Starting phenix.real_space_refine on Sat Mar 16 23:18:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqg_20847/03_2024/6uqg_20847_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqg_20847/03_2024/6uqg_20847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqg_20847/03_2024/6uqg_20847.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqg_20847/03_2024/6uqg_20847.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqg_20847/03_2024/6uqg_20847_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqg_20847/03_2024/6uqg_20847_updated.pdb" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.054 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 116 5.16 5 C 10388 2.51 5 N 2756 2.21 5 O 2712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 146": "OD1" <-> "OD2" Residue "A PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A ASP 312": "OD1" <-> "OD2" Residue "A ASP 371": "OD1" <-> "OD2" Residue "A ASP 401": "OD1" <-> "OD2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A GLU 409": "OE1" <-> "OE2" Residue "A TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 446": "OE1" <-> "OE2" Residue "A PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 146": "OD1" <-> "OD2" Residue "B PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "B ASP 371": "OD1" <-> "OD2" Residue "B ASP 401": "OD1" <-> "OD2" Residue "B ARG 404": "NH1" <-> "NH2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B GLU 409": "OE1" <-> "OE2" Residue "B TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 446": "OE1" <-> "OE2" Residue "B PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 146": "OD1" <-> "OD2" Residue "C PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 282": "OE1" <-> "OE2" Residue "C ASP 312": "OD1" <-> "OD2" Residue "C ASP 371": "OD1" <-> "OD2" Residue "C ASP 401": "OD1" <-> "OD2" Residue "C ARG 404": "NH1" <-> "NH2" Residue "C ARG 405": "NH1" <-> "NH2" Residue "C GLU 409": "OE1" <-> "OE2" Residue "C TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 446": "OE1" <-> "OE2" Residue "C PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 146": "OD1" <-> "OD2" Residue "D PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 282": "OE1" <-> "OE2" Residue "D ASP 312": "OD1" <-> "OD2" Residue "D ASP 371": "OD1" <-> "OD2" Residue "D ASP 401": "OD1" <-> "OD2" Residue "D ARG 404": "NH1" <-> "NH2" Residue "D ARG 405": "NH1" <-> "NH2" Residue "D GLU 409": "OE1" <-> "OE2" Residue "D TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 446": "OE1" <-> "OE2" Residue "D PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15976 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 3972 Classifications: {'peptide': 530} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 16, 'TRANS': 513} Chain breaks: 2 Unresolved non-hydrogen bonds: 371 Unresolved non-hydrogen angles: 465 Unresolved non-hydrogen dihedrals: 294 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 4, 'GLU:plan': 15, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 218 Chain: "B" Number of atoms: 3972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 3972 Classifications: {'peptide': 530} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 16, 'TRANS': 513} Chain breaks: 2 Unresolved non-hydrogen bonds: 371 Unresolved non-hydrogen angles: 465 Unresolved non-hydrogen dihedrals: 294 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 4, 'GLU:plan': 15, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 218 Chain: "C" Number of atoms: 3972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 3972 Classifications: {'peptide': 530} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 16, 'TRANS': 513} Chain breaks: 2 Unresolved non-hydrogen bonds: 371 Unresolved non-hydrogen angles: 465 Unresolved non-hydrogen dihedrals: 294 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 4, 'GLU:plan': 15, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 218 Chain: "D" Number of atoms: 3972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 3972 Classifications: {'peptide': 530} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 16, 'TRANS': 513} Chain breaks: 2 Unresolved non-hydrogen bonds: 371 Unresolved non-hydrogen angles: 465 Unresolved non-hydrogen dihedrals: 294 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 4, 'GLU:plan': 15, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 218 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 8.28, per 1000 atoms: 0.52 Number of scatterers: 15976 At special positions: 0 Unit cell: (107.12, 108.15, 128.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 116 16.00 P 4 15.00 O 2712 8.00 N 2756 7.00 C 10388 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 6.04 Conformation dependent library (CDL) restraints added in 3.0 seconds 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4040 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 8 sheets defined 67.4% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'A' and resid 95 through 102 Processing helix chain 'A' and resid 108 through 114 Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 140 through 166 Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 173 through 194 Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 222 through 229 removed outlier: 4.726A pdb=" N SER A 228 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 241 removed outlier: 3.709A pdb=" N LEU A 237 " --> pdb=" O ASP A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 285 removed outlier: 4.341A pdb=" N SER A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ARG A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ARG A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU A 271 " --> pdb=" O ARG A 267 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N SER A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ARG A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 322 removed outlier: 3.993A pdb=" N PHE A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 330 through 334 Processing helix chain 'A' and resid 341 through 