Starting phenix.real_space_refine on Fri Feb 16 02:40:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm0_20382/02_2024/6pm0_20382_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm0_20382/02_2024/6pm0_20382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm0_20382/02_2024/6pm0_20382.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm0_20382/02_2024/6pm0_20382.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm0_20382/02_2024/6pm0_20382_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm0_20382/02_2024/6pm0_20382_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9165 2.51 5 N 2250 2.21 5 O 2565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 268": "NH1" <-> "NH2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A ARG 407": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ARG 268": "NH1" <-> "NH2" Residue "B ARG 287": "NH1" <-> "NH2" Residue "B ARG 407": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 229": "NH1" <-> "NH2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C ARG 287": "NH1" <-> "NH2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D ARG 229": "NH1" <-> "NH2" Residue "D ARG 268": "NH1" <-> "NH2" Residue "D ARG 287": "NH1" <-> "NH2" Residue "D ARG 407": "NH1" <-> "NH2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 229": "NH1" <-> "NH2" Residue "E ARG 268": "NH1" <-> "NH2" Residue "E ARG 287": "NH1" <-> "NH2" Residue "E ARG 407": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14080 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2770 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2770 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2770 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2770 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2770 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 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: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.60, per 1000 atoms: 0.61 Number of scatterers: 14080 At special positions: 0 Unit cell: (104.521, 105.344, 135.795, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2565 8.00 N 2250 7.00 C 9165 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=2.03 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=2.03 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=2.03 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=2.03 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG 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: 5.70 Conformation dependent library (CDL) restraints added in 2.4 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... running ksdssp... Secondary structure from input PDB file: 55 helices and 25 sheets defined 36.1% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'A' and resid 26 through 31 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.610A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASP A 107 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 108 " --> pdb=" O MET A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 236 through 242 Processing helix chain 'A' and resid 244 through 259 removed outlier: 3.986A pdb=" N ILE A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP A 259 " --> pdb=" O TRP A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 284 removed outlier: 4.108A pdb=" N LEU A 271 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 274 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 277 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR A 278 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR A 280 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN A 282 " --> pdb=" O MET A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 301 No H-bonds generated for 'chain 'A' and resid 298 through 301' Processing helix chain 'A' and resid 303 through 324 removed outlier: 3.656A pdb=" N VAL A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 426 removed outlier: 3.662A pdb=" N PHE A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A 399 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 3.525A pdb=" N ILE A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE A 417 " --> pdb=" O VAL A 413 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE A 423 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR A 425 " --> pdb=" O TYR A 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 31 Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.611A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASP B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 108 " --> pdb=" O MET B 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 108' Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 236 through 242 Processing helix chain 'B' and resid 244 through 259 removed outlier: 3.986A pdb=" N ILE B 250 " --> pdb=" O PRO B 246 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP B 259 " --> pdb=" O TRP B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 284 removed outlier: 4.107A pdb=" N LEU B 271 " --> pdb=" O ARG B 268 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR B 274 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 277 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR B 278 