASN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN D 83 GLN D 131 ASN D 141 ASN D 231 HIS ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN E 83 GLN E 131 ASN E 141 ASN E 202 GLN E 231 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14395 Z= 0.260 Angle : 0.788 6.390 19555 Z= 0.404 Chirality : 0.044 0.193 2260 Planarity : 0.005 0.037 2430 Dihedral : 12.098 74.121 2185 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 21.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.26 % Allowed : 9.17 % Favored : 89.57 % 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: -3.26 (0.18), residues: 1710 helix: -1.76 (0.18), residues: 595 sheet: -2.42 (0.23), residues: 370 loop : -2.21 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 110 HIS 0.003 0.001 HIS A 231 PHE 0.013 0.002 PHE C 230 TYR 0.021 0.002 TYR E 238 ARG 0.004 0.000 ARG C 268 *********************** 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 184 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 165 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.9309 (m-30) cc_final: 0.8999 (m-30) REVERT: A 134 LEU cc_start: 0.9630 (tp) cc_final: 0.9368 (tt) REVERT: A 311 PHE cc_start: 0.9379 (m-80) cc_final: 0.9065 (m-80) REVERT: A 391 MET cc_start: 0.8265 (mmm) cc_final: 0.7973 (ttp) REVERT: A 417 PHE cc_start: 0.9708 (t80) cc_final: 0.9499 (t80) REVERT: B 82 GLN cc_start: 0.9620 (mt0) cc_final: 0.9091 (mt0) REVERT: B 130 ASP cc_start: 0.9295 (m-30) cc_final: 0.8970 (m-30) REVERT: B 134 LEU cc_start: 0.9638 (tp) cc_final: 0.9337 (tt) REVERT: B 170 MET cc_start: 0.9343 (ppp) cc_final: 0.9123 (ppp) REVERT: B 262 MET cc_start: 0.8591 (tpt) cc_final: 0.8365 (tpt) REVERT: B 391 MET cc_start: 0.8321 (mmm) cc_final: 0.8111 (ttp) REVERT: B 417 PHE cc_start: 0.9711 (t80) cc_final: 0.9450 (t80) REVERT: C 130 ASP cc_start: 0.9303 (m-30) cc_final: 0.8966 (m-30) REVERT: C 134 LEU cc_start: 0.9606 (tp) cc_final: 0.9371 (tt) REVERT: C 170 MET cc_start: 0.9344 (ppp) cc_final: 0.9113 (ppp) REVERT: C 262 MET cc_start: 0.8593 (tpt) cc_final: 0.8372 (tpt) REVERT: C 391 MET cc_start: 0.8281 (mmm) cc_final: 0.8020 (ttp) REVERT: C 417 PHE cc_start: 0.9679 (t80) cc_final: 0.9447 (t80) REVERT: D 130 ASP cc_start: 0.9300 (m-30) cc_final: 0.8972 (m-30) REVERT: D 391 MET cc_start: 0.8342 (mmm) cc_final: 0.8096 (ttp) REVERT: E 130 ASP cc_start: 0.9250 (m-30) cc_final: 0.8924 (m-30) outliers start: 19 outliers final: 12 residues processed: 175 average time/residue: 0.2391 time to fit residues: 64.5431 Evaluate side-chains 155 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 143 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 168 CYS Chi-restraints excluded: chain E residue 251 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 167 optimal weight: 8.9990 chunk 137 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14395 Z= 0.276 Angle : 0.721 8.685 19555 Z= 0.364 Chirality : 0.042 0.182 2260 Planarity : 0.004 0.034 2430 Dihedral : 9.163 52.544 2185 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 23.