356 Processing helix chain 'A' and resid 369 through 400 Processing helix chain 'A' and resid 402 through 421 Processing helix chain 'A' and resid 425 through 439 removed outlier: 3.504A pdb=" N LYS A 430 " --> pdb=" O ASP A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 452 Processing helix chain 'A' and resid 455 through 465 Processing helix chain 'A' and resid 467 through 472 removed outlier: 3.662A pdb=" N ALA A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 481 through 489 Processing helix chain 'A' and resid 540 through 545 Processing helix chain 'A' and resid 566 through 575 Processing helix chain 'A' and resid 578 through 594 Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 616 through 634 Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 108 through 114 Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 140 through 166 Proline residue: B 161 - end of helix Processing helix chain 'B' and resid 173 through 194 Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 222 through 229 removed outlier: 4.727A pdb=" N SER B 228 " --> pdb=" O VAL B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 241 removed outlier: 3.708A pdb=" N LEU B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 285 removed outlier: 4.342A pdb=" N SER B 264 " --> pdb=" O THR B 260 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU B 266 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ARG B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU B 268 " --> pdb=" O SER B 264 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ARG B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU B 271 " --> pdb=" O ARG B 267 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N SER B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ARG B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 322 removed outlier: 3.993A pdb=" N PHE B 317 " --> pdb=" O GLY B 313 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 330 through 334 Processing helix chain 'B' and resid 341 through 356 Processing helix chain 'B' and resid 369 through 400 Processing helix chain 'B' and resid 402 through 421 Processing helix chain 'B' and resid 425 through 439 removed outlier: 3.504A pdb=" N LYS B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 452 Processing helix chain 'B' and resid 455 through 465 Processing helix chain 'B' and resid 467 through 472 removed outlier: 3.662A pdb=" N ALA B 471 " --> pdb=" O ARG B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 478 Processing helix chain 'B' and resid 481 through 489 Processing helix chain 'B' and resid 540 through 545 Processing helix chain 'B' and resid 566 through 575 Processing helix chain 'B' and resid 578 through 594 Processing helix chain 'B' and resid 599 through 609 Processing helix chain 'B' and resid 616 through 634 Processing helix chain 'C' and resid 95 through 102 Processing helix chain 'C' and resid 108 through 114 Processing helix chain 'C' and resid 117 through 128 Processing helix chain 'C' and resid 140 through 166 Proline residue: C 161 - end of helix Processing helix chain 'C' and resid 173 through 194 Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 222 through 229 removed outlier: 4.726A pdb=" N SER C 228 " --> pdb=" O VAL C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 241 removed outlier: 3.708A pdb=" N LEU C 237 " --> pdb=" O ASP C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 285 removed outlier: 4.341A pdb=" N SER C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LEU C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU C 266 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ARG C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ARG C 270 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU C 271 " --> pdb=" O ARG C 267 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N SER C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ARG C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 274 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN C 280 " --> pdb=" O ARG C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 322 removed outlier: 3.994A pdb=" N PHE C 317 " --> pdb=" O GLY C 313 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 330 through 334 Processing helix chain 'C' and resid 341 through 356 Processing helix chain 'C' and resid 369 through 400 Processing helix chain 'C' and resid 402 through 421 Processing helix chain 'C' and resid 425 through 439 removed outlier: 3.505A pdb=" N LYS C 430 " --> pdb=" O ASP C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 452 Processing helix chain 'C' and resid 455 through 465 Processing helix chain 'C' and resid 467 through 472 removed outlier: 3.662A pdb=" N ALA C 471 " --> pdb=" O ARG C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 478 Processing helix chain 'C' and resid 481 through 489 Processing helix chain 'C' and resid 540 through 545 Processing helix chain 'C' and resid 566 through 575 Processing helix chain 'C' and resid 578 through 594 Processing helix chain 'C' and resid 599 through 609 Processing helix chain 'C' and resid 616 through 634 Processing helix chain 'D' and resid 95 through 102 Processing helix chain 'D' and resid 108 through 114 Processing helix chain 'D' and resid 117 through 128 Processing helix chain 'D' and resid 140 through 166 Proline residue: D 161 - end of helix Processing helix chain 'D' and resid 173 through 194 Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 222 through 229 removed outlier: 4.726A pdb=" N SER D 228 " --> pdb=" O VAL D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 241 removed outlier: 3.709A pdb=" N LEU D 237 " --> pdb=" O ASP D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 285 removed outlier: 4.341A pdb=" N SER D 264 " --> pdb=" O THR D 260 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU D 265 " --> pdb=" O LYS D 261 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU D 266 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ARG D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU