Starting phenix.real_space_refine on Sun Dec 10 09:37:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm4_20386/12_2023/6pm4_20386.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm4_20386/12_2023/6pm4_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_20386/12_2023/6pm4_20386.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm4_20386/12_2023/6pm4_20386.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm4_20386/12_2023/6pm4_20386.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm4_20386/12_2023/6pm4_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-1.21rc1-5172/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: 6 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: 6 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: 6 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: 6 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: 6 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: 7.39, per 1000 atoms: 0.53 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: 5.90 Conformation dependent library (CDL) restraints added in 2.2 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: 1.66 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: 5.18 Time building geometry restraints manager: 6.27 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 - 14.94: 8125 14.94 - 29.87: 430 29.87 - 44.81: 105 44.81 - 59.75: 15 59.75 - 74.68: 15 Dihedral angle restraints: 8690 sinusoidal: 3575 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 8687 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: 1.320 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: 7.310 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 38.640 Find NCS groups from input model: 0.920 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.600 ------------------------------------------------------------------------------- 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 : 10.349 74.684 5340 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 : 1.666 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 outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.2672 time to fit residues: 112.3151 Evaluate side-chains 143 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.708 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1425 ------------------------------------------------------------------------------- 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: 6.9990 chunk 71 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 HIS ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS C 62 ASN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 83 GLN ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 HIS ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 HIS ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN E 131 ASN E 141 ASN ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14395 Z= 0.342 Angle : 0.842 7.292 19555 Z= 0.436 Chirality : 0.043 0.195 2260 Planarity : 0.005 0.040 2430 Dihedral : 7.492 56.209 2090 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 24.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 1.99 % Allowed : 10.43 % Favored : 87.57 % 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: -3.08 (0.18), residues: 1710 helix: -1.54 (0.18), residues: 595 sheet: -2.08 (0.24), residues: 325 loop : -2.34 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 110 HIS 0.003 0.001 HIS E 125 PHE 0.015 0.002 PHE C 230 TYR 0.023 0.002 TYR C 238 ARG 0.006 0.001 ARG D 287 *********************** 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 177 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 147 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 17 residues processed: 161 average time/residue: 0.2227 time to fit residues: 55.8607 Evaluate side-chains 141 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 1.482 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1206 time to fit residues: 5.9989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 154 optimal weight: 8.9990 chunk 167 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 153 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14395 Z= 0.220 Angle : 0.761 11.048 19555 Z= 0.381 Chirality : 0.042 0.191 2260 Planarity : 0.004 0.030 2430 Dihedral : 6.880 46.329 2090 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 22.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.06 % Allowed : 10.03 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.19), residues: 1710 helix: -0.54 (0.20), residues: 590 sheet: -2.35 (0.22), residues: 390 loop : -1.95 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 84 HIS 0.003 0.002 HIS D 125 PHE 0.009 0.001 PHE D 203 TYR 0.030 0.002 TYR B 144 ARG 0.003 0.000 ARG A 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 160 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 14 residues processed: 157 average time/residue: 0.2249 time to fit residues: 55.6399 Evaluate side-chains 139 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 1.576 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1186 time to fit residues: 5.3224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 17 optimal weight: 0.0770 chunk 73 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 164 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 147 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 overall best weight: 4.6146 ------------------------------------------------------------------------------- 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: 0.8654 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 14395 Z= 0.307 Angle : 0.743 11.618 19555 Z= 0.376 Chirality : 0.041 0.234 2260 Planarity : 0.005 0.038 2430 Dihedral : 6.439 32.960 2090 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 24.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 1.40 % Allowed : 10.76 % Favored : 87.84 % 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: 0.05 (0.21), residues: 590 sheet: -2.16 (0.22), residues: 390 loop : -1.76 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 110 HIS 0.005 0.002 HIS E 231 PHE 0.015 0.002 PHE A 311 TYR 0.031 0.002 TYR B 144 ARG 0.004 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 149 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 128 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 143 average time/residue: 0.2290 time to fit residues: 51.1141 Evaluate side-chains 132 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 1.587 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1245 time to fit residues: 4.3321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.5980 chunk 93 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14395 Z= 0.242 Angle : 0.719 8.217 19555 Z= 0.361 Chirality : 0.042 0.208 2260 Planarity : 0.004 0.033 2430 Dihedral : 6.205 26.743 2090 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.86 % Allowed : 12.09 % Favored : 87.04 % 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: 0.20 (0.21), residues: 590 sheet: -1.95 (0.23), residues: 390 loop : -1.63 (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 C 231 PHE 0.033 0.001 PHE B 311 TYR 0.025 0.002 TYR B 144 ARG 0.004 0.000 ARG A 43 *********************** 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 144 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 131 time to evaluate : 1.607 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 141 average time/residue: 0.2435 time to fit residues: 52.9271 Evaluate side-chains 125 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 1.594 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1338 time to fit residues: 4.3721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 164 optimal weight: 9.9990 chunk 136 optimal weight: 0.0170 chunk 76 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 overall best weight: 4.