Starting phenix.real_space_refine on Thu Nov 16 16:45:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqg_20847/11_2023/6uqg_20847_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqg_20847/11_2023/6uqg_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_20847/11_2023/6uqg_20847.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqg_20847/11_2023/6uqg_20847.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqg_20847/11_2023/6uqg_20847_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqg_20847/11_2023/6uqg_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-1.21rc1-5144/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: 9.37, per 1000 atoms: 0.59 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: 6.31 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: 3.77 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: 5.04 Time building geometry restraints manager: 6.89 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: 1.970 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: 0.020 Extract box with map and model: 7.860 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 45.950 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.090 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.160 ------------------------------------------------------------------------------- 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 *********************** 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 : 1.947 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.2846 time to fit residues: 122.1183 Evaluate side-chains 221 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.618 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4256 ------------------------------------------------------------------------------- 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: 3.9990 chunk 89 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 chunk 85 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 GLN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN B 517 HIS B 628 HIS C 416 GLN ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16348 Z= 0.192 Angle : 0.576 9.609 22228 Z= 0.295 Chirality : 0.039 0.184 2548 Planarity : 0.005 0.056 2788 Dihedral : 8.111 146.605 2336 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.24 % Allowed : 12.40 % Favored : 85.37 % 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: -0.96 (0.17), residues: 2096 helix: 0.18 (0.12), residues: 1520 sheet: -1.84 (0.38), residues: 140 loop : -2.83 (0.24), residues: 436 *********************** 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 271 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 238 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 18 residues processed: 257 average time/residue: 0.2626 time to fit residues: 101.6202 Evaluate side-chains 231 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 213 time to evaluate : 1.872 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1461 time to fit residues: 7.3579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 160 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 53 optimal weight: 20.0000 chunk 192 optimal weight: 1.9990 chunk 208 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 chunk 191 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 154 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 ASN ** 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 156 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16348 Z= 0.227 Angle : 0.570 8.708 22228 Z= 0.291 Chirality : 0.040 0.128 2548 Planarity : 0.004 0.047 2788 Dihedral : 7.525 138.491 2336 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.54 % Allowed : 16.19 % Favored : 83.27 % 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: 0.15 (0.18), residues: 2096 helix: 0.99 (0.13), residues: 1520 sheet: -0.12 (0.51), residues: 88 loop : -2.67 (0.24), residues: 488 *********************** 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 242 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 234 time to evaluate : 1.898 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 234 average time/residue: 0.2669 time to fit residues: 94.7148 Evaluate side-chains 214 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 209 time to evaluate : 1.830 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1646 time to fit residues: 4.1073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 chunk 100 optimal weight: 0.0670 chunk 21 optimal weight: 0.2980 chunk 92 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 193 optimal weight: 0.0670 chunk 204 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- 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: 0.7699 moved from start: 0.2521 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= 0.140 Angle : 0.520 7.687 22228 Z= 0.261 Chirality : 0.038 0.124 2548 Planarity : 0.003 0.040 2788 Dihedral : 7.110 134.359 2336 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.42 % Allowed : 16.80 % Favored : 81.78 % 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: 0.77 (0.18), residues: 2096 helix: 1.43 (0.13), residues: 1520 sheet: 0.36 (0.57), residues: 88 loop : -2.46 (0.25), residues: 488 *********************** 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 265 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 244 time to evaluate : 2.018 Fit side-chains outliers start: 21 outliers final: 11 residues processed: 253 average time/residue: 0.2544 time to fit residues: 98.8878 Evaluate side-chains 214 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 203 time to evaluate : 1.837 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1568 time to fit residues: 5.4126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0570 chunk 2 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 174 optimal weight: 0.9990 chunk 141 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 104 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 overall best weight: 0.9304 ------------------------------------------------------------------------------- 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 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: 0.7723 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16348 Z= 0.180 Angle : 0.546 8.198 22228 Z= 0.273 Chirality : 0.039 0.125 2548 Planarity : 0.003 0.038 2788 Dihedral : 7.041 133.696 2336 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.02 % Allowed : 18.56 % Favored : 80.42 % 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: 1.10 (0.19), residues: 2096 helix: 1.65 (0.13), residues: 1520 sheet: 0.65 (0.58), residues: 88 loop : -2.30 (0.25), residues: 488 *********************** 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 239 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 224 time to evaluate : 1.961 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 231 average time/residue: 0.2616 time to fit residues: 92.6871 Evaluate side-chains 211 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 205 time to evaluate : 1.982 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1461 time to fit residues: 4.0515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 4.9990 chunk 184 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 205 optimal weight: 3.9990 chunk 170 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 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: 0.7790 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16348 