Starting phenix.real_space_refine on Sat Mar 16 16:00:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsw_32769/03_2024/7wsw_32769_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsw_32769/03_2024/7wsw_32769.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsw_32769/03_2024/7wsw_32769.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsw_32769/03_2024/7wsw_32769.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsw_32769/03_2024/7wsw_32769_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsw_32769/03_2024/7wsw_32769_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 3 8.98 5 P 4 5.49 5 S 88 5.16 5 C 9802 2.51 5 N 2518 2.21 5 O 2636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 103": "OD1" <-> "OD2" Residue "B PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 103": "OD1" <-> "OD2" Residue "D PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 387": "OE1" <-> "OE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 337": "OD1" <-> "OD2" Residue "C PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15051 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3735 Classifications: {'peptide': 472} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 16, 'TRANS': 455} Chain breaks: 1 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 75 Chain: "B" Number of atoms: 3709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3709 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 16, 'TRANS': 445} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 34 Chain: "D" Number of atoms: 3709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3709 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 16, 'TRANS': 445} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3735 Classifications: {'peptide': 472} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 16, 'TRANS': 455} Chain breaks: 1 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 75 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' K': 3, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Time building chain proxies: 8.20, per 1000 atoms: 0.54 Number of scatterers: 15051 At special positions: 0 Unit cell: (107.167, 115.827, 132.065, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 3 19.00 S 88 16.00 P 4 15.00 O 2636 8.00 N 2518 7.00 C 9802 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.05 Conformation dependent library (CDL) restraints added in 3.1 seconds 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3580 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 78 helices and 8 sheets defined 60.3% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'A' and resid 7 through 13 Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.786A pdb=" N TRP A 60 " --> pdb=" O LYS A 56 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE A 63 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A 65 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL A 66 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 67 " --> pdb=" O PHE A 63 " (cutoff:3.500A) Proline residue: A 76 - end of helix Processing helix chain 'A' and resid 87 through 109 removed outlier: 4.204A pdb=" N THR A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N PHE A 109 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 135 removed outlier: 3.819A pdb=" N ARG A 133 " --> pdb=" O PHE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 143 removed outlier: 3.723A pdb=" N THR A 143 " --> pdb=" O ASP A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 152 Processing helix chain 'A' and resid 161 through 179 removed outlier: 3.597A pdb=" N ARG A 169 " --> pdb=" O TRP A 166 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG A 170 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 171 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 214 Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 236 through 251 Processing helix chain 'A' and resid 264 through 292 removed outlier: 3.787A pdb=" N GLY A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 314 removed outlier: 3.721A pdb=" N ASN A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE A 302 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 346 removed outlier: 3.515A pdb=" N LEU A 327 " --> pdb=" O GLN A 323 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER A 338 " --> pdb=" O TYR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 369 removed outlier: 3.765A pdb=" N SER A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N SER A 365 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LEU