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR B 280 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN B 282 " --> pdb=" O MET B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 301 No H-bonds generated for 'chain 'B' and resid 298 through 301' Processing helix chain 'B' and resid 303 through 324 removed outlier: 3.656A pdb=" N VAL B 310 " --> pdb=" O CYS B 306 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 318 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 426 removed outlier: 3.662A pdb=" N PHE B 395 " --> pdb=" O MET B 391 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA B 399 " --> pdb=" O PHE B 395 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Proline residue: B 411 - end of helix removed outlier: 3.526A pdb=" N ILE B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE B 417 " --> pdb=" O VAL B 413 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE B 423 " --> pdb=" O ILE B 419 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR B 425 " --> pdb=" O TYR B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 31 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.611A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C 108 " --> pdb=" O MET C 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 108' Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 236 through 242 Processing helix chain 'C' and resid 244 through 259 removed outlier: 3.986A pdb=" N ILE C 250 " --> pdb=" O PRO C 246 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP C 259 " --> pdb=" O TRP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 284 removed outlier: 4.108A pdb=" N LEU C 271 " --> pdb=" O ARG C 268 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR C 274 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 277 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR C 278 " --> pdb=" O THR C 275 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR C 280 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLN C 282 " --> pdb=" O MET C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 301 No H-bonds generated for 'chain 'C' and resid 298 through 301' Processing helix chain 'C' and resid 303 through 324 removed outlier: 3.656A pdb=" N VAL C 310 " --> pdb=" O CYS C 306 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA C 313 " --> pdb=" O PHE C 309 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 318 " --> pdb=" O LEU C 314 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE C 323 " --> pdb=" O ALA C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 426 removed outlier: 3.661A pdb=" N PHE C 395 " --> pdb=" O MET C 391 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA C 399 " --> pdb=" O PHE C 395 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 3.526A pdb=" N ILE C 416 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE C 417 " --> pdb=" O VAL C 413 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE C 423 " --> pdb=" O ILE C 419 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR C 425 " --> pdb=" O TYR C 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.611A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASP D 107 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER D 108 " --> pdb=" O MET D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'D' and resid 161 through 163 No H-bonds generated for 'chain 'D' and resid 161 through 163' Processing helix chain 'D' and resid 236 through 242 Processing helix chain 'D' and resid 244 through 259 removed outlier: 3.986A pdb=" N ILE D 250 " --> pdb=" O PRO D 246 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE D 258 " --> pdb=" O SER D 254 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP D 259 " --> pdb=" O TRP D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 284 removed outlier: 4.107A pdb=" N LEU D 271 " --> pdb=" O ARG D 268 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR D 274 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU D 277 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR D 278 " --> pdb=" O THR D 275 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR D 280 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLN D 282 " --> pdb=" O MET D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 301 No H-bonds generated for 'chain 'D' and resid 298 through 301' Processing helix chain 'D' and resid 303 through 324 removed outlier: 3.656A pdb=" N VAL D 310 " --> pdb=" O CYS D 306 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 318 " --> pdb=" O LEU D 314 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 426 removed outlier: 3.662A pdb=" N PHE D 395 " --> pdb=" O MET D 391 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA D 399 " --> pdb=" O PHE D 395 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL D 405 " --> pdb=" O ARG D 401 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) Proline residue: D 411 - end of helix removed outlier: 3.525A pdb=" N ILE D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE D 417 " --> pdb=" O VAL D 413 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE D 423 " --> pdb=" O ILE D 419 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR D 424 " --> pdb=" O PHE D 420 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR D 425 " --> pdb=" O TYR D 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 31 Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 87 through 89 No H-bonds generated for 'chain 'E' and resid 87 through 89' Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.610A pdb=" N LEU E 106 " --> pdb=" O PRO E 103 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASP E 107 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER E 108 " --> pdb=" O MET E 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 103 through 108' Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 236 through 242 Processing helix chain 'E' and resid 244 through 259 removed outlier: 3.986A pdb=" N ILE E 250 " --> pdb=" O PRO E 246 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE E 258 " --> pdb=" O SER E 254 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP E 259 " --> pdb=" O TRP E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 284 removed outlier: 4.108A pdb=" N LEU E 271 " --> pdb=" O ARG E 268 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR E 274 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU E 277 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR E 278 " --> pdb=" O THR E 275 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR E 280 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLN E 282 " --> pdb=" O MET E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 301 No H-bonds generated for 'chain 'E' and resid 298 through 301' Processing helix chain 'E' and resid 303 through 324 removed outlier: 3.656A pdb=" N VAL E 310 " --> pdb=" O CYS E 306 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA E 313 " --> pdb=" O PHE E 309 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA E 318 " --> pdb=" O LEU E 314 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 426 removed outlier: 3.662A pdb=" N PHE E 395 " --> pdb=" O MET E 391 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA E 399 " --> pdb=" O PHE E 395 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL E 405 " --> pdb=" O ARG E 401 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) Proline residue: E 411 - end of helix removed outlier: 3.526A pdb=" N ILE E 416 " --> pdb=" O LEU E 412 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE E 417 " --> pdb=" O VAL E 413 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE E 423 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR E 424 " --> pdb=" O PHE E 420 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR E 425 " --> pdb=" O TYR E 421 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 182 through 186 removed outlier: 6.066A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 59 through 61 Processing sheet with id= C, first strand: chain 'A' and resid 98 through 100 Processing sheet with id= D, first strand: chain 'A' and resid 114 through 116 Processing sheet with id= E, first strand: chain 'A' and resid 210 through 213 Processing sheet with id= F, first strand: chain 'B' and resid 182 through 186 removed outlier: 6.066A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 59 through 61 Processing sheet with id= H, first strand: chain 'B' and resid 98 through 100 Processing sheet with id= I, first strand: chain 'B' and resid 114 through 116 Processing sheet with id= J, first strand: chain 'B' and resid 210 through 213 Processing sheet with id= K, first strand: chain 'C' and resid 182 through 186 removed outlier: 6.066A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 59 through 61 Processing sheet with id= M, first strand: chain 'C' and resid 98 through 100 Processing sheet with id= N, first strand: chain 'C' and resid 114 through 116 Processing sheet with id= O, first strand: chain 'C' and resid 210 through 213 Processing sheet with id= P, first strand: chain 'D' and resid 182 through 186 removed outlier: 6.066A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 59 through 61 Processing sheet with id= R, first strand: chain 'D' and resid 98 through 100 Processing sheet with id= S, first strand: chain 'D' and resid 114 through 116 Processing sheet with id= T, first strand: chain 'D' and resid 210 through 213 Processing sheet with id= U, first strand: chain 'E' and resid 182 through 186 removed outlier: 6.066A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 59 through 61 Processing sheet with id= W, first strand: chain 'E' and resid 98 through 100 Processing sheet with id= X, first strand: chain 'E' and resid 114 through 116 Processing sheet with id= Y, first strand: chain 'E' and resid 210 through 213 495 hydrogen bonds defined for protein. 1320 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.08 Time building geometry restraints manager: 6.