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 2.19 % Allowed : 7.84 % Favored : 89.97 % 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: -2.36 (0.19), residues: 1710 helix: -0.44 (0.20), residues: 590 sheet: -2.35 (0.23), residues: 370 loop : -1.97 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 110 HIS 0.005 0.002 HIS E 231 PHE 0.015 0.001 PHE E 223 TYR 0.017 0.002 TYR E 238 ARG 0.004 0.000 ARG E 75 *********************** 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 187 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 154 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.9192 (ttp) cc_final: 0.8861 (tmm) REVERT: A 130 ASP cc_start: 0.9367 (m-30) cc_final: 0.9001 (m-30) REVERT: A 152 LEU cc_start: 0.9843 (mt) cc_final: 0.9300 (tt) REVERT: A 202 GLN cc_start: 0.9460 (mt0) cc_final: 0.9038 (tm-30) REVERT: A 391 MET cc_start: 0.8305 (mmm) cc_final: 0.8092 (ttm) REVERT: A 415 LEU cc_start: 0.9338 (tp) cc_final: 0.9112 (pp) REVERT: B 72 MET cc_start: 0.9153 (ttp) cc_final: 0.8859 (tmm) REVERT: B 130 ASP cc_start: 0.9344 (m-30) cc_final: 0.8987 (m-30) REVERT: B 134 LEU cc_start: 0.9675 (tp) cc_final: 0.9410 (tt) REVERT: B 152 LEU cc_start: 0.9832 (mt) cc_final: 0.9250 (tt) REVERT: B 170 MET cc_start: 0.9404 (ppp) cc_final: 0.8978 (ppp) REVERT: B 202 GLN cc_start: 0.9507 (mt0) cc_final: 0.9066 (tm-30) REVERT: B 262 MET cc_start: 0.8620 (tpt) cc_final: 0.8401 (tpt) REVERT: B 417 PHE cc_start: 0.9736 (t80) cc_final: 0.9441 (t80) REVERT: C 72 MET cc_start: 0.9071 (ttp) cc_final: 0.8781 (tmm) REVERT: C 130 ASP cc_start: 0.9349 (m-30) cc_final: 0.8706 (p0) REVERT: C 134 LEU cc_start: 0.9647 (tp) cc_final: 0.9447 (tt) REVERT: C 152 LEU cc_start: 0.9832 (mt) cc_final: 0.9338 (tt) REVERT: C 170 MET cc_start: 0.9437 (ppp) cc_final: 0.9209 (ppp) REVERT: C 202 GLN cc_start: 0.9527 (mt0) cc_final: 0.9036 (tm-30) REVERT: C 262 MET cc_start: 0.8590 (tpt) cc_final: 0.8373 (tpt) REVERT: C 417 PHE cc_start: 0.9738 (t80) cc_final: 0.9494 (t80) REVERT: D 72 MET cc_start: 0.9223 (ttp) cc_final: 0.8910 (tmm) REVERT: D 119 GLU cc_start: 0.8442 (tp30) cc_final: 0.8155 (tm-30) REVERT: D 130 ASP cc_start: 0.9331 (m-30) cc_final: 0.8778 (p0) REVERT: D 152 LEU cc_start: 0.9834 (mt) cc_final: 0.9263 (tt) REVERT: D 202 GLN cc_start: 0.9542 (mt0) cc_final: 0.9084 (tm-30) REVERT: E 72 MET cc_start: 0.9232 (ttp) cc_final: 0.8929 (tmm) REVERT: E 82 GLN cc_start: 0.9668 (mt0) cc_final: 0.9128 (mt0) REVERT: E 130 ASP cc_start: 0.9281 (m-30) cc_final: 0.8955 (m-30) REVERT: E 152 LEU cc_start: 0.9826 (mt) cc_final: 0.9323 (tt) REVERT: E 202 GLN cc_start: 0.9497 (mt0) cc_final: 0.9068 (tm-30) REVERT: E 391 MET cc_start: 0.6583 (ttp) cc_final: 0.6381 (tmm) outliers start: 33 outliers final: 26 residues processed: 184 average time/residue: 0.2127 time to fit residues: 61.6991 Evaluate side-chains 168 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 142 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 168 CYS Chi-restraints excluded: chain E residue 225 CYS Chi-restraints excluded: chain E residue 251 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 147 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 GLN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14395 Z= 0.366 Angle : 0.756 11.293 19555 Z= 0.385 Chirality : 0.042 0.190 2260 Planarity : 0.005 0.047 2430 Dihedral : 7.425 59.760 2185 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 26.