A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 387 removed outlier: 3.726A pdb=" N GLU A 387 " --> pdb=" O GLN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 493 removed outlier: 3.573A pdb=" N LYS A 493 " --> pdb=" O LEU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 509 Processing helix chain 'B' and resid 58 through 81 removed outlier: 3.776A pdb=" N VAL B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 67 " --> pdb=" O PHE B 63 " (cutoff:3.500A) Proline residue: B 76 - end of helix Processing helix chain 'B' and resid 87 through 109 removed outlier: 3.760A pdb=" N ILE B 91 " --> pdb=" O PRO B 87 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N THR B 92 " --> pdb=" O PRO B 88 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE B 108 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N PHE B 109 " --> pdb=" O ILE B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 131 No H-bonds generated for 'chain 'B' and resid 128 through 131' Processing helix chain 'B' and resid 136 through 143 removed outlier: 4.287A pdb=" N THR B 143 " --> pdb=" O ASP B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 152 removed outlier: 4.005A pdb=" N ARG B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 180 removed outlier: 3.836A pdb=" N LEU B 163 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG B 164 " --> pdb=" O PHE B 160 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N LEU B 165 " --> pdb=" O ASN B 161 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N TRP B 166 " --> pdb=" O MET B 162 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ARG B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LEU B 168 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ARG B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ARG B 170 " --> pdb=" O TRP B 166 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 214 removed outlier: 3.605A pdb=" N ALA B 192 " --> pdb=" O TRP B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'B' and resid 236 through 251 Processing helix chain 'B' and resid 264 through 295 removed outlier: 3.599A pdb=" N PHE B 272 " --> pdb=" O ILE B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 315 Processing helix chain 'B' and resid 320 through 335 removed outlier: 4.161A pdb=" N GLN B 325 " --> pdb=" O ARG B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 349 removed outlier: 4.287A pdb=" N GLN B 344 " --> pdb=" O GLY B 340 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ALA B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'B' and resid 365 through 369 removed outlier: 3.575A pdb=" N LYS B 369 " --> pdb=" O SER B 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 369' Processing helix chain 'B' and resid 380 through 387 Processing helix chain 'B' and resid 441 through 444 No H-bonds generated for 'chain 'B' and resid 441 through 444' Processing helix chain 'B' and resid 467 through 476 Processing helix chain 'B' and resid 478 through 491 removed outlier: 3.687A pdb=" N THR B 482 " --> pdb=" O VAL B 478 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE B 483 " --> pdb=" O GLY B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 508 removed outlier: 3.786A pdb=" N GLU B 508 " --> pdb=" O LEU B 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 81 removed outlier: 3.820A pdb=" N VAL D 66 " --> pdb=" O ALA D 62 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU D 67 " --> pdb=" O PHE D 63 " (cutoff:3.500A) Proline residue: D 76 - end of helix Processing helix chain 'D' and resid 87 through 109 removed outlier: 3.756A pdb=" N ILE D 91 " --> pdb=" O PRO D 87 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N THR D 92 " --> pdb=" O PRO D 88 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N PHE D 108 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N PHE D 109 " --> pdb=" O ILE D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 131 No H-bonds generated for 'chain 'D' and resid 128 through 131' Processing helix chain 'D' and resid 136 through 143 removed outlier: 4.287A pdb=" N THR D 143 " --> pdb=" O ASP D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 152 removed outlier: 4.004A pdb=" N ARG D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 179 removed outlier: 3.827A pdb=" N LEU D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG D 164 " --> pdb=" O PHE D 160 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N LEU D 165 " --> pdb=" O ASN D 161 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N