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2221 1.32 - 1.46: 4953 1.46 - 1.59: 7086 1.59 - 1.73: 5 1.73 - 1.87: 160 Bond restraints: 14425 Sorted by residual: bond pdb=" C MET B 34 " pdb=" O MET B 34 " ideal model delta sigma weight residual 1.237 1.180 0.057 1.43e-02 4.89e+03 1.59e+01 bond pdb=" C MET D 34 " pdb=" O MET D 34 " ideal model delta sigma weight residual 1.237 1.180 0.057 1.43e-02 4.89e+03 1.58e+01 bond pdb=" C MET A 34 " pdb=" O MET A 34 " ideal model delta sigma weight residual 1.237 1.180 0.057 1.43e-02 4.89e+03 1.58e+01 bond pdb=" C MET E 34 " pdb=" O MET E 34 " ideal model delta sigma weight residual 1.237 1.180 0.057 1.43e-02 4.89e+03 1.58e+01 bond pdb=" C MET C 34 " pdb=" O MET C 34 " ideal model delta sigma weight residual 1.237 1.181 0.056 1.43e-02 4.89e+03 1.54e+01 ... (remaining 14420 not shown) Histogram of bond angle deviations from ideal: 95.46 - 103.17: 177 103.17 - 110.89: 5028 110.89 - 118.61: 6222 118.61 - 126.33: 7928 126.33 - 134.05: 245 Bond angle restraints: 19600 Sorted by residual: angle pdb=" C VAL B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 121.54 132.72 -11.18 1.91e+00 2.74e-01 3.43e+01 angle pdb=" C VAL D 127 " pdb=" N THR D 128 " pdb=" CA THR D 128 " ideal model delta sigma weight residual 121.54 132.72 -11.18 1.91e+00 2.74e-01 3.43e+01 angle pdb=" C VAL A 127 " pdb=" N THR A 128 " pdb=" CA THR A 128 " ideal model delta sigma weight residual 121.54 132.72 -11.18 1.91e+00 2.74e-01 3.42e+01 angle pdb=" C VAL E 127 " pdb=" N THR E 128 " pdb=" CA THR E 128 " ideal model delta sigma weight residual 121.54 132.71 -11.17 1.91e+00 2.74e-01 3.42e+01 angle pdb=" CB MET E 34 " pdb=" CG MET E 34 " pdb=" SD MET E 34 " ideal model delta sigma weight residual 112.70 95.46 17.24 3.00e+00 1.11e-01 3.30e+01 ... (remaining 19595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.76: 8470 20.76 - 41.51: 250 41.51 - 62.27: 15 62.27 - 83.02: 35 83.02 - 103.78: 20 Dihedral angle restraints: 8790 sinusoidal: 3675 harmonic: 5115 Sorted by residual: dihedral pdb=" CA ASN E 160 " pdb=" C ASN E 160 " pdb=" N PHE E 161 " pdb=" CA PHE E 161 " ideal model delta harmonic sigma weight residual 180.00 -155.50 -24.50 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA ASN C 160 " pdb=" C ASN C 160 " pdb=" N PHE C 161 " pdb=" CA PHE C 161 " ideal model delta harmonic sigma weight residual -180.00 -155.51 -24.49 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA ASN A 160 " pdb=" C ASN A 160 " pdb=" N PHE A 161 " pdb=" CA PHE A 161 " ideal model delta harmonic sigma weight residual 180.00 -155.52 -24.48 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 8787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1687 0.059 - 0.117: 470 0.117 - 0.176: 88 0.176 - 0.235: 10 0.235 - 0.294: 5 Chirality restraints: 2260 Sorted by residual: 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 -2.57 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.13e+00 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 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 2257 not shown) Planarity restraints: 2430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR E 128 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.57e+00 pdb=" C THR E 128 " -0.037 2.00e-02 2.50e+03 pdb=" O THR E 128 " 0.014 2.00e-02 2.50e+03 pdb=" N THR E 129 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 128 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.54e+00 pdb=" C THR B 128 " 0.037 2.00e-02 2.50e+03 pdb=" O THR B 128 " -0.014 2.00e-02 2.50e+03 pdb=" N THR B 129 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 128 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.54e+00 pdb=" C THR C 128 " -0.037 2.00e-02 2.50e+03 pdb=" O THR C 128 " 0.014 2.00e-02 2.50e+03 pdb=" N THR C 129 " 0.012 2.00e-02 2.50e+03 ... (remaining 2427 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4364 2.82 - 3.34: 12226 3.34 - 3.86: 23088 3.86 - 4.38: 27229 4.38 - 4.90: 45320 Nonbonded interactions: 112227 Sorted by model distance: nonbonded pdb=" OG SER D 27 " pdb=" NE ARG E 43 " model vdw 2.298 2.520 nonbonded pdb=" O THR E 281 " pdb=" OG SER E 284 " model vdw 2.333 2.440 nonbonded pdb=" O THR D 281 " pdb=" OG SER D 284 " model vdw 2.334 2.440 nonbonded pdb=" O THR A 281 " pdb=" OG SER A 284 " model vdw 2.334 2.440 nonbonded pdb=" O THR C 281 " pdb=" OG SER C 284 " model vdw 2.334 2.440 ... (remaining 112222 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 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: 7.330 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 40.430 Find NCS groups from input model: 0.910 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: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 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 0.072 14425 Z= 0.466 Angle : 1.034 17.244 19600 Z= 0.527 Chirality : 0.057 0.294 2260 Planarity : 0.007 0.049 2425 Dihedral : 12.784 103.778 5440 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.55 (0.15), residues: 1710 helix: -4.56 (0.10), residues: 565 sheet: -0.97 (0.26), residues: 350 loop : -2.71 (0.16), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 110 HIS 0.002 0.001 HIS E 231 PHE 0.024 0.003 PHE C 115 TYR 0.025 0.003 TYR E 144 ARG 0.005 0.001 ARG E 147 *********************** 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 383 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 383 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 VAL cc_start: 0.6445 (t) cc_final: 0.5698 (t) REVERT: B 130 ASP cc_start: 0.7179 (m-30) cc_final: 0.6979 (m-30) REVERT: E 320 VAL cc_start: 0.6564 (t) cc_final: 0.5838 (t) outliers start: 0 outliers final: 0 residues processed: 383 average time/residue: 0.2641 time to fit residues: 144.6705 Evaluate side-chains 210 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.534 ------------------------------------------------------------------------------- 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: 2.9990 chunk 128 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 133 optimal weight: 30.0000 chunk 51 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 99 optimal weight: 0.4980 chunk 154 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 82 GLN B 62 ASN B 82 GLN B 131 ASN C 62 ASN C 82 GLN D 62 ASN D 82 GLN D 131 ASN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN E 82 GLN E 131 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14425 Z= 0.179 Angle : 0.631 7.939 19600 Z= 0.321 Chirality : 0.043 0.164 2260 Planarity : 0.004 0.028 2425 Dihedral : 9.939 63.013 2185 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.59 % Allowed : 10.86 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.17), residues: 1710 helix: -3.15 (0.15), residues: 590 sheet: -0.49 (0.26), residues: 345 loop : -2.39 (0.18), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 255 HIS 0.003 0.001 HIS E 125 PHE 0.017 0.001 PHE A 414 TYR 0.016 0.001 TYR B 317 ARG 0.013 0.001 ARG C 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 273 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 249 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7474 (tt) REVERT: B 105 MET cc_start: 0.7371 (mmm) cc_final: 0.6969 (mmm) REVERT: E 314 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7310 (tt) outliers start: 24 outliers final: 12 residues processed: 255 average time/residue: 0.2399 time to fit residues: 93.1186 Evaluate side-chains 207 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 193 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 314 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 chunk 154 optimal weight: 5.9990 chunk 167 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 chunk 153 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 GLN C 231 HIS D 193 GLN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14425 Z= 0.207 Angle : 0.574 6.261 19600 Z= 0.295 Chirality : 0.043 0.159 2260 Planarity : 0.004 0.039 2425 Dihedral : 7.104 37.493 2185 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.25 % Allowed : 12.58 % Favored : 84.17 % 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: -2.64 (0.18), residues: 1710 helix: -2.18 (0.18), residues: 595 sheet: -0.19 (0.27), residues: 350 loop : -2.08 (0.19), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 255 HIS 0.003 0.001 HIS E 125 PHE 0.027 0.001 PHE E 258 TYR 0.010 0.001 TYR A 144 ARG 0.011 0.001 ARG A 287 *********************** 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 265 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 216 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 GLN cc_start: 0.8877 (mm-40) cc_final: 0.8647 (mp10) REVERT: A 314 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7559 (tt) REVERT: B 314 LEU cc_start: 0.8219 (mt) cc_final: 0.7738 (tt) REVERT: C 242 GLN cc_start: 0.7300 (tt0) cc_final: 0.7047 (tp40) REVERT: D 314 LEU cc_start: 0.8254 (mt) cc_final: 0.7736 (tt) REVERT: E 314 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7436 (tt) outliers start: 49 outliers final: 30 residues processed: 236 average time/residue: 0.2249 time to fit residues: 81.6513 Evaluate side-chains 217 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 185 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 202 GLN Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 314 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 17 optimal weight: 0.0170 chunk 73 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS B 193 GLN B 231 HIS ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 HIS ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14425 Z= 0.195 Angle : 0.573 7.789 19600 Z= 0.287 Chirality : 0.043 0.159 2260 Planarity : 0.003 0.021 2425 Dihedral : 5.727 28.447 2185 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.11 % Allowed : 13.91 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.19), residues: 1710 helix: -1.36 (0.20), residues: 580 sheet: 0.05 (0.28), residues: 350 loop : -1.86 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 255 HIS 0.003 0.001 HIS E 125 PHE 0.009 0.001 PHE E 258 TYR 0.010 0.001 TYR A 317 ARG 0.005 0.000 ARG B 287 *********************** 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 252 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 205 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.7823 (mmm) cc_final: 0.7391 (mmt) REVERT: A 282 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8322 (mp10) REVERT: A 314 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7523 (tt) REVERT: B 314 LEU cc_start: 0.8252 (mt) cc_final: 0.7759 (tt) REVERT: B 320 VAL cc_start: 0.5734 (t) cc_final: 0.5505 (t) REVERT: C 282 GLN cc_start: 0.8823 (mp10) cc_final: 0.8619 (mp10) REVERT: C 314 LEU cc_start: 0.8239 (mt) cc_final: 