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 2.46 % Allowed : 9.77 % Favored : 87.77 % 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: -1.92 (0.19), residues: 1710 helix: 0.09 (0.21), residues: 590 sheet: -2.25 (0.24), residues: 370 loop : -1.78 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 110 HIS 0.006 0.002 HIS E 231 PHE 0.030 0.002 PHE A 311 TYR 0.019 0.002 TYR B 144 ARG 0.003 0.001 ARG D 75 *********************** 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 183 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 146 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.9308 (ttp) cc_final: 0.8847 (tmm) REVERT: A 119 GLU cc_start: 0.8471 (tp30) cc_final: 0.8209 (tp30) REVERT: A 130 ASP cc_start: 0.9378 (m-30) cc_final: 0.8870 (p0) REVERT: A 152 LEU cc_start: 0.9868 (mt) cc_final: 0.9293 (tt) REVERT: A 202 GLN cc_start: 0.9468 (mt0) cc_final: 0.9010 (tm-30) REVERT: A 391 MET cc_start: 0.8375 (mmm) cc_final: 0.8173 (ttm) REVERT: B 72 MET cc_start: 0.9305 (ttp) cc_final: 0.8883 (tmm) REVERT: B 119 GLU cc_start: 0.8493 (tp30) cc_final: 0.8228 (tp30) REVERT: B 130 ASP cc_start: 0.9380 (m-30) cc_final: 0.8866 (p0) REVERT: B 202 GLN cc_start: 0.9514 (mt0) cc_final: 0.9046 (tm-30) REVERT: B 262 MET cc_start: 0.8571 (tpt) cc_final: 0.8311 (tpp) REVERT: B 391 MET cc_start: 0.7369 (ttm) cc_final: 0.7096 (ttp) REVERT: C 72 MET cc_start: 0.9242 (ttp) cc_final: 0.8802 (tmm) REVERT: C 130 ASP cc_start: 0.9383 (m-30) cc_final: 0.8823 (p0) REVERT: C 202 GLN cc_start: 0.9540 (mt0) cc_final: 0.9033 (tm-30) REVERT: C 262 MET cc_start: 0.8713 (tpt) cc_final: 0.8459 (tpt) REVERT: C 391 MET cc_start: 0.7270 (ttm) cc_final: 0.6965 (ttp) REVERT: C 417 PHE cc_start: 0.9793 (t80) cc_final: 0.9528 (t80) REVERT: D 119 GLU cc_start: 0.8460 (tp30) cc_final: 0.8150 (tp30) REVERT: D 130 ASP cc_start: 0.9388 (m-30) cc_final: 0.8882 (p0) REVERT: D 152 LEU cc_start: 0.9852 (mt) cc_final: 0.9332 (tt) REVERT: D 202 GLN cc_start: 0.9485 (mt0) cc_final: 0.9046 (tm-30) REVERT: D 391 MET cc_start: 0.7706 (ttm) cc_final: 0.7363 (ttp) REVERT: E 72 MET cc_start: 0.9328 (ttp) cc_final: 0.8832 (tmm) REVERT: E 130 ASP cc_start: 0.9325 (m-30) cc_final: 0.8864 (p0) REVERT: E 202 GLN cc_start: 0.9490 (mt0) cc_final: 0.9020 (tm-30) REVERT: E 391 MET cc_start: 0.6686 (ttp) cc_final: 0.6327 (ttp) outliers start: 37 outliers final: 27 residues processed: 178 average time/residue: 0.2178 time to fit residues: 60.9288 Evaluate side-chains 166 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 168 CYS Chi-restraints excluded: chain E residue 225 CYS Chi-restraints excluded: chain E residue 251 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.0050 chunk 93 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 overall best weight: 4.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 14395 Z= 0.301 Angle : 0.720 8.616 19555 Z= 0.365 Chirality : 0.041 0.197 2260 Planarity : 0.005 0.038 2430 Dihedral : 6.544 41.026 2185 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 24.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 1.79 % Allowed : 11.63 % Favored : 86.58 % 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: -1.68 (0.20), residues: 1710 helix: 0.23 (0.21), residues: 610 sheet: -2.04 (0.24), residues: 370 loop : -1.69 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 84 HIS 0.004 0.001 HIS E 231 PHE 0.031 0.002 PHE C 311 TYR 0.017 0.002 TYR E 144 ARG 0.004 0.001 ARG B 75 *********************** 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 167 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 140 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.9280 (ptp) cc_final: 0.8934 (pmm) REVERT: A 119 GLU cc_start: 0.8501 (tp30) cc_final: 0.8199 (tp30) REVERT: A 130 ASP cc_start: 0.9382 (m-30) cc_final: 0.8835 (p0) REVERT: A 152 LEU cc_start: 0.9870 (mt) cc_final: 0.9342 (tt) REVERT: A 202 GLN cc_start: 0.9463 (mt0) cc_final: 0.9011 (tm-30) REVERT: A 391 MET cc_start: 0.8363 (mmm) cc_final: 0.8090 (ttp) REVERT: B 130 ASP cc_start: 0.9383 (m-30) cc_final: 0.8890 (p0) REVERT: B 202 GLN cc_start: 0.9499 (mt0) cc_final: 0.9045 (tm-30) REVERT: B 262 MET cc_start: 0.8680 (tpt) cc_final: 0.8402 (tpp) REVERT: B 391 MET cc_start: 0.7405 (ttm) cc_final: 0.7184 (ttp) REVERT: C 72 MET cc_start: 0.9302 (ttp) cc_final: 0.8870 (tmm) REVERT: C 130 ASP cc_start: 0.9392 (m-30) cc_final: 0.8891 (p0) REVERT: C 202 GLN cc_start: 0.9529 (mt0) cc_final: 0.9034 (tm-30) REVERT: C 391 MET cc_start: 0.7255 (ttm) cc_final: 0.7028 (ttp) REVERT: D 130 ASP cc_start: 0.9409 (m-30) cc_final: 0.8913 (p0) REVERT: D 202 GLN cc_start: 0.9475 (mt0) cc_final: 0.9053 (tm-30) REVERT: D 391 MET cc_start: 0.7825 (ttm) cc_final: 0.7541 (ttp) REVERT: E 105 MET cc_start: 0.9350 (ptp) cc_final: 0.9096 (mpp) REVERT: E 130 ASP cc_start: 0.9368 (m-30) cc_final: 0.8892 (p0) REVERT: E 202 GLN cc_start: 0.9467 (mt0) cc_final: 0.9031 (tm-30) REVERT: E 391 MET cc_start: 0.6668 (ttp) cc_final: 0.6447 (tmm) outliers start: 27 outliers final: 24 residues processed: 166 average time/residue: 0.2186 time to fit residues: 56.7134 Evaluate side-chains 161 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 137 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 168 CYS Chi-restraints excluded: chain E residue 225 CYS Chi-restraints excluded: chain E residue 251 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 136 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 ASN E 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14395 Z= 0.176 Angle : 0.691 8.361 19555 Z= 0.340 Chirality : 0.043 0.193 2260 Planarity : 0.004 0.031 2430 Dihedral : 6.101 30.840 2185 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.79 % Allowed : 11.89 % Favored : 86.31 % 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: -1.52 (0.20), residues: 1710 helix: 0.21 (0.21), residues: 610 sheet: -1.85 (0.25), residues: 370 loop : -1.49 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 84 HIS 0.002 0.001 HIS D 231 PHE 0.008 0.001 PHE A 311 TYR 0.017 0.002 TYR E 144 ARG 0.004 0.000 ARG C 75 *********************** 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 170 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.9301 (ttp) cc_final: 0.8840 (tmm) REVERT: A 105 MET cc_start: 0.9261 (ptp) cc_final: 0.8960 (pmm) REVERT: A 119 GLU cc_start: 0.8452 (tp30) cc_final: 0.8162 (tm-30) REVERT: A 130 ASP cc_start: 0.9385 (m-30) cc_final: 0.8822 (p0) REVERT: A 160 ASN cc_start: 0.9092 (OUTLIER) cc_final: 0.8845 (p0) REVERT: A 202 GLN cc_start: 0.9437 (mt0) cc_final: 0.9032 (tm-30) REVERT: A 391 MET cc_start: 0.8344 (mmm) cc_final: 0.8089 (ttp) REVERT: B 72 MET cc_start: 0.9352 (ttp) cc_final: 0.8871 (tmm) REVERT: B 105 MET cc_start: 0.9077 (ptp) cc_final: 0.8785 (pmm) REVERT: B 119 GLU cc_start: 0.8484 (tp30) cc_final: 0.8126 (tp30) REVERT: B 130 ASP cc_start: 0.9404 (m-30) cc_final: 0.8860 (p0) REVERT: B 202 GLN cc_start: 0.9479 (mt0) cc_final: 0.9072 (tm-30) REVERT: B 262 MET cc_start: 0.8456 (tpt) cc_final: 0.8185 (tpp) REVERT: B 