TRP D 166 " --> pdb=" O MET D 162 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ARG D 167 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LEU D 168 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ARG D 169 " --> pdb=" O LEU D 165 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ARG D 170 " --> pdb=" O TRP D 166 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL D 171 " --> pdb=" O ARG D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 214 removed outlier: 3.597A pdb=" N ALA D 192 " --> pdb=" O TRP D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 233 No H-bonds generated for 'chain 'D' and resid 231 through 233' Processing helix chain 'D' and resid 236 through 251 Processing helix chain 'D' and resid 264 through 295 removed outlier: 3.600A pdb=" N PHE D 272 " --> pdb=" O ILE D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 315 Processing helix chain 'D' and resid 320 through 335 removed outlier: 4.164A pdb=" N GLN D 325 " --> pdb=" O ARG D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 349 removed outlier: 4.239A pdb=" N GLN D 344 " --> pdb=" O GLY D 340 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ALA D 349 " --> pdb=" O GLU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 362 Processing helix chain 'D' and resid 365 through 369 removed outlier: 3.609A pdb=" N LYS D 369 " --> pdb=" O SER D 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 365 through 369' Processing helix chain 'D' and resid 380 through 387 Processing helix chain 'D' and resid 441 through 444 No H-bonds generated for 'chain 'D' and resid 441 through 444' Processing helix chain 'D' and resid 467 through 476 Processing helix chain 'D' and resid 478 through 491 removed outlier: 3.663A pdb=" N THR D 482 " --> pdb=" O VAL D 478 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE D 483 " --> pdb=" O GLY D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 508 removed outlier: 3.721A pdb=" N GLU D 508 " --> pdb=" O LEU D 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 13 Processing helix chain 'C' and resid 55 through 81 removed outlier: 3.785A pdb=" N TRP C 60 " --> pdb=" O LYS C 56 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE C 63 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL C 66 " --> pdb=" O ALA C 62 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C 67 " --> pdb=" O PHE C 63 " (cutoff:3.500A) Proline residue: C 76 - end of helix Processing helix chain 'C' and resid 87 through 109 removed outlier: 4.202A pdb=" N THR C 92 " --> pdb=" O PRO C 88 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE C 108 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N PHE C 109 " --> pdb=" O ILE C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 135 removed outlier: 3.817A pdb=" N ARG C 133 " --> pdb=" O PHE C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 143 removed outlier: 3.727A pdb=" N THR C 143 " --> pdb=" O ASP C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 152 Processing helix chain 'C' and resid 161 through 179 removed outlier: 3.597A pdb=" N ARG C 169 " --> pdb=" O TRP C 166 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG C 170 " --> pdb=" O ARG C 167 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL C 171 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 214 Processing helix chain 'C' and resid 219 through 221 No H-bonds generated for 'chain 'C' and resid 219 through 221' Processing helix chain 'C' and resid 236 through 251 Processing helix chain 'C' and resid 264 through 292 removed outlier: 3.734A pdb=" N GLY C 279 " --> pdb=" O LEU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 314 removed outlier: 3.622A pdb=" N ASN C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N PHE C 302 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA C 309 " --> pdb=" O THR C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 346 Processing helix chain 'C' and resid 352 through 369 removed outlier: 3.761A pdb=" N SER C 357 " --> pdb=" O ALA C 353 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N SER C 365 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LEU C 366 " --> pdb=" O LEU C 362 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS C 369 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 387 removed outlier: 3.645A pdb=" N GLU C 387 " --> pdb=" O GLN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 446 Processing helix chain 'C' and resid 467 through 475 Processing helix chain 'C' and resid 