0.7753 (tt) REVERT: D 314 LEU cc_start: 0.8363 (mt) cc_final: 0.7885 (tt) REVERT: E 314 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7475 (tt) outliers start: 47 outliers final: 34 residues processed: 228 average time/residue: 0.2256 time to fit residues: 78.2273 Evaluate side-chains 223 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 187 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 314 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 140 optimal weight: 0.0980 chunk 113 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 41 optimal weight: 0.0070 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14425 Z= 0.178 Angle : 0.562 7.796 19600 Z= 0.280 Chirality : 0.042 0.160 2260 Planarity : 0.003 0.020 2425 Dihedral : 5.241 22.269 2185 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.98 % Allowed : 14.57 % Favored : 82.45 % 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: -1.60 (0.19), residues: 1710 helix: -0.89 (0.21), residues: 585 sheet: 0.36 (0.28), residues: 345 loop : -1.84 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 255 HIS 0.002 0.001 HIS E 125 PHE 0.009 0.001 PHE D 115 TYR 0.012 0.001 TYR A 317 ARG 0.006 0.000 ARG A 268 *********************** 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 245 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 200 time to evaluate : 1.654 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: C 314 LEU cc_start: 0.8288 (mt) cc_final: 0.7787 (tt) REVERT: D 72 MET cc_start: 0.8211 (mmm) cc_final: 0.7993 (mmm) REVERT: D 282 GLN cc_start: 0.8757 (mp10) cc_final: 0.8508 (mp10) REVERT: D 314 LEU cc_start: 0.8390 (mt) cc_final: 0.7882 (tt) outliers start: 45 outliers final: 35 residues processed: 219 average time/residue: 0.2330 time to fit residues: 77.4150 Evaluate side-chains 216 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 181 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 310 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 96 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 76 optimal weight: 0.2980 chunk 13 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN C 166 GLN D 231 HIS ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 GLN ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14425 Z= 0.162 Angle : 0.550 8.348 19600 Z= 0.274 Chirality : 0.042 0.161 2260 Planarity : 0.003 0.029 2425 Dihedral : 5.121 22.187 2185 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.31 % Allowed : 14.50 % Favored : 82.19 % 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: -1.18 (0.20), residues: 1710 helix: -0.45 (0.22), residues: 590 sheet: 0.53 (0.29), residues: 345 loop : -1.64 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 255 HIS 0.002 0.001 HIS E 125 PHE 0.010 0.001 PHE D 115 TYR 0.009 0.001 TYR D 144 ARG 0.002 0.000 ARG A 268 *********************** 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 255 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 205 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7265 (tmm) REVERT: A 314 LEU cc_start: 0.8067 (mt) cc_final: 0.7424 (tt) REVERT: C 262 MET cc_start: 0.2030 (tpt) cc_final: 0.1805 (tpt) REVERT: C 314 LEU cc_start: 0.8270 (mt) cc_final: 0.7787 (tt) outliers start: 50 outliers final: 36 residues processed: 231 average time/residue: 0.2334 time to fit residues: 81.4129 Evaluate side-chains 219 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 182 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 310 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 120 optimal weight: 0.0670 chunk 138 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 75 optimal weight: 0.0170 chunk 101 optimal weight: 4.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN D 235 GLN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 GLN ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14425 Z= 0.142 Angle : 0.543 8.433 19600 Z= 0.271 Chirality : 0.041 0.163 2260 Planarity : 0.003 0.043 2425 Dihedral : 4.952 21.870 2185 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.52 % Allowed : 15.96 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.20), residues: 1710 helix: -0.18 (0.23), residues: 590 sheet: 0.74 (0.29), residues: 345 loop : -1.50 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 255 HIS 0.002 0.001 HIS B 125 PHE 0.009 0.001 PHE D 115 TYR 0.009 0.001 TYR D 317 ARG 0.011 0.000 ARG D 268 *********************** 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 228 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 190 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7264 (tmm) REVERT: A 314 LEU cc_start: 0.8030 (mt) cc_final: 0.7403 (tt) REVERT: C 314 LEU cc_start: 0.8317 (mt) cc_final: 0.8005 (mp) outliers start: 38 outliers final: 33 residues processed: 205 average time/residue: 0.2238 time to fit residues: 70.9705 Evaluate side-chains 211 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 177 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 202 GLN Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 310 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 128 optimal weight: 0.0570 chunk 149 optimal weight: 0.8980 overall best weight: 1.