391 MET cc_start: 0.7423 (ttm) cc_final: 0.7196 (ttp) REVERT: C 30 LEU cc_start: 0.9613 (tt) cc_final: 0.9409 (pp) REVERT: C 72 MET cc_start: 0.9317 (ttp) cc_final: 0.8891 (tmm) REVERT: C 130 ASP cc_start: 0.9415 (m-30) cc_final: 0.8869 (p0) REVERT: C 170 MET cc_start: 0.9303 (ppp) cc_final: 0.8919 (ppp) REVERT: C 202 GLN cc_start: 0.9508 (mt0) cc_final: 0.9076 (tm-30) REVERT: C 391 MET cc_start: 0.7281 (ttm) cc_final: 0.7048 (ttp) REVERT: C 417 PHE cc_start: 0.9753 (t80) cc_final: 0.9456 (t80) REVERT: D 82 GLN cc_start: 0.9590 (mt0) cc_final: 0.9319 (mp10) REVERT: D 119 GLU cc_start: 0.8375 (tp30) cc_final: 0.8138 (tm-30) REVERT: D 130 ASP cc_start: 0.9409 (m-30) cc_final: 0.8878 (p0) REVERT: D 202 GLN cc_start: 0.9459 (mt0) cc_final: 0.9081 (tm-30) REVERT: D 391 MET cc_start: 0.7807 (ttm) cc_final: 0.7512 (ttp) REVERT: E 130 ASP cc_start: 0.9362 (m-30) cc_final: 0.8885 (p0) REVERT: E 202 GLN cc_start: 0.9448 (mt0) cc_final: 0.9079 (tm-30) REVERT: E 391 MET cc_start: 0.6674 (ttp) cc_final: 0.6449 (tmm) outliers start: 27 outliers final: 24 residues processed: 169 average time/residue: 0.2206 time to fit residues: 58.6474 Evaluate side-chains 164 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 168 CYS Chi-restraints excluded: chain E residue 225 CYS Chi-restraints excluded: chain E residue 251 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14395 Z= 0.268 Angle : 0.720 14.291 19555 Z= 0.358 Chirality : 0.041 0.185 2260 Planarity : 0.004 0.033 2430 Dihedral : 5.887 27.334 2185 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 23.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 1.99 % Allowed : 12.29 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.20), residues: 1710 helix: 0.27 (0.21), residues: 610 sheet: -1.69 (0.25), residues: 370 loop : -1.54 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 84 HIS 0.003 0.001 HIS E 231 PHE 0.062 0.001 PHE C 311 TYR 0.015 0.002 TYR E 144 ARG 0.002 0.000 ARG A 407 *********************** 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 165 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 135 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.9345 (ttp) cc_final: 0.8858 (tmm) REVERT: A 82 GLN cc_start: 0.9575 (mt0) cc_final: 0.9314 (mp10) REVERT: A 105 MET cc_start: 0.9290 (ptp) cc_final: 0.8993 (pmm) REVERT: A 130 ASP cc_start: 0.9395 (m-30) cc_final: 0.8902 (p0) REVERT: A 202 GLN cc_start: 0.9462 (mt0) cc_final: 0.9026 (tm-30) REVERT: A 391 MET cc_start: 0.8351 (mmm) cc_final: 0.8100 (ttp) REVERT: B 72 MET cc_start: 0.9394 (ttp) cc_final: 0.8892 (tmm) REVERT: B 130 ASP cc_start: 0.9406 (m-30) cc_final: 0.8939 (p0) REVERT: B 202 GLN cc_start: 0.9494 (mt0) cc_final: 0.9061 (tm-30) REVERT: B 391 MET cc_start: 0.7485 (ttm) cc_final: 0.7257 (ttp) REVERT: C 72 MET cc_start: 0.9342 (ttp) cc_final: 0.8905 (tmm) REVERT: C 130 ASP cc_start: 0.9418 (m-30) cc_final: 0.8921 (p0) REVERT: C 170 MET cc_start: 0.9248 (ppp) cc_final: 0.8883 (ppp) REVERT: C 202 GLN cc_start: 0.9527 (mt0) cc_final: 0.9076 (tm-30) REVERT: C 391 MET cc_start: 0.7401 (ttm) cc_final: 0.7140 (ttp) REVERT: D 130 ASP cc_start: 0.9433 (m-30) cc_final: 0.8945 (p0) REVERT: D 202 GLN cc_start: 0.9492 (mt0) cc_final: 0.9083 (tm-30) REVERT: D 391 MET cc_start: 0.7860 (ttm) cc_final: 0.7561 (ttp) REVERT: E 130 ASP cc_start: 0.9363 (m-30) cc_final: 0.8937 (p0) REVERT: E 202 