481 through 493 removed outlier: 3.599A pdb=" N LYS C 493 " --> pdb=" O LEU C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 509 Processing sheet with id= A, first strand: chain 'A' and resid 390 through 393 removed outlier: 3.625A pdb=" N ASN A 414 " --> pdb=" O GLN A 461 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU A 463 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU A 412 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N MET A 465 " --> pdb=" O TYR A 410 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TYR A 410 " --> pdb=" O MET A 465 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 397 through 400 removed outlier: 3.753A pdb=" N GLU A 397 " --> pdb=" O THR A 456 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL A 454 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG A 431 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASP A 421 " --> pdb=" O ILE A 429 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE A 429 " --> pdb=" O ASP A 421 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 389 through 393 removed outlier: 3.502A pdb=" N ASN B 414 " --> pdb=" O GLN B 461 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU B 463 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU B 412 " --> pdb=" O LEU B 463 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N MET B 465 " --> pdb=" O TYR B 410 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N TYR B 410 " --> pdb=" O MET B 465 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP B 437 " --> pdb=" O LEU B 412 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 453 through 456 Processing sheet with id= E, first strand: chain 'D' and resid 389 through 393 removed outlier: 3.532A pdb=" N GLN D 461 " --> pdb=" O ASN D 414 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU D 463 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU D 412 " --> pdb=" O LEU D 463 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N MET D 465 " --> pdb=" O TYR D 410 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N TYR D 410 " --> pdb=" O MET D 465 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP D 437 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 453 through 456 Processing sheet with id= G, first strand: chain 'C' and resid 390 through 393 removed outlier: 3.573A pdb=" N ASN C 414 " --> pdb=" O GLN C 461 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU C 463 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU C 412 " --> pdb=" O LEU C 463 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N MET C 465 " --> pdb=" O TYR C 410 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N TYR C 410 " --> pdb=" O MET C 465 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 397 through 400 removed outlier: 3.754A pdb=" N GLU C 397 " --> pdb=" O THR C 456 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL C 454 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG C 431 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASP C 421 " --> pdb=" O ILE C 429 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE C 429 " --> pdb=" O ASP C 421 " (cutoff:3.500A) 765 hydrogen bonds defined for protein. 2181 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.37 Time building geometry restraints manager: 6.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2507 1.32 - 1.45: 4177 1.45 - 1.57: 8560 1.57 - 1.69: 8 1.69 - 1.82: 148 Bond restraints: 15400 Sorted by residual: bond pdb=" C5 PTY D 901 " pdb=" O14 PTY D 901 " ideal model delta sigma weight residual 1.409 1.454 -0.045 2.00e-02 2.50e+03 5.11e+00 bond pdb=" C5 PTY B 901 " pdb=" O14 PTY B 901 " ideal model delta sigma weight residual 1.409 1.454 -0.045 2.00e-02 2.50e+03 5.08e+00 bond pdb=" C5 PTY A 901 " pdb=" O14 PTY A 901 " ideal model delta sigma weight residual 1.409 1.453 -0.044 2.00e-02 2.50e+03 4.91e+00 bond pdb=" C5 PTY C 901 " pdb=" O14 PTY C 901 " ideal model delta sigma weight residual 1.409 1.453 -0.044 2.00e-02 2.50e+03 4.84e+00 bond pdb=" O14 PTY B 901 " pdb=" P1 PTY B 901 " ideal model delta sigma weight residual 1.646 1.605 0.041 2.00e-02 2.50e+03 4.21e+00 ... (remaining 15395 not shown) Histogram of bond angle deviations from ideal: 99.96 - 106.77: 375 106.77 - 113.59: 8403 113.59 - 120.40: 5938 120.40 - 127.22: 6032 127.22 - 134.03: 154 Bond angle restraints: 20902 Sorted by residual: angle pdb=" N ASP B 379 " pdb=" CA ASP B 379 " pdb=" C ASP B 379 " ideal model delta sigma weight residual 114.04 109.73 4.31 1.24e+00 6.50e-01 