D 269 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ARG D 270 " --> pdb=" O LEU D 266 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU D 271 " --> pdb=" O ARG D 267 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N SER D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ARG D 273 " --> pdb=" O LEU D 269 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU D 274 " --> pdb=" O ARG D 270 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN D 280 " --> pdb=" O ARG D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 322 removed outlier: 3.993A pdb=" N PHE D 317 " --> pdb=" O GLY D 313 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 330 through 334 Processing helix chain 'D' and resid 341 through 356 Processing helix chain 'D' and resid 369 through 400 Processing helix chain 'D' and resid 402 through 421 Processing helix chain 'D' and resid 425 through 439 removed outlier: 3.504A pdb=" N LYS D 430 " --> pdb=" O ASP D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 452 Processing helix chain 'D' and resid 455 through 465 Processing helix chain 'D' and resid 467 through 472 removed outlier: 3.661A pdb=" N ALA D 471 " --> pdb=" O ARG D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 478 Processing helix chain 'D' and resid 481 through 489 Processing helix chain 'D' and resid 540 through 545 Processing helix chain 'D' and resid 566 through 575 Processing helix chain 'D' and resid 578 through 594 Processing helix chain 'D' and resid 599 through 609 Processing helix chain 'D' and resid 616 through 634 Processing sheet with id= A, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.027A pdb=" N TYR A 562 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ILE A 515 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU A 564 " --> pdb=" O TYR A 513 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N TYR A 513 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER A 536 " --> pdb=" O ILE A 515 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 530 through 532 removed outlier: 3.828A pdb=" N SER A 552 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 492 through 496 removed outlier: 6.026A pdb=" N TYR B 562 " --> pdb=" O ILE B 515 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ILE B 515 " --> pdb=" O TYR B 562 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU B 564 " --> pdb=" O TYR B 513 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N TYR B 513 " --> pdb=" O LEU B 564 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER B 536 " --> pdb=" O ILE B 515 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 530 through 532 removed outlier: 3.828A pdb=" N SER B 552 " --> pdb=" O ILE B 523 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.027A pdb=" N TYR C 562 " --> pdb=" O ILE C 515 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ILE C 515 " --> pdb=" O TYR C 562 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU C 564 " --> pdb=" O TYR C 513 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N TYR C 513 " --> pdb=" O LEU C 564 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER C 536 " --> pdb=" O ILE C 515 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 530 through 532 removed outlier: 3.828A pdb=" N SER C 552 " --> pdb=" O ILE C 523 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.027A pdb=" N TYR D 562 " --> pdb=" O ILE D 515 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ILE D 515 " --> pdb=" O TYR D 562 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU D 564 " --> pdb=" O TYR D 513 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N TYR D 513 " --> pdb=" O LEU D 564 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER D 536 " --> pdb=" O ILE D 515 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 530 through 532 removed outlier: 3.828A pdb=" N SER D 552 " --> pdb=" O ILE D 523 " (cutoff:3.500A) 1008 hydrogen bonds defined for protein. 2976 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.31 Time building geometry restraints manager: 6.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4439 1.34 - 1.45: 2947 1.45 - 1.57: 8750 1.57 - 1.69: 8 1.69 - 1.81: 204 Bond restraints: 16348 Sorted by residual: bond pdb=" CG1 ILE D 374 " pdb=" CD1 ILE D 374 " ideal model delta sigma weight residual 1.513 1.411 0.102 3.90e-02 6.57e+02 6.82e+00 bond pdb=" CG1 ILE B 374 " pdb=" CD1 ILE B 374 " ideal model delta sigma weight residual 1.513 1.412 0.101 3.90e-02 6.57e+02 6.75e+00 bond pdb=" CG1 ILE A 374 " pdb=" CD1 ILE A 374 " ideal model delta sigma weight residual 1.513 1.412 0.101 3.90e-02 6.57e+02 6.75e+00 bond pdb=" CG1 ILE C 374 " pdb=" CD1 ILE C 374 " ideal model delta sigma weight residual 1.513 1.412 0.101 3.90e-02 6.57e+02 6.73e+00 bond pdb=" CA ILE B 160 " pdb=" C ILE B 160 " ideal model delta sigma weight residual 1.524 1.550 -0.025 1.05e-02 9.07e+03 5.77e+00 ... (remaining 16343 not shown) Histogram of bond angle deviations from ideal: 97.04 - 104.94: 309 104.94 - 112.83: 8708 112.83 - 120.73: 8231 120.73 - 128.62: 4845 128.62 - 136.52: 135 Bond angle restraints: 22228 Sorted by residual: angle pdb=" N ILE D 359 " pdb=" CA ILE D 359 " pdb=" C ILE D 359 " ideal model delta sigma weight residual 110.53 117.62 -7.09 9.40e-01 1.13e+00 5.69e+01 angle pdb=" N ILE B 359 " pdb=" CA ILE B 359 " pdb=" C ILE B 359 " ideal model delta sigma weight residual 110.53 117.62 -7.09 9.40e-01 1.13e+00 5.69e+01 angle pdb=" N ILE A 359 " pdb=" CA ILE A 359 " pdb=" C ILE A 359 " ideal model delta sigma weight residual 110.53 117.61 -7.08 9.40e-01 1.13e+00 5.67e+01 angle pdb=" N ILE C 359 " pdb=" CA ILE C 359 " pdb=" C ILE C 359 " ideal model delta sigma weight residual 110.53 117.60 -7.07 9.40e-01 1.13e+00 5.65e+01 angle pdb=" N ILE B 164 " pdb=" CA ILE B 164 " pdb=" C ILE B 164 " ideal model delta sigma weight residual 110.42 117.59 -7.17 9.60e-01 1.09e+00 5.58e+01 ... (remaining 22223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.77: 9327 30.77 - 61.54: 289 61.54 - 92.32: 12 92.32 - 123.09: 4 123.09 - 