GLN cc_start: 0.9468 (mt0) cc_final: 0.9074 (tm-30) REVERT: E 391 MET cc_start: 0.6744 (ttp) cc_final: 0.6374 (ttp) outliers start: 30 outliers final: 28 residues processed: 165 average time/residue: 0.2190 time to fit residues: 56.7072 Evaluate side-chains 161 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 133 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 168 CYS Chi-restraints excluded: chain E residue 225 CYS Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 296 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 15 optimal weight: 20.0000 chunk 128 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 14395 Z= 0.248 Angle : 0.719 15.514 19555 Z= 0.355 Chirality : 0.041 0.194 2260 Planarity : 0.004 0.033 2430 Dihedral : 5.830 28.071 2185 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 22.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 1.86 % Allowed : 12.62 % Favored : 85.51 % 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: -1.22 (0.20), residues: 1710 helix: 0.37 (0.21), residues: 610 sheet: -1.53 (0.26), residues: 370 loop : -1.32 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 84 HIS 0.003 0.001 HIS D 231 PHE 0.045 0.001 PHE C 311 TYR 0.016 0.002 TYR E 144 ARG 0.003 0.000 ARG C 75 *********************** 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 163 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.9371 (ttp) cc_final: 0.8862 (tmm) REVERT: A 82 GLN cc_start: 0.9570 (mt0) cc_final: 0.9315 (mp10) REVERT: A 105 MET cc_start: 0.9291 (ptp) cc_final: 0.8980 (pmm) REVERT: A 130 ASP cc_start: 0.9393 (m-30) cc_final: 0.8918 (p0) REVERT: A 202 GLN cc_start: 0.9454 (mt0) cc_final: 0.9020 (tm-30) REVERT: A 391 MET cc_start: 0.8350 (mmm) cc_final: 0.8109 (ttp) REVERT: B 72 MET cc_start: 0.9408 (ttp) cc_final: 0.8894 (tmm) REVERT: B 130 ASP cc_start: 0.9410 (m-30) cc_final: 0.8920 (p0) REVERT: B 202 GLN cc_start: 0.9477 (mt0) cc_final: 0.9048 (tm-30) REVERT: C 30 LEU cc_start: 0.9625 (tt) cc_final: 0.9405 (pp) REVERT: C 119 GLU cc_start: 0.8507 (tp30) cc_final: 0.8207 (tm-30) REVERT: C 130 ASP cc_start: 0.9426 (m-30) cc_final: 0.8890 (p0) REVERT: C 170 MET cc_start: 0.9248 (ppp) cc_final: 0.8889 (ppp) REVERT: C 202 GLN cc_start: 0.9523 (mt0) cc_final: 0.9067 (tm-30) REVERT: C 391 MET cc_start: 0.7625 (ttm) cc_final: 0.7379 (ttp) REVERT: D 82 GLN cc_start: 0.9591 (mt0) cc_final: 0.9258 (mp10) REVERT: D 130 ASP cc_start: 0.9443 (m-30) cc_final: 0.8939 (p0) REVERT: D 202 GLN cc_start: 0.9475 (mt0) cc_final: 0.9075 (tm-30) REVERT: D 391 MET cc_start: 0.7889 (ttm) cc_final: 0.7462 (ttp) REVERT: E 130 ASP cc_start: 0.9374 (m-30) cc_final: 0.8969 (p0) REVERT: E 202 GLN cc_start: 0.9456 (mt0) cc_final: 0.9047 (tm-30) REVERT: E 391 MET cc_start: 0.6814 (ttp) cc_final: 0.6435 (ttp) outliers start: 28 outliers final: 26 residues processed: 163 average time/residue: 0.2201 time to fit residues: 56.1204 Evaluate side-chains 158 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 168 CYS Chi-restraints excluded: chain E residue 225 CYS Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 296 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 9.9990 chunk 143 optimal weight: 7.9990 chunk 152 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14395 Z= 0.215 Angle : 0.717 9.214 19555 Z= 0.352 Chirality : 0.042 0.190 2260 Planarity : 0.004 0.033 2430 Dihedral : 5.766 27.279 2185 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 21.