1.21e+01 angle pdb=" O11 PTY B 901 " pdb=" P1 PTY B 901 " pdb=" O14 PTY B 901 " ideal model delta sigma weight residual 92.90 102.99 -10.09 3.00e+00 1.11e-01 1.13e+01 angle pdb=" O11 PTY D 901 " pdb=" P1 PTY D 901 " pdb=" O14 PTY D 901 " ideal model delta sigma weight residual 92.90 102.97 -10.07 3.00e+00 1.11e-01 1.13e+01 angle pdb=" O11 PTY C 901 " pdb=" P1 PTY C 901 " pdb=" O14 PTY C 901 " ideal model delta sigma weight residual 92.90 102.96 -10.06 3.00e+00 1.11e-01 1.12e+01 angle pdb=" O11 PTY A 901 " pdb=" P1 PTY A 901 " pdb=" O14 PTY A 901 " ideal model delta sigma weight residual 92.90 102.96 -10.06 3.00e+00 1.11e-01 1.12e+01 ... (remaining 20897 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 8187 16.52 - 33.04: 800 33.04 - 49.56: 111 49.56 - 66.09: 29 66.09 - 82.61: 11 Dihedral angle restraints: 9138 sinusoidal: 3614 harmonic: 5524 Sorted by residual: dihedral pdb=" CA MET B 495 " pdb=" C MET B 495 " pdb=" N ASN B 496 " pdb=" CA ASN B 496 " ideal model delta harmonic sigma weight residual 180.00 160.92 19.08 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA GLU B 494 " pdb=" C GLU B 494 " pdb=" N MET B 495 " pdb=" CA MET B 495 " ideal model delta harmonic sigma weight residual -180.00 -162.13 -17.87 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA GLN B 126 " pdb=" C GLN B 126 " pdb=" N ILE B 127 " pdb=" CA ILE B 127 " ideal model delta harmonic sigma weight residual 180.00 162.56 17.44 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 9135 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1873 0.044 - 0.088: 434 0.088 - 0.132: 69 0.132 - 0.176: 2 0.176 - 0.220: 2 Chirality restraints: 2380 Sorted by residual: chirality pdb=" C6 PTY D 901 " pdb=" C1 PTY D 901 " pdb=" C5 PTY D 901 " pdb=" O7 PTY D 901 " both_signs ideal model delta sigma weight residual False 2.49 2.27 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C6 PTY B 901 " pdb=" C1 PTY B 901 " pdb=" C5 PTY B 901 " pdb=" O7 PTY B 901 " both_signs ideal model delta sigma weight residual False 2.49 2.27 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ILE C 144 " pdb=" N ILE C 144 " pdb=" C ILE C 144 " pdb=" CB ILE C 144 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 ... (remaining 2377 not shown) Planarity restraints: 2612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 497 " 0.049 5.00e-02 4.00e+02 7.40e-02 8.76e+00 pdb=" N PRO A 498 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 498 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 498 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 87 " 0.041 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO D 88 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO D 88 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 88 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 87 " -0.040 5.00e-02 4.00e+02 6.13e-02 6.00e+00 pdb=" N PRO B 88 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 88 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 88 " -0.034 5.00e-02 4.00e+02 ... (remaining 2609 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.75: 1677 2.75 - 3.35: 18413 3.35 - 3.94: 28138 3.94 - 4.54: 38256 4.54 - 5.14: 57304 Nonbonded interactions: 143788 Sorted by model distance: nonbonded pdb=" OD2 ASP A 379 " pdb=" OH TYR B 447 " model vdw 2.149 2.440 nonbonded pdb=" OH TYR D 447 " pdb=" OD2 ASP C 379 " model vdw 2.150 2.440 nonbonded pdb=" OG SER A 377 " pdb=" OD1 ASP A 379 " model vdw 2.204 2.440 nonbonded pdb=" O TYR A 273 " pdb=" ND2 ASN A 277 " model vdw 2.213 2.520 nonbonded pdb=" OH TYR A 70 " pdb=" OG1 THR A 92 " model vdw 2.222 2.440 ... (remaining 143783 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' and (resid 49 through 113 or (resid 114 through 115 and (name N or na \ me CA or name C or name O or name CB )) or resid 116 or (resid 117 through 120 a \ nd (name N or name CA or name C or name O or name CB )) or resid 121 or (resid 1 \ 22 and (name N or name CA or name C or name O or name CB )) or resid 123 through \ 336 or (resid 337 and (name N or name CA or name C or name O or name CB )) or r \ esid 338 through 341 or (resid 342 and (name N or name CA or name C or name O or \ name CB )) or resid 343 or (resid 344 through 345 and (name N or name CA or nam \ e C or name O or name CB )) or resid 346 through 395 or (resid 396 and (name N o \ r name CA or name C or name O or name CB )) or resid 397 through 510 or resid 90 \ 1)) selection = (chain 'B' and (resid 49 through 300 or (resid 301 and (name N or name CA or nam \ e C