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 GLN ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14425 Z= 0.224 Angle : 0.572 9.433 19600 Z= 0.287 Chirality : 0.042 0.158 2260 Planarity : 0.003 0.059 2425 Dihedral : 5.026 23.355 2185 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.85 % Allowed : 16.09 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.21), residues: 1710 helix: -0.06 (0.23), residues: 590 sheet: 1.07 (0.30), residues: 320 loop : -1.29 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 255 HIS 0.002 0.001 HIS D 125 PHE 0.011 0.001 PHE C 203 TYR 0.010 0.001 TYR B 144 ARG 0.003 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 177 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7230 (tmm) REVERT: A 314 LEU cc_start: 0.8058 (mt) cc_final: 0.7361 (tt) REVERT: E 314 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7608 (tt) outliers start: 43 outliers final: 35 residues processed: 197 average time/residue: 0.2209 time to fit residues: 67.6575 Evaluate side-chains 214 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 177 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 202 GLN Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 314 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 5.9990 chunk 143 optimal weight: 0.0060 chunk 152 optimal weight: 0.0470 chunk 91 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 144 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 overall best weight: 1.2098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 GLN ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14425 Z= 0.191 Angle : 0.562 8.392 19600 Z= 0.281 Chirality : 0.042 0.163 2260 Planarity : 0.003 0.042 2425 Dihedral : 5.025 23.431 2185 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.45 % Allowed : 16.56 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.21), residues: 1710 helix: 0.04 (0.23), residues: 590 sheet: 1.11 (0.31), residues: 320 loop : -1.25 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 255 HIS 0.002 0.000 HIS D 125 PHE 0.010 0.001 PHE D 115 TYR 0.009 0.001 TYR B 144 ARG 0.006 0.000 ARG B 268 *********************** 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 218 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 181 time to evaluate : 1.638 Fit side-chains revert: symmetry clash REVERT: A 24 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7311 (tmm) REVERT: A 314 LEU cc_start: 0.8085 (mt) cc_final: 0.7405 (tt) outliers start: 37 outliers final: 31 residues processed: 199 average time/residue: 0.2273 time to fit residues: 69.9754 Evaluate side-chains 212 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 180 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 310 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.1980 chunk 76 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 GLN ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14425 Z= 0.165 Angle : 0.577 12.917 19600 Z= 0.286 Chirality : 0.042 0.176 2260 Planarity : 0.003 0.037 2425 Dihedral : 5.040 36.641 2185 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.32 % Allowed : 17.02 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.21), residues: 1710 helix: 0.08 (0.23), residues: 590 sheet: 1.13 (0.31), residues: 320 loop : -1.25 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 255 HIS 0.002 0.000 HIS D 125 PHE 0.009 0.001 PHE B 322 TYR 0.013 0.001 TYR D 213 ARG 0.002 0.000 ARG C 212 ********************** 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 216 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 181 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7327 (tmm) REVERT: A 314 LEU cc_start: 0.8085 (mt) cc_final: 0.7412 (tt) REVERT: D 308 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7857 (mt) outliers start: 35 outliers final: 32 residues processed: 199 average time/residue: 0.2201 time to fit residues: 68.0910 Evaluate side-chains 211 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 177 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 310 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 4.9990 chunk 124 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 118 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN E 193 GLN ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.106722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.075399 restraints weight = 29795.267| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 3.17 r_work: 0.2885 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14425 Z= 0.164 Angle : 0.570 9.720 19600 Z= 0.283 Chirality : 0.042 0.162 2260 Planarity : 0.003 0.031 2425 Dihedral : 5.012 44.888 2185 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.32 % Allowed : 16.95 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.21), residues: 1710 helix: 0.14 (0.23), residues: 590 sheet: 1.14 (0.31), residues: 320 loop : -1.22 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 255 HIS 0.002 0.000 HIS D 125 PHE 0.022 0.001 PHE B 322 TYR 0.009 0.001 TYR B 144 ARG 0.004 0.000 ARG B 268 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3026.96 seconds wall clock time: 55 minutes 38.90 seconds (3338.90 seconds total)