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 1.79 % Allowed : 12.96 % Favored : 85.25 % 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: -1.14 (0.20), residues: 1710 helix: 0.34 (0.21), residues: 615 sheet: -1.47 (0.26), residues: 370 loop : -1.21 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 84 HIS 0.002 0.001 HIS E 231 PHE 0.065 0.002 PHE C 311 TYR 0.022 0.002 TYR E 144 ARG 0.003 0.000 ARG B 75 *********************** 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 161 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 134 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.9399 (ttp) cc_final: 0.8884 (tmm) REVERT: A 82 GLN cc_start: 0.9570 (mt0) cc_final: 0.9301 (mp10) REVERT: A 105 MET cc_start: 0.9273 (ptp) cc_final: 0.9000 (pmm) REVERT: A 130 ASP cc_start: 0.9400 (m-30) cc_final: 0.8899 (p0) REVERT: A 202 GLN cc_start: 0.9449 (mt0) cc_final: 0.9035 (tm-30) REVERT: A 391 MET cc_start: 0.8359 (mmm) cc_final: 0.8113 (ttp) REVERT: B 72 MET cc_start: 0.9420 (ttp) cc_final: 0.8890 (tmm) REVERT: B 130 ASP cc_start: 0.9423 (m-30) cc_final: 0.8923 (p0) REVERT: B 202 GLN cc_start: 0.9476 (mt0) cc_final: 0.9063 (tm-30) REVERT: B 391 MET cc_start: 0.7098 (ttp) cc_final: 0.6787 (tmm) REVERT: C 30 LEU cc_start: 0.9618 (tt) cc_final: 0.9399 (pp) REVERT: C 72 MET cc_start: 0.9379 (ttp) cc_final: 0.8861 (tmm) REVERT: C 119 GLU cc_start: 0.8444 (tp30) cc_final: 0.8219 (tm-30) REVERT: C 130 ASP cc_start: 0.9440 (m-30) cc_final: 0.8891 (p0) REVERT: C 170 MET cc_start: 0.9260 (ppp) cc_final: 0.8877 (ppp) REVERT: C 202 GLN cc_start: 0.9519 (mt0) cc_final: 0.9077 (tm-30) REVERT: C 391 MET cc_start: 0.7722 (ttm) cc_final: 0.7468 (ttp) REVERT: D 72 MET cc_start: 0.9580 (tpp) cc_final: 0.9275 (tpp) REVERT: D 130 ASP cc_start: 0.9441 (m-30) cc_final: 0.8965 (p0) REVERT: D 202 GLN cc_start: 0.9473 (mt0) cc_final: 0.9075 (tm-30) REVERT: E 130 ASP cc_start: 0.9375 (m-30) cc_final: 0.8976 (p0) REVERT: E 202 GLN cc_start: 0.9451 (mt0) cc_final: 0.9070 (tm-30) REVERT: E 391 MET cc_start: 0.6845 (ttp) cc_final: 0.6467 (ttp) outliers start: 27 outliers final: 25 residues processed: 161 average time/residue: 0.2177 time to fit residues: 55.1372 Evaluate side-chains 155 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 225 CYS Chi-restraints excluded: chain E residue 251 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 7.9990 chunk 76 optimal weight: 0.5980 chunk 112 optimal weight: 9.9990 chunk 169 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 134 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 chunk 82 optimal weight: 0.5980 chunk 107 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14395 Z= 0.182 Angle : 0.738 13.184 19555 Z= 0.357 Chirality : 0.042 0.187 2260 Planarity : 0.004 0.040 2430 Dihedral : 5.663 25.318 2185 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 1.86 % Allowed : 12.82 % Favored : 85.32 % 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: -1.14 (0.20), residues: 1710 helix: 0.24 (0.21), residues: 615 sheet: -1.40 (0.26), residues: 370 loop : -1.14 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 84 HIS 0.002 0.001 HIS E 231 PHE 0.048 0.001 PHE A 311 TYR 0.022 0.002 TYR E 144 ARG 0.004 0.000 ARG D 75 ********************** REFINEMENT MACRO_CYCLE 10 