or name O or name CB )) or resid 302 through 313 or (resid 314 through 318 a \ nd (name N or name CA or name C or name O or name CB )) or resid 319 through 320 \ or (resid 321 and (name N or name CA or name C or name O or name CB )) or resid \ 322 through 323 or (resid 324 and (name N or name CA or name C or name O or nam \ e CB )) or resid 325 through 425 or (resid 426 through 427 and (name N or name C \ A or name C or name O or name CB )) or resid 428 through 499 or (resid 500 and ( \ name N or name CA or name C or name O or name CB )) or resid 501 through 503 or \ (resid 504 and (name N or name CA or name C or name O or name CB )) or resid 505 \ or (resid 506 through 510 and (name N or name CA or name C or name O or name CB \ )) or resid 901)) selection = (chain 'C' and (resid 49 through 113 or (resid 114 through 115 and (name N or na \ me CA or name C or name O or name CB )) or resid 116 or (resid 117 through 120 a \ nd (name N or name CA or name C or name O or name CB )) or resid 121 or (resid 1 \ 22 and (name N or name CA or name C or name O or name CB )) or resid 123 through \ 336 or (resid 337 and (name N or name CA or name C or name O or name CB )) or r \ esid 338 through 341 or (resid 342 and (name N or name CA or name C or name O or \ name CB )) or resid 343 or (resid 344 through 345 and (name N or name CA or nam \ e C or name O or name CB )) or resid 346 through 395 or (resid 396 and (name N o \ r name CA or name C or name O or name CB )) or resid 397 through 510 or resid 90 \ 1)) selection = (chain 'D' and (resid 49 through 300 or (resid 301 and (name N or name CA or nam \ e C or name O or name CB )) or resid 302 through 313 or (resid 314 through 318 a \ nd (name N or name CA or name C or name O or name CB )) or resid 319 through 320 \ or (resid 321 and (name N or name CA or name C or name O or name CB )) or resid \ 322 through 323 or (resid 324 and (name N or name CA or name C or name O or nam \ e CB )) or resid 325 through 425 or (resid 426 through 427 and (name N or name C \ A or name C or name O or name CB )) or resid 428 through 499 or (resid 500 and ( \ name N or name CA or name C or name O or name CB )) or resid 501 through 503 or \ (resid 504 and (name N or name CA or name C or name O or name CB )) or resid 505 \ or (resid 506 through 510 and (name N or name CA or name C or name O or name CB \ )) or resid 901)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 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: 7.640 Check model and map are aligned: 0.310 Set scattering table: 0.170 Process input model: 42.050 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 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 : 0.003 0.045 15400 Z= 0.190 Angle : 0.550 10.091 20902 Z= 0.287 Chirality : 0.038 0.220 2380 Planarity : 0.004 0.074 2612 Dihedral : 13.261 82.608 5558 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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: 0.70 (0.20), residues: 1856 helix: 1.60 (0.16), residues: 1110 sheet: 0.59 (0.54), residues: 84 loop : -1.59 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 135 HIS 0.008 0.001 HIS C 491 PHE 0.008 0.001 PHE D 409 TYR 0.018 0.001 TYR D 209 ARG 0.009 0.000 ARG D 458 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.906 Fit side-chains REVERT: A 59 ILE cc_start: 0.9397 (tt) cc_final: 0.9120 (tp) REVERT: A 238 MET cc_start: 0.7626 (tmm) cc_final: 0.7359 (ttt) REVERT: C 59 ILE cc_start: 0.9389 (tt) cc_final: 0.9121 (tp) REVERT: C 238 MET cc_start: 0.7642 (tmm) cc_final: 0.7372 (ttt) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2463 time to fit residues: 47.6789 Evaluate side-chains 104 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 145 optimal weight: 4.9990 chunk 56 optimal weight: 0.0170 chunk 88 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 overall best weight: 1.4022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15400 Z= 0.202 Angle : 0.503 7.307 20902 Z= 0.260 Chirality : 0.039 0.137 2380 Planarity : 0.004 0.060 2612 Dihedral : 5.554 57.375 2188 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.51 % Allowed : 4.63 % Favored : 94.86 % 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: 0.62 (0.20), residues: 1856 helix: 1.48 (0.16), residues: 1138 sheet: 0.82 (0.58), residues: 64 loop : -1.60 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 60 HIS 0.004 0.001 HIS A 294 PHE 0.017 0.001 PHE D 160 TYR 0.014 0.001 TYR C 209 ARG 0.010 0.000 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 