Z= 0.323 Angle : 0.626 8.158 22228 Z= 0.317 Chirality : 0.041 0.131 2548 Planarity : 0.004 0.042 2788 Dihedral : 7.202 133.967 2336 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.56 % Allowed : 18.63 % Favored : 79.81 % 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: 1.12 (0.18), residues: 2096 helix: 1.69 (0.13), residues: 1496 sheet: 0.72 (0.54), residues: 88 loop : -2.17 (0.24), residues: 512 *********************** 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 244 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 221 time to evaluate : 1.899 Fit side-chains outliers start: 23 outliers final: 8 residues processed: 230 average time/residue: 0.2572 time to fit residues: 91.0230 Evaluate side-chains 216 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 208 time to evaluate : 2.021 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1537 time to fit residues: 4.8073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 0.9990 chunk 23 optimal weight: 0.0030 chunk 116 optimal weight: 0.0010 chunk 149 optimal weight: 2.9990 chunk 172 optimal weight: 0.0370 chunk 114 optimal weight: 0.9980 chunk 204 optimal weight: 0.9980 chunk 127 optimal weight: 0.0030 chunk 124 optimal weight: 0.0370 chunk 94 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 overall best weight: 0.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 628 HIS ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16348 Z= 0.134 Angle : 0.538 8.059 22228 Z= 0.266 Chirality : 0.037 0.129 2548 Planarity : 0.004 0.048 2788 Dihedral : 6.860 131.925 2336 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.81 % Allowed : 19.65 % Favored : 79.54 % 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: 1.46 (0.19), residues: 2096 helix: 1.90 (0.13), residues: 1512 sheet: 0.84 (0.58), residues: 88 loop : -2.07 (0.25), residues: 496 *********************** 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 265 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 253 time to evaluate : 2.027 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 260 average time/residue: 0.2471 time to fit residues: 99.7218 Evaluate side-chains 223 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 220 time to evaluate : 1.841 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1293 time to fit residues: 3.3546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 chunk 129 optimal weight: 0.0020 chunk 139 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 185 optimal weight: 1.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 628 HIS ** 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 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 HIS ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16348 Z= 0.157 Angle : 0.562 8.727 22228 Z= 0.274 Chirality : 0.038 0.123 2548 Planarity : 0.003 0.043 2788 Dihedral : 6.843 132.205 2336 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.42 % Allowed : 20.39 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.19), residues: 2096 helix: 2.01 (0.13), residues: 1508 sheet: 0.85 (0.58), residues: 88 loop : -1.99 (0.26), residues: 500 *********************** 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 245 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 224 time to evaluate : 1.946 Fit side-chains outliers start: 21 outliers final: 8 residues processed: 230 average time/residue: 0.2455 time to fit residues: 88.2599 Evaluate side-chains 224 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 216 time to evaluate : 1.955 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1520 time to fit residues: 4.8556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 190 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 172 optimal weight: 0.5980 chunk 180 optimal weight: 0.3980 chunk 189 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 628 HIS ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 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** C 628 HIS ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16348 Z= 0.178 Angle : 0.573 9.044 22228 Z= 0.280 Chirality : 0.039 0.143 2548 Planarity : 0.003 0.042 2788 Dihedral : 6.839 132.238 2336 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.47 % Allowed : 20.60 % Favored : 78.93 % 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: 1.74 (0.19), residues: 2096 helix: 2.09 (0.13), residues: 1512 sheet: 0.86 (0.58), residues: 88 loop : -1.87 (0.27), residues: 496 *********************** 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 227 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 220 time to evaluate : 2.017 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 222 average time/residue: 0.2523 time to fit residues: 87.7015 Evaluate side-chains 216 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 213 time to evaluate : 1.769 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1502 time to fit residues: 3.2465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 0.9980 chunk 122 optimal weight: 0.1980 chunk 95 optimal weight: 0.8980 chunk 139 optimal weight: 0.5980 chunk 211 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 129 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 133 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 628 HIS ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 517 HIS B 628 HIS ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16348 Z= 0.164 Angle : 0.575 9.672 22228 Z= 0.280 Chirality : 0.038 0.165 2548 Planarity : 0.003 0.042 2788 Dihedral : 6.809 131.921 2336 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.41 % Allowed : 21.41 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.19), residues: 2096 helix: 2.14 (0.13), residues: 1508 sheet: 0.79 (0.57), residues: 88 loop : -1.76 (0.27), residues: 500 ********************** 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 226 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 220 time to evaluate : 2.062 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 221 average time/residue: 0.2566 time to fit residues: 88.4918 Evaluate side-chains 219 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 218 time to evaluate : 1.957 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1568 time to fit residues: 2.9848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 155 optimal weight: 0.1980 chunk 24 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 517 HIS A 628 HIS ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 HIS ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.129365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.099711 restraints weight = 30446.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.102975 restraints weight = 15882.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.105031 restraints weight = 10645.779| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16348 Z= 0.174 Angle : 0.581 9.126 22228 Z= 0.282 Chirality : 0.038 0.132 2548 Planarity : 0.003 0.041 2788 Dihedral : 6.811 131.920 2336 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.88 % Allowed : 20.73 % Favored : 78.39 % 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: 1.89 (0.19), residues: 2096 helix: 2.17 (0.13), residues: 1512 sheet: 0.79 (0.57), residues: 88 loop : -1.70 (0.27), residues: 496 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2934.91 seconds wall clock time: 54 minutes 10.74 seconds (3250.74 seconds total)