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 166 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 138 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.9382 (ttp) cc_final: 0.8886 (tmm) REVERT: A 82 GLN cc_start: 0.9564 (mt0) cc_final: 0.9298 (mp10) REVERT: A 105 MET cc_start: 0.9267 (ptp) cc_final: 0.9008 (pmm) REVERT: A 130 ASP cc_start: 0.9401 (m-30) cc_final: 0.8875 (p0) REVERT: A 202 GLN cc_start: 0.9443 (mt0) cc_final: 0.9046 (tm-30) REVERT: A 391 MET cc_start: 0.8374 (mmm) cc_final: 0.8133 (ttp) REVERT: B 30 LEU cc_start: 0.9657 (tt) cc_final: 0.9438 (pp) REVERT: B 72 MET cc_start: 0.9412 (ttp) cc_final: 0.8879 (tmm) REVERT: B 105 MET cc_start: 0.9081 (ptp) cc_final: 0.8693 (pmm) REVERT: B 130 ASP cc_start: 0.9431 (m-30) cc_final: 0.8922 (p0) REVERT: B 202 GLN cc_start: 0.9477 (mt0) cc_final: 0.9080 (tm-30) REVERT: B 391 MET cc_start: 0.7145 (ttp) cc_final: 0.6836 (tmm) REVERT: C 30 LEU cc_start: 0.9620 (tt) cc_final: 0.9408 (pp) REVERT: C 72 MET cc_start: 0.9344 (ttp) cc_final: 0.8815 (tmm) REVERT: C 119 GLU cc_start: 0.8426 (tp30) cc_final: 0.8162 (tm-30) REVERT: C 130 ASP cc_start: 0.9435 (m-30) cc_final: 0.8844 (p0) REVERT: C 170 MET cc_start: 0.9185 (ppp) cc_final: 0.8848 (ppp) REVERT: C 202 GLN cc_start: 0.9513 (mt0) cc_final: 0.9091 (tm-30) REVERT: C 391 MET cc_start: 0.7730 (ttm) cc_final: 0.7476 (ttp) REVERT: D 130 ASP cc_start: 0.9445 (m-30) cc_final: 0.8900 (p0) REVERT: D 202 GLN cc_start: 0.9466 (mt0) cc_final: 0.9096 (tm-30) REVERT: D 391 MET cc_start: 0.7056 (ttt) cc_final: 0.6773 (tmm) REVERT: E 130 ASP cc_start: 0.9379 (m-30) cc_final: 0.8919 (p0) REVERT: E 202 GLN cc_start: 0.9453 (mt0) cc_final: 0.9083 (tm-30) REVERT: E 391 MET cc_start: 0.6841 (ttp) cc_final: 0.6468 (ttp) outliers start: 28 outliers final: 26 residues processed: 166 average time/residue: 0.2186 time to fit residues: 57.0293 Evaluate side-chains 161 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 135 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 225 CYS Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 296 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 138 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 118 optimal weight: 0.3980 chunk 7 optimal weight: 6.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.041558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.030727 restraints weight = 107023.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.031785 restraints weight = 70528.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.032549 restraints weight = 52534.486| |-----------------------------------------------------------------------------| r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14395 Z= 0.164 Angle : 0.747 14.756 19555 Z= 0.358 Chirality : 0.043 0.181 2260 Planarity : 0.004 0.042 2430 Dihedral : 5.504 21.547 2185 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.40 % Allowed : 13.49 % Favored : 85.12 % 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: -1.13 (0.20), residues: 1710 helix: 0.19 (0.21), residues: 610 sheet: -1.30 (0.26), residues: 370 loop : -1.13 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 84 HIS 0.002 0.001 HIS D 231 PHE 0.058 0.001 PHE C 311 TYR 0.022 0.001 TYR E 144 ARG 0.004 0.000 ARG D 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2304.29 seconds wall clock time: 43 minutes 37.28 seconds (2617.28 seconds total)