153.86: 4 Dihedral angle restraints: 9636 sinusoidal: 3404 harmonic: 6232 Sorted by residual: dihedral pdb=" C5' CMP D 901 " pdb=" O5' CMP D 901 " pdb=" P CMP D 901 " pdb=" O1P CMP D 901 " ideal model delta sinusoidal sigma weight residual 60.00 166.17 -106.17 1 2.00e+01 2.50e-03 3.07e+01 dihedral pdb=" C5' CMP A 901 " pdb=" O5' CMP A 901 " pdb=" P CMP A 901 " pdb=" O1P CMP A 901 " ideal model delta sinusoidal sigma weight residual 60.00 166.15 -106.15 1 2.00e+01 2.50e-03 3.07e+01 dihedral pdb=" C5' CMP C 901 " pdb=" O5' CMP C 901 " pdb=" P CMP C 901 " pdb=" O1P CMP C 901 " ideal model delta sinusoidal sigma weight residual 60.00 166.15 -106.15 1 2.00e+01 2.50e-03 3.07e+01 ... (remaining 9633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1839 0.055 - 0.110: 590 0.110 - 0.166: 89 0.166 - 0.221: 22 0.221 - 0.276: 8 Chirality restraints: 2548 Sorted by residual: chirality pdb=" CA CYS B 358 " pdb=" N CYS B 358 " pdb=" C CYS B 358 " pdb=" CB CYS B 358 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA CYS A 358 " pdb=" N CYS A 358 " pdb=" C CYS A 358 " pdb=" CB CYS A 358 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA CYS D 358 " pdb=" N CYS D 358 " pdb=" C CYS D 358 " pdb=" CB CYS D 358 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 2545 not shown) Planarity restraints: 2788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 319 " 0.056 5.00e-02 4.00e+02 8.35e-02 1.11e+01 pdb=" N PRO C 320 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO C 320 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 320 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 319 " -0.056 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO D 320 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO D 320 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 320 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 319 " -0.056 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO A 320 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 320 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 320 " -0.047 5.00e-02 4.00e+02 ... (remaining 2785 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4737 2.81 - 3.33: 14906 3.33 - 3.85: 26174 3.85 - 4.38: 27505 4.38 - 4.90: 49038 Nonbonded interactions: 122360 Sorted by model distance: nonbonded pdb=" OG SER A 403 " pdb=" NE2 GLN D 416 " model vdw 2.286 2.520 nonbonded pdb=" OG SER C 565 " pdb=" OD1 ASN C 568 " model vdw 2.300 2.440 nonbonded pdb=" OG SER A 565 " pdb=" OD1 ASN A 568 " model vdw 2.300 2.440 nonbonded pdb=" OG SER B 565 " pdb=" OD1 ASN B 568 " model vdw 2.301 2.440 nonbonded pdb=" OG SER D 565 " pdb=" OD1 ASN D 568 " model vdw 2.301 2.440 ... (remaining 122355 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 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: 7.400 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 42.980 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 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 : 0.009 0.102 16348 Z= 0.569 Angle : 0.968 9.745 22228 Z= 0.571 Chirality : 0.055 0.276 2548 Planarity : 0.008 0.083 2788 Dihedral : 15.113 153.860 5596 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.14), residues: 2096 helix: -2.07 (0.10), residues: 1516 sheet: -2.03 (0.39), residues: 124 loop : -2.76 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 330 HIS 0.005 0.002 HIS C 421 PHE 0.029 0.003 PHE C 194 TYR 0.023 0.002 TYR C 347 ARG 0.003 0.001 ARG D 593 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.8178 (mmm) cc_final: 0.7478 (mtt) REVERT: A 152 MET cc_start: 0.7631 (tpp) cc_final: 0.7388 (tpp) REVERT: A 401 ASP cc_start: 0.8492 (t0) cc_final: 0.7312 (t70) REVERT: A 410 LYS cc_start: 0.8663 (tttt) cc_final: 0.8417 (ttpt) REVERT: A 624 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7863 (tm-30) REVERT: A 628 HIS cc_start: 0.8277 (t-90) cc_final: 0.7785 (t-170) REVERT: B 281 TRP cc_start: 0.7768 (t60) cc_final: 0.7476 (t60) REVERT: B 386 TYR cc_start: 0.8735 (t80) cc_final: 0.8363 (t80) REVERT: B 451 ASN cc_start: 0.9140 (t0) cc_final: 0.8936 (t0) REVERT: B 624 GLN cc_start: 0.7974 (tm-30) cc_final: 0.7730 (tp40) REVERT: B 628 HIS cc_start: 0.7496 (t-90) cc_final: 0.6443 (t-170) REVERT: C 149 MET cc_start: 0.7406 (mmp) cc_final: 0.7141 (mmp) REVERT: C 281 TRP cc_start: 0.7766 (t60) cc_final: 0.7476 (t60) REVERT: C 347 TYR cc_start: 0.8697 (t80) cc_final: 0.8404 (t80) REVERT: C 386 TYR cc_start: 0.8587 (t80) cc_final: 0.8265 (t80) REVERT: C 401 ASP cc_start: 0.8126 (t0) cc_final: 0.6859 (t70) REVERT: C 624 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7728 (tp40) REVERT: C 628 HIS cc_start: 0.7558 (t-90) cc_final: 0.7259 (t-170) REVERT: D 281 TRP cc_start: 0.7789 (t60) cc_final: 0.7489 (t60) REVERT: D 386 TYR cc_start: 0.8667 (t80) cc_final: 0.8341 (t80) REVERT: D 409 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8480 (mm-30) REVERT: D 624 GLN cc_start: 0.7925 (tm-30) cc_final: 0.7693 (tp40) REVERT: D 628 HIS cc_start: 0.7496 (t-90) cc_final: 0.6456 (t-170) outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.2806 time to fit residues: 121.3095 Evaluate side-chains 228 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.9980 chunk 160 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 166 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS A 416 GLN B 310 HIS ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN B 517 HIS C 310 HIS C 416 GLN D 310 HIS ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16348 Z= 0.191 Angle : 0.570 9.682 22228 Z= 0.291 Chirality : 0.039 0.163 2548 Planarity : 0.005 0.055 2788 Dihedral : 8.217 148.507 2336 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.24 % Allowed : 12.33 % Favored : 85.43 % 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: -0.97 (0.17), residues: 2096 helix: 0.17 (0.12), residues: 1520 sheet: -1.83 (0.38), residues: 140 loop : -2.84 (0.24), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 341 HIS 0.004 0.001 HIS D 628 PHE 0.017 0.001 PHE A 109 TYR 0.012 0.001 TYR D 347 ARG 0.004 0.000 ARG B 