1.708 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 115 average time/residue: 0.2380 time to fit residues: 42.9191 Evaluate side-chains 107 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain C residue 60 TRP Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 169 optimal weight: 10.0000 chunk 182 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 135 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN A 491 HIS ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 15400 Z= 0.379 Angle : 0.594 7.329 20902 Z= 0.310 Chirality : 0.042 0.162 2380 Planarity : 0.005 0.060 2612 Dihedral : 6.381 56.682 2188 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.82 % Allowed : 9.45 % Favored : 89.72 % 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: 0.39 (0.20), residues: 1856 helix: 1.27 (0.16), residues: 1128 sheet: 0.48 (0.58), residues: 64 loop : -1.55 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 135 HIS 0.007 0.001 HIS A 294 PHE 0.022 0.001 PHE B 160 TYR 0.012 0.002 TYR B 210 ARG 0.006 0.001 ARG D 455 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 1.912 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 112 average time/residue: 0.2414 time to fit residues: 42.6685 Evaluate side-chains 107 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain C residue 60 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 0.0970 chunk 127 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 18 optimal weight: 0.2980 chunk 80 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 169 optimal weight: 0.9980 chunk 179 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15400 Z= 0.132 Angle : 0.482 7.857 20902 Z= 0.248 Chirality : 0.037 0.146 2380 Planarity : 0.004 0.061 2612 Dihedral : 5.744 58.068 2188 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.51 % Allowed : 11.23 % Favored : 88.26 % 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: 0.74 (0.21), residues: 1856 helix: 1.64 (0.16), residues: 1126 sheet: 0.43 (0.57), residues: 64 loop : -1.56 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 60 HIS 0.003 0.001 HIS A 294 PHE 0.008 0.001 PHE A 409 TYR 0.014 0.001 TYR D 210 ARG 0.002 0.000 ARG D 458 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 1.485 Fit side-chains REVERT: D 376 VAL cc_start: 0.7822 (OUTLIER) cc_final: 0.7588 (p) outliers start: 8 outliers final: 4 residues processed: 114 average time/residue: 0.2414 time to fit residues: 43.3820 Evaluate side-chains 107 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain C residue 60 TRP Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 91 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 HIS ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15400 Z= 0.213 Angle : 0.505 8.049 20902 Z= 0.259 Chirality : 0.038 0.148 2380 Planarity : 0.004 0.061 2612 Dihedral : 5.778 58.241 2188 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.57 % Allowed : 12.63 % Favored : 86.80 % 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 (0.20), residues: 1856 helix: 1.69 (0.16), residues: 1120 sheet: 0.54 (0.58), residues: 64 loop : -1.59 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 60 HIS 0.004 0.001 HIS A 294 PHE 0.009 0.001 PHE A 269 TYR 0.014 0.001 TYR D 210 ARG 0.005 0.000 ARG C 300 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 1.873 Fit side-chains REVERT: A 485 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.6736 (mpp) outliers start: 9 outliers final: 4 residues processed: 109 average time/residue: 0.2436 time to fit residues: 41.7470 Evaluate side-chains 104 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain C residue 60 TRP Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 0.6980 chunk 161 optimal weight: 0.0980 chunk 35 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 44 optimal weight: 0.0770 chunk 179 optimal weight: 3.9990 chunk 149 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15400 Z= 0.123 Angle : 0.472 8.169 20902 Z= 0.240 Chirality : 0.037 0.137 2380 Planarity : 0.004 0.061 2612 Dihedral : 5.280 50.686 2188 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.51 % Allowed : 13.32 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.21), residues: 1856 helix: 1.83 (0.16), residues: 1120 sheet: 0.46 (0.58), residues: 64 loop : -1.48 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 60 HIS 0.002 0.001 HIS A 491 PHE 0.019 0.001 PHE B 160 TYR 0.013 0.001 TYR D 210 ARG 0.002 0.000 ARG B 448 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 1.779 