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14395 Z= 0.285 Angle : 0.763 13.029 19555 Z= 0.384 Chirality : 0.042 0.191 2260 Planarity : 0.004 0.032 2430 Dihedral : 6.145 27.673 2090 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 24.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 1.26 % Allowed : 13.55 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.20), residues: 1710 helix: 0.25 (0.21), residues: 590 sheet: -1.84 (0.23), residues: 390 loop : -1.44 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 84 HIS 0.004 0.002 HIS E 231 PHE 0.021 0.002 PHE D 203 TYR 0.022 0.002 TYR B 144 ARG 0.004 0.000 ARG D 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 140 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 121 time to evaluate : 1.690 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 17 residues processed: 136 average time/residue: 0.2307 time to fit residues: 49.0672 Evaluate side-chains 135 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 1.612 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1277 time to fit residues: 6.1782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 93 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 138 optimal weight: 0.0770 chunk 91 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14395 Z= 0.205 Angle : 0.746 14.161 19555 Z= 0.367 Chirality : 0.042 0.192 2260 Planarity : 0.004 0.031 2430 Dihedral : 6.002 26.589 2090 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 20.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.47 % Allowed : 13.89 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.20), residues: 1710 helix: 0.15 (0.21), residues: 610 sheet: -1.68 (0.24), residues: 390 loop : -1.47 (0.23), residues: 710 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 0.019 0.001 PHE D 203 TYR 0.024 0.002 TYR E 144 ARG 0.004 0.000 ARG C 75 *********************** 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 130 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 123 time to evaluate : 1.621 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 127 average time/residue: 0.2365 time to fit residues: 46.5169 Evaluate side-chains 125 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 1.618 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1235 time to fit residues: 3.0995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 128 optimal weight: 0.4980 chunk 149 optimal weight: 0.0870 overall best weight: 1.7164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14395 Z= 0.188 Angle : 0.734 12.158 19555 Z= 0.358 Chirality : 0.042 0.187 2260 Planarity : 0.004 0.030 2430 Dihedral : 5.854 24.246 2090 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.33 % Allowed : 14.35 % 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: -1.41 (0.20), residues: 1710 helix: 0.15 (0.21), residues: 610 sheet: -1.48 (0.25), residues: 390 loop : -1.46 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 84 HIS 0.002 0.001 HIS E 125 PHE 0.015 0.001 PHE C 311 TYR 0.027 0.002 TYR A 144 ARG 0.003 0.000 ARG B 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 131 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 126 time to evaluate : 1.594 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 126 average time/residue: 0.2391 time to fit residues: 47.0095 Evaluate side-chains 123 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 120 time to evaluate : 1.558 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1257 time to fit residues: 2.6859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 137 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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: 0.8624 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14395 Z= 0.205 Angle : 0.745 12.900 19555 Z= 0.363 Chirality : 0.041 0.185 2260 Planarity : 0.004 0.032 2430 Dihedral : 5.765 22.911 2090 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.20 % Allowed : 15.02 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.20), residues: 1710 helix: 0.30 (0.21), residues: 590 sheet: -1.35 (0.25), residues: 390 loop : -1.35 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 84 HIS 0.005 0.001 HIS C 125 PHE 0.021 0.001 PHE B 311 TYR 0.020 0.002 TYR B 144 ARG 0.003 0.000 ARG A 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 128 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 1.629 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 126 average time/residue: 0.2435 time to fit residues: 47.5809 Evaluate side-chains 119 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 1.753 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1289 time to fit residues: 2.4394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.0000 chunk 76 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 169 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 104 optimal weight: 0.0980 chunk 82 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- 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** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.5152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14395 Z= 0.175 Angle : 0.762 11.116 19555 Z= 0.367 Chirality : 0.043 0.187 2260 Planarity : 0.004 0.044 2430 Dihedral : 5.687 21.142 2090 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.07 % Allowed : 15.35 % Favored : 84.58 % 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: -1.29 (0.20), residues: 1710 helix: 0.10 (0.21), residues: 610 sheet: -1.26 (0.25), residues: 390 loop : -1.34 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 84 HIS 0.004 0.001 HIS A 125 PHE 0.049 0.001 PHE B 311 TYR 0.019 0.002 TYR E 144 ARG 0.004 0.000 ARG C 43 ********************** 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 128 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.2470 time to fit residues: 48.7025 Evaluate side-chains 124 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.527 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 138 optimal weight: 6.9990 chunk 17 optimal weight: 0.0770 chunk 24 optimal weight: 8.9990 chunk 118 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.9344 ------------------------------------------------------------------------------- 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** ** E 282 GLN ** 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 = 0.3139 r_free = 0.3139 target = 0.041366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.031097 restraints weight = 110877.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.032157 restraints weight = 71963.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.032906 restraints weight = 52885.332| |-----------------------------------------------------------------------------| r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14395 Z= 0.189 Angle : 0.758 13.932 19555 Z= 0.364 Chirality : 0.042 0.181 2260 Planarity : 0.004 0.046 2430 Dihedral : 5.615 20.677 2090 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.20 % Allowed : 15.55 % Favored : 84.25 % 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: -1.26 (0.20), residues: 1710 helix: 0.10 (0.21), residues: 610 sheet: -1.22 (0.25), residues: 390 loop : -1.31 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 84 HIS 0.003 0.001 HIS A 125 PHE 0.052 0.001 PHE C 311 TYR 0.018 0.001 TYR E 144 ARG 0.003 0.000 ARG D 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2241.94 seconds wall clock time: 42 minutes 37.49 seconds (2557.49 seconds total)