492 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 243 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.8189 (mmm) cc_final: 0.7566 (mtt) REVERT: A 109 PHE cc_start: 0.8736 (t80) cc_final: 0.8508 (t80) REVERT: A 281 TRP cc_start: 0.7504 (t60) cc_final: 0.7196 (t60) REVERT: A 305 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7386 (tpp) REVERT: A 401 ASP cc_start: 0.8239 (t0) cc_final: 0.7099 (t70) REVERT: A 624 GLN cc_start: 0.7998 (tm-30) cc_final: 0.7743 (tm-30) REVERT: A 628 HIS cc_start: 0.8065 (t-90) cc_final: 0.7841 (t-170) REVERT: B 156 ASN cc_start: 0.8117 (t0) cc_final: 0.7908 (t0) REVERT: B 281 TRP cc_start: 0.7566 (t60) cc_final: 0.7329 (t60) REVERT: B 305 MET cc_start: 0.7642 (ttm) cc_final: 0.7100 (tpt) REVERT: B 386 TYR cc_start: 0.8566 (t80) cc_final: 0.8362 (t80) REVERT: B 451 ASN cc_start: 0.9110 (t0) cc_final: 0.8900 (t0) REVERT: B 490 LYS cc_start: 0.8781 (mttt) cc_final: 0.8452 (mttm) REVERT: B 530 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.6279 (mtp) REVERT: B 628 HIS cc_start: 0.7569 (t-90) cc_final: 0.6834 (t-170) REVERT: C 101 MET cc_start: 0.8089 (mtm) cc_final: 0.7726 (mtp) REVERT: C 227 ILE cc_start: 0.8408 (mt) cc_final: 0.8207 (tp) REVERT: C 347 TYR cc_start: 0.8686 (t80) cc_final: 0.8393 (t80) REVERT: C 386 TYR cc_start: 0.8392 (t80) cc_final: 0.8174 (t80) REVERT: C 401 ASP cc_start: 0.8019 (t0) cc_final: 0.6821 (t70) REVERT: C 487 MET cc_start: 0.8656 (ttm) cc_final: 0.8378 (ttm) REVERT: C 530 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.6508 (mtp) REVERT: C 628 HIS cc_start: 0.7422 (t-90) cc_final: 0.7080 (t-170) REVERT: D 156 ASN cc_start: 0.8092 (t0) cc_final: 0.7861 (t0) REVERT: D 281 TRP cc_start: 0.7635 (t60) cc_final: 0.7417 (t60) REVERT: D 305 MET cc_start: 0.7593 (ttm) cc_final: 0.7061 (tpt) REVERT: D 490 LYS cc_start: 0.8764 (mttt) cc_final: 0.8436 (mttm) REVERT: D 530 MET cc_start: 0.7346 (OUTLIER) cc_final: 0.6320 (mtp) REVERT: D 628 HIS cc_start: 0.7558 (t-90) cc_final: 0.6846 (t-170) outliers start: 33 outliers final: 18 residues processed: 262 average time/residue: 0.2624 time to fit residues: 103.9943 Evaluate side-chains 239 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 217 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 530 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 20.0000 chunk 59 optimal weight: 0.4980 chunk 160 optimal weight: 0.3980 chunk 131 optimal weight: 0.2980 chunk 53 optimal weight: 20.0000 chunk 192 optimal weight: 0.7980 chunk 208 optimal weight: 6.9990 chunk 171 optimal weight: 7.9990 chunk 191 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 154 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16348 Z= 0.147 Angle : 0.529 8.296 22228 Z= 0.265 Chirality : 0.038 0.124 2548 Planarity : 0.004 0.045 2788 Dihedral : 7.320 136.337 2336 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.56 % Allowed : 15.92 % Favored : 82.52 % 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: 0.26 (0.18), residues: 2096 helix: 1.08 (0.13), residues: 1520 sheet: -0.02 (0.55), residues: 88 loop : -2.67 (0.24), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 281 HIS 0.002 0.000 HIS B 392 PHE 0.011 0.001 PHE A 109 TYR 0.008 0.001 TYR A 347 ARG 0.008 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 231 time to evaluate : 1.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.8178 (mmm) cc_final: 0.7570 (mtt) REVERT: A 305 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.7373 (tpp) REVERT: A 624 GLN cc_start: 0.8016 (tm-30) cc_final: 0.7736 (tm-30) REVERT: A 628 HIS cc_start: 0.8057 (t-90) cc_final: 0.7829 (t-170) REVERT: B 156 ASN cc_start: 0.8016 (t0) cc_final: 0.7788 (t0) REVERT: B 386 TYR cc_start: 0.8625 (t80) cc_final: 0.8280 (t80) REVERT: B 388 MET cc_start: 0.8324 (mmt) cc_final: 0.7994 (mmt) REVERT: B 451 ASN cc_start: 0.9064 (t0) cc_final: 0.8856 (t0) REVERT: B 530 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.6192 (mtp) REVERT: B 628 HIS cc_start: 0.7855 (t-90) cc_final: 0.7336 (t-170) REVERT: C 101 MET cc_start: 0.8254 (mtm) cc_final: 0.7878 (mtp) REVERT: C 192 MET cc_start: 0.7719 (mpp) cc_final: 0.7409 (mpp) REVERT: C 530 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.6344 (mtp) REVERT: C 628 HIS cc_start: 0.7458 (t-90) cc_final: 0.7125 (t-170) REVERT: D 490 LYS cc_start: 0.8753 (mttt) cc_final: 0.8535 (mttm) REVERT: D 530 MET cc_start: 0.7225 (OUTLIER) cc_final: 0.6149 (mtp) REVERT: D 628 HIS cc_start: 0.7822 (t-90) cc_final: 0.7295 (t-170) outliers start: 23 outliers final: 14 residues processed: 240 average time/residue: 0.2566 time to fit residues: 92.9938 Evaluate side-chains 229 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 211 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 530 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 193 optimal weight: 3.9990 chunk 204 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 183 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 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 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16348 Z= 0.165 Angle : 0.526 7.613 22228 Z= 0.264 Chirality : 0.038 0.124 2548 Planarity : 0.003 0.040 2788 Dihedral : 7.106 134.108 2336 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.69 % Allowed : 16.06 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.18), residues: 2096 helix: 1.52 (0.13), residues: 1520 sheet: 0.40 (0.57), residues: 88 loop : -2.45 (0.24), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 281 HIS 0.003 0.000 HIS D 628 PHE 0.011 0.001 PHE A 538 TYR 0.011 0.001 TYR D 347 ARG 0.007 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 233 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.8148 (mmm) cc_final: 0.7628 (mtt) REVERT: A 305 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7378 (tpp) REVERT: A 624 GLN cc_start: 0.8069 (tm-30) cc_final: 0.7788 (tm-30) REVERT: A 628 HIS cc_start: 0.8036 (t-90) cc_final: 0.7812 (t-170) REVERT: B 386 TYR cc_start: 0.8588 (t80) cc_final: 0.8303 (t80) REVERT: B 388 MET cc_start: 0.8317 (mmt) cc_final: 0.7946 (mmt) REVERT: B 530 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.6196 (mtp) REVERT: C 101 MET cc_start: 0.8259 (mtm) cc_final: 0.7777 (mtp) REVERT: C 192 MET cc_start: 0.7772 (mpp) cc_final: 0.7247 (mmt) REVERT: C 530 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.6433 (mtp) REVERT: C 624 GLN cc_start: 0.7743 (tm-30) cc_final: 0.7537 (tp40) REVERT: C 628 HIS cc_start: 0.7477 (t-90) cc_final: 0.7168 (t-170) REVERT: D 376 MET cc_start: 0.9118 (mmm) cc_final: 0.8463 (mmm) REVERT: D 404 ARG cc_start: 0.7636 (tmt170) cc_final: 0.7069 (tmm-80) REVERT: D 530 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.6203 (mtp) REVERT: D 628 HIS cc_start: 0.7888 (t-90) cc_final: 0.7493 (t-170) outliers start: 25 outliers final: 16 residues processed: 242 average time/residue: 0.2663 time to fit residues: 98.1750 Evaluate side-chains 229 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 209 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 530 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 104 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16348 Z= 0.225 Angle : 0.555 7.274 22228 Z= 0.280 Chirality : 0.039 0.126 2548 Planarity : 0.003 0.039 2788 Dihedral : 7.068 133.125 2336 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.78 % Allowed : 16.26 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.19), residues: 2096 helix: 1.70 (0.13), residues: 1520 sheet: 0.63 (0.57), residues: 88 loop : -2.33 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 373 HIS 0.005 0.001 HIS B 628 PHE 0.013 0.001 PHE A 538 TYR 0.016 0.001 TYR B 347 ARG 0.005 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 225 time to evaluate : 1.657 Fit side-chains REVERT: A 101 MET cc_start: 0.8152 (mmm) cc_final: 0.7628 (mtt) REVERT: A 305 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.7316 (tpp) REVERT: A 361 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.7861 (m-10) REVERT: A 624 GLN cc_start: 0.8078 (tm-30) cc_final: 0.7781 (tm-30) REVERT: A 628 HIS cc_start: 0.8005 (t-90) cc_final: 0.7777 (t-170) REVERT: B 259 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.8058 (m-80) REVERT: B 361 TYR cc_start: 0.8990 (OUTLIER) cc_final: 0.8038 (m-80) REVERT: B 386 TYR cc_start: 0.8623 (t80) cc_final: 0.8335 (t80) REVERT: B 530 MET cc_start: 0.7438 (OUTLIER) cc_final: 0.6411 (mtp) REVERT: B 628 HIS cc_start: 0.7480 (t-170) cc_final: 0.6458 (t-170) REVERT: C 101 MET cc_start: 0.8294 (mtm) cc_final: 0.7823 (mtp) REVERT: C 192 MET cc_start: 0.7804 (mpp) cc_final: 0.7238 (mmt) REVERT: C 530 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.6936 (mtp) REVERT: C 624 GLN cc_start: 0.7754 (tm-30) cc_final: 0.7524 (tp40) REVERT: C 628 HIS cc_start: 0.7544 (t-90) cc_final: 0.7224 (t-170) REVERT: D 149 MET cc_start: 0.7247 (OUTLIER) cc_final: 0.7003 (mmp) REVERT: D 259 PHE cc_start: 0.8290 (OUTLIER) cc_final: 0.8084 (m-80) REVERT: D 361 TYR cc_start: 0.8991 (OUTLIER) cc_final: 0.7938 (m-80) REVERT: D 404 ARG cc_start: 0.7713 (tmt170) cc_final: 0.7122 (tmm-80) REVERT: D 530 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.6374 (mtp) REVERT: D 628 HIS cc_start: 0.7920 (t-90) cc_final: 0.7559 (t-170) outliers start: 41 outliers final: 23 residues processed: 241 average time/residue: 0.2481 time to fit residues: 90.9990 Evaluate side-chains 247 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 214 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 361 TYR Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 530 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 9.9990 chunk 184 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 120 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 205 optimal weight: 3.9990 chunk 170 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 GLN ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 16348 Z= 0.448 Angle : 0.698 7.519 22228 Z= 0.359 Chirality : 0.044 0.149 2548 Planarity : 0.004 0.043 2788 Dihedral : 7.412 133.327 2336 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.05 % Allowed : 18.09 % Favored : 78.86 % 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: 0.84 (0.18), residues: 2096 helix: 1.46 (0.13), residues: 1496 sheet: 0.75 (0.51), residues: 88 loop : -2.24 (0.24), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 373 HIS 0.008 0.001 HIS B 628 PHE 0.017 0.002 PHE A 538 TYR 0.029 0.002 TYR B 347 ARG 0.005 0.001 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 214 time to evaluate : 1.955 Fit side-chains REVERT: A 306 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8670 (mm) REVERT: A 361 TYR cc_start: 0.8833 (OUTLIER) cc_final: 0.7972 (m-10) REVERT: A 624 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7759 (tm-30) REVERT: A 628 HIS cc_start: 0.8159 (t-90) cc_final: 0.7896 (t-170) REVERT: B 233 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.8053 (m-30) REVERT: B 361 TYR cc_start: 0.8866 (OUTLIER) cc_final: 0.7963 (m-80) REVERT: B 386 TYR cc_start: 0.8635 (t80) cc_final: 0.8311 (t80) REVERT: B 388 MET cc_start: 0.8606 (mmt) cc_final: 0.8313 (mmt) REVERT: B 530 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.6913 (mtp) REVERT: B 624 GLN cc_start: 0.7944 (tm-30) cc_final: 0.7725 (tp40) REVERT: C 101 MET cc_start: 0.8354 (mtm) cc_final: 0.7877 (mtp) REVERT: C 361 TYR cc_start: 0.8840 (OUTLIER) cc_final: 0.7775 (m-10) REVERT: C 530 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7191 (mtp) REVERT: C 624 GLN cc_start: 0.7872 (tm-30) cc_final: 0.7650 (tp40) REVERT: C 628 HIS cc_start: 0.7514 (t-90) cc_final: 0.7185 (t-170) REVERT: D 233 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.8130 (m-30) REVERT: D 361 TYR cc_start: 0.8884 (OUTLIER) cc_final: 0.7863 (m-80) REVERT: D 376 MET cc_start: 0.9146 (mmm) cc_final: 0.8487 (mmm) REVERT: D 404 ARG cc_start: 0.7796 (tmt170) cc_final: 0.7206 (tmm-80) REVERT: D 530 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.6955 (mtp) REVERT: D 624 GLN cc_start: 0.7941 (tm-30) cc_final: 0.7722 (tp40) outliers start: 45 outliers final: 21 residues processed: 235 average time/residue: 0.2701 time to fit residues: 98.3706 Evaluate side-chains 242 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 211 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 361 TYR Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 530 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 0.8980 chunk 23 optimal weight: 0.0770 chunk 116 optimal weight: 10.0000 chunk 149 optimal weight: 0.9980 chunk 172 optimal weight: 8.9990 chunk 114 optimal weight: 0.6980 chunk 204 optimal weight: 1.9990 chunk 127 optimal weight: 0.4980 chunk 124 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 517 HIS ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16348 Z= 0.157 Angle : 0.539 7.195 22228 Z= 0.270 Chirality : 0.038 0.129 2548 Planarity : 0.003 0.047 2788 Dihedral : 7.015 132.569 2336 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.10 % Allowed : 19.31 % Favored : 78.59 % 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: 1.39 (0.18), residues: 2096 helix: 1.92 (0.13), residues: 1488 sheet: 0.92 (0.55), residues: 88 loop : -2.15 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 330 HIS 0.006 0.001 HIS B 628 PHE 0.016 0.001 PHE C 186 TYR 0.005 0.001 TYR C 347 ARG 0.005 0.000 ARG D 270 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 233 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 ILE cc_start: 0.8546 (mt) cc_final: 0.8344 (tp) REVERT: A 305 MET cc_start: 0.7535 (mmm) cc_final: 0.7159 (tpt) REVERT: A 624 GLN cc_start: 0.8014 (tm-30) cc_final: 0.7712 (tm-30) REVERT: A 628 HIS cc_start: 0.7894 (t-90) cc_final: 0.7657 (t-170) REVERT: B 336 MET cc_start: 0.8172 (ptp) cc_final: 0.7972 (ptm) REVERT: B 361 TYR cc_start: 0.8847 (OUTLIER) cc_final: 0.7742 (m-80) REVERT: B 388 MET cc_start: 0.8591 (mmt) cc_final: 0.8342 (mmt) REVERT: B 530 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.6449 (mtp) REVERT: C 101 MET cc_start: 0.8301 (mtm) cc_final: 0.7863 (mtp) REVERT: C 530 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.6965 (mtp) REVERT: C 624 GLN cc_start: 0.7769 (tm-30) cc_final: 0.7510 (tp40) REVERT: C 628 HIS cc_start: 0.7481 (t-90) cc_final: 0.7175 (t-170) REVERT: D 376 MET cc_start: 0.9076 (mmm) cc_final: 0.8397 (mmt) REVERT: D 530 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.6444 (mtp) outliers start: 31 outliers final: 21 residues processed: 250 average time/residue: 0.2536 time to fit residues: 96.9768 Evaluate side-chains 241 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 216 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 530 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 129 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 160 optimal weight: 8.9990 chunk 185 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 HIS ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16348 Z= 0.181 Angle : 0.561 8.110 22228 Z= 0.279 Chirality : 0.039 0.135 2548 Planarity : 0.003 0.043 2788 Dihedral : 6.990 132.470 2336 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.57 % Allowed : 19.65 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.19), residues: 2096 helix: 1.99 (0.13), residues: 1488 sheet: 1.12 (0.57), residues: 88 loop : -2.05 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 281 HIS 0.006 0.001 HIS B 628 PHE 0.015 0.001 PHE A 186 TYR 0.012 0.001 TYR B 347 ARG 0.005 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 225 time to evaluate : 1.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7412 (mtp) cc_final: 0.7173 (ttm) REVERT: A 227 ILE cc_start: 0.8555 (mt) cc_final: 0.8345 (tp) REVERT: A 274 LEU cc_start: 0.9007 (tp) cc_final: 0.8787 (tp) REVERT: A 305 MET cc_start: 0.7517 (mmm) cc_final: 0.7116 (tpt) REVERT: A 624 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7684 (tm-30) REVERT: A 628 HIS cc_start: 0.7917 (t-90) cc_final: 0.7681 (t-170) REVERT: B 361 TYR cc_start: 0.8908 (OUTLIER) cc_final: 0.7855 (m-80) REVERT: B 388 MET cc_start: 0.8605 (mmt) cc_final: 0.8342 (mmt) REVERT: B 530 MET cc_start: 0.7434 (OUTLIER) cc_final: 0.6815 (mtp) REVERT: C 101 MET cc_start: 0.8326 (mtm) cc_final: 0.7937 (mtp) REVERT: C 233 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.8107 (m-30) REVERT: C 353 MET cc_start: 0.8739 (ttp) cc_final: 0.8536 (ttp) REVERT: C 530 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.7050 (mtp) REVERT: C 624 GLN cc_start: 0.7772 (tm-30) cc_final: 0.7505 (tp40) REVERT: C 628 HIS cc_start: 0.7447 (t-90) cc_final: 0.7142 (t-170) REVERT: D 361 TYR cc_start: 0.8895 (OUTLIER) cc_final: 0.7619 (m-80) REVERT: D 376 MET cc_start: 0.9119 (mmm) cc_final: 0.8474 (mmm) REVERT: D 388 MET cc_start: 0.8464 (mmt) cc_final: 0.8195 (mmt) REVERT: D 530 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.6432 (mtp) REVERT: D 624 GLN cc_start: 0.7853 (tm-30) cc_final: 0.7628 (tp40) outliers start: 38 outliers final: 22 residues processed: 245 average time/residue: 0.2472 time to fit residues: 93.4121 Evaluate side-chains 242 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 214 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 361 TYR Chi-restraints excluded: chain D residue 530 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 0.0980 chunk 178 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 172 optimal weight: 9.9990 chunk 180 optimal weight: 0.5980 chunk 189 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 517 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16348 Z= 0.163 Angle : 0.555 7.978 22228 Z= 0.275 Chirality : 0.039 0.149 2548 Planarity : 0.003 0.045 2788 Dihedral : 6.909 132.149 2336 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.90 % Allowed : 20.60 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.19), residues: 2096 helix: 2.01 (0.13), residues: 1492 sheet: 1.10 (0.58), residues: 88 loop : -1.87 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 330 HIS 0.005 0.001 HIS D 628 PHE 0.012 0.001 PHE A 186 TYR 0.008 0.001 TYR B 347 ARG 0.004 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 226 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 ILE cc_start: 0.8563 (mt) cc_final: 0.8361 (tp) REVERT: A 305 MET cc_start: 0.7512 (mmm) cc_final: 0.7102 (tpt) REVERT: A 361 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.7617 (m-80) REVERT: A 624 GLN cc_start: 0.7942 (tm-30) cc_final: 0.7607 (tm-30) REVERT: A 628 HIS cc_start: 0.7911 (t-90) cc_final: 0.7675 (t-170) REVERT: B 152 MET cc_start: 0.7251 (tpp) cc_final: 0.7044 (tpt) REVERT: B 305 MET cc_start: 0.7635 (tpt) cc_final: 0.7053 (tpt) REVERT: B 361 TYR cc_start: 0.8890 (OUTLIER) cc_final: 0.7747 (m-80) REVERT: B 388 MET cc_start: 0.8594 (mmt) cc_final: 0.8317 (mmt) REVERT: B 512 MET cc_start: 0.8752 (ptp) cc_final: 0.8512 (ptp) REVERT: B 530 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.6831 (mtp) REVERT: B 632 MET cc_start: 0.3855 (mtm) cc_final: 0.3417 (tmm) REVERT: C 101 MET cc_start: 0.8326 (mtm) cc_final: 0.7949 (mtp) REVERT: C 336 MET cc_start: 0.8150 (ptp) cc_final: 0.7805 (ptm) REVERT: C 530 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.7094 (mtp) REVERT: C 624 GLN cc_start: 0.7764 (tm-30) cc_final: 0.7488 (tp40) REVERT: C 628 HIS cc_start: 0.7533 (t-90) cc_final: 0.7233 (t-170) REVERT: D 152 MET cc_start: 0.7235 (tpp) cc_final: 0.7030 (tpt) REVERT: D 361 TYR cc_start: 0.8859 (OUTLIER) cc_final: 0.7497 (m-80) REVERT: D 376 MET cc_start: 0.9127 (mmm) cc_final: 0.8471 (mmt) REVERT: D 388 MET cc_start: 0.8455 (mmt) cc_final: 0.8191 (mmt) REVERT: D 512 MET cc_start: 0.8755 (ptp) cc_final: 0.8520 (ptp) REVERT: D 530 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.6489 (mtp) REVERT: D 624 GLN cc_start: 0.7776 (tm-30) cc_final: 0.7548 (tp40) outliers start: 28 outliers final: 19 residues processed: 241 average time/residue: 0.2467 time to fit residues: 91.5765 Evaluate side-chains 243 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 218 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 361 TYR Chi-restraints excluded: chain D residue 530 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 chunk 211 optimal weight: 7.9990 chunk 194 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 chunk 103 optimal weight: 8.9990 chunk 133 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16348 Z= 0.172 Angle : 0.561 7.919 22228 Z= 0.278 Chirality : 0.038 0.147 2548 Planarity : 0.003 0.047 2788 Dihedral : 6.886 132.105 2336 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.96 % Allowed : 20.46 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.19), residues: 2096 helix: 2.05 (0.13), residues: 1492 sheet: 1.00 (0.57), residues: 88 loop : -1.81 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 281 HIS 0.009 0.001 HIS B 628 PHE 0.011 0.001 PHE C 483 TYR 0.009 0.001 TYR B 347 ARG 0.006 0.000 ARG A 270 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 223 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 ILE cc_start: 0.8567 (mt) cc_final: 0.8343 (tp) REVERT: A 305 MET cc_start: 0.7472 (mmm) cc_final: 0.7127 (tpt) REVERT: A 361 TYR cc_start: 0.8819 (OUTLIER) cc_final: 0.7789 (m-10) REVERT: A 624 GLN cc_start: 0.7947 (tm-30) cc_final: 0.7745 (tm-30) REVERT: A 628 HIS cc_start: 0.7903 (t-90) cc_final: 0.7668 (t-170) REVERT: B 152 MET cc_start: 0.7242 (tpp) cc_final: 0.7021 (tpt) REVERT: B 361 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.7769 (m-80) REVERT: B 388 MET cc_start: 0.8570 (mmt) cc_final: 0.8305 (mmt) REVERT: B 512 MET cc_start: 0.8738 (ptp) cc_final: 0.8478 (ptp) REVERT: B 530 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.6910 (mtp) REVERT: B 632 MET cc_start: 0.3805 (mtm) cc_final: 0.3422 (tmm) REVERT: C 101 MET cc_start: 0.8327 (mtm) cc_final: 0.7952 (mtp) REVERT: C 336 MET cc_start: 0.8101 (ptp) cc_final: 0.7753 (ptm) REVERT: C 376 MET cc_start: 0.9087 (mmm) cc_final: 0.8304 (mmm) REVERT: C 512 MET cc_start: 0.8740 (ptp) cc_final: 0.8495 (ptp) REVERT: C 530 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.7152 (mtp) REVERT: C 624 GLN cc_start: 0.7791 (tm-30) cc_final: 0.7511 (tp40) REVERT: C 628 HIS cc_start: 0.7532 (t-90) cc_final: 0.7229 (t-170) REVERT: D 233 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.8080 (m-30) REVERT: D 361 TYR cc_start: 0.8891 (OUTLIER) cc_final: 0.7686 (m-80) REVERT: D 376 MET cc_start: 0.9134 (mmm) cc_final: 0.8480 (mmt) REVERT: D 388 MET cc_start: 0.8400 (mmt) cc_final: 0.8117 (mmt) REVERT: D 512 MET cc_start: 0.8742 (ptp) cc_final: 0.8486 (ptp) REVERT: D 530 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.6850 (mtp) REVERT: D 624 GLN cc_start: 0.7797 (tm-30) cc_final: 0.7565 (tp40) outliers start: 29 outliers final: 18 residues processed: 238 average time/residue: 0.2512 time to fit residues: 91.7756 Evaluate side-chains 241 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 216 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 361 TYR Chi-restraints excluded: chain D residue 530 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 155 optimal weight: 0.0980 chunk 24 optimal weight: 0.5980 chunk 46 optimal weight: 0.0770 chunk 168 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.130628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.100263 restraints weight = 30288.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.103577 restraints weight = 15769.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.105729 restraints weight = 10621.569| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16348 Z= 0.148 Angle : 0.558 7.885 22228 Z= 0.274 Chirality : 0.038 0.128 2548 Planarity : 0.003 0.044 2788 Dihedral : 6.807 131.778 2336 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.90 % Allowed : 20.60 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.19), residues: 2096 helix: 2.15 (0.13), residues: 1492 sheet: 0.92 (0.57), residues: 88 loop : -1.70 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 330 HIS 0.013 0.001 HIS B 628 PHE 0.013 0.001 PHE A 186 TYR 0.006 0.001 TYR D 347 ARG 0.004 0.000 ARG A 270 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2878.85 seconds wall clock time: 52 minutes 53.48 seconds (3173.48 seconds total)