Fit side-chains REVERT: D 382 PHE cc_start: 0.8341 (t80) cc_final: 0.8123 (t80) outliers start: 8 outliers final: 5 residues processed: 114 average time/residue: 0.2268 time to fit residues: 41.4326 Evaluate side-chains 106 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 101 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 456 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 101 optimal weight: 0.2980 chunk 151 optimal weight: 3.9990 chunk 100 optimal weight: 0.0470 chunk 179 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.2684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15400 Z= 0.189 Angle : 0.491 7.743 20902 Z= 0.251 Chirality : 0.038 0.140 2380 Planarity : 0.004 0.061 2612 Dihedral : 5.307 46.661 2188 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.08 % Allowed : 13.83 % Favored : 85.09 % 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 (0.21), residues: 1856 helix: 1.82 (0.16), residues: 1120 sheet: 0.56 (0.59), residues: 64 loop : -1.46 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 60 HIS 0.003 0.001 HIS A 294 PHE 0.019 0.001 PHE D 160 TYR 0.013 0.001 TYR D 210 ARG 0.005 0.000 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 1.812 Fit side-chains REVERT: A 485 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.6669 (mpp) REVERT: D 382 PHE cc_start: 0.8372 (t80) cc_final: 0.8144 (t80) outliers start: 17 outliers final: 11 residues processed: 116 average time/residue: 0.2376 time to fit residues: 43.7522 Evaluate side-chains 113 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain C residue 60 TRP Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 chunk 54 optimal weight: 0.1980 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 140 optimal weight: 0.0020 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15400 Z= 0.142 Angle : 0.478 7.823 20902 Z= 0.243 Chirality : 0.037 0.131 2380 Planarity : 0.004 0.062 2612 Dihedral : 5.163 45.144 2188 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.02 % Allowed : 14.02 % Favored : 84.96 % 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: 1.01 (0.21), residues: 1856 helix: 1.85 (0.16), residues: 1120 sheet: 0.55 (0.59), residues: 64 loop : -1.43 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 60 HIS 0.002 0.001 HIS A 294 PHE 0.008 0.001 PHE A 409 TYR 0.013 0.001 TYR D 210 ARG 0.003 0.000 ARG C 300 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 1.815 Fit side-chains REVERT: A 485 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.6649 (mpp) REVERT: D 382 PHE cc_start: 0.8355 (t80) cc_final: 0.8131 (t80) outliers start: 16 outliers final: 12 residues processed: 118 average time/residue: 0.2294 time to fit residues: 43.2032 Evaluate side-chains 115 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain C residue 60 TRP Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 0.6980 chunk 171 optimal weight: 8.9990 chunk 156 optimal weight: 0.4980 chunk 167 optimal weight: 2.9990 chunk 100 optimal weight: 0.0020 chunk 72 optimal weight: 0.8980 chunk 131 optimal weight: 0.0010 chunk 51 optimal weight: 4.9990 chunk 150 optimal weight: 0.5980 chunk 158 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 15400 Z= 0.124 Angle : 0.478 8.591 20902 Z= 0.242 Chirality : 0.037 0.129 2380 Planarity : 0.004 0.063 2612 Dihedral : 4.872 40.014 2188 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.70 % Allowed : 14.02 % Favored : 85.28 % 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: 0.93 (0.21), residues: 1856 helix: 1.84 (0.16), residues: 1114 sheet: 0.52 (0.59), residues: 64 loop : -1.53 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 60 HIS 0.002 0.001 HIS D 491 PHE 0.008 0.001 PHE A 409 TYR 0.012 0.001 TYR B 210 ARG 0.002 0.000 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 1.922 Fit side-chains REVERT: A 485 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.6669 (mpp) REVERT: D 382 PHE cc_start: 0.8313 (t80) cc_final: 0.8092 (t80) outliers start: 11 outliers final: 9 residues processed: 120 average time/residue: 0.2284 time to fit residues: 44.0911 Evaluate side-chains 114 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain C residue 60 TRP Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 147 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15400 Z= 0.279 Angle : 0.540 8.249 20902 Z= 0.276 Chirality : 0.040 0.136 2380 Planarity : 0.004 0.063 2612 Dihedral : 5.412 51.175 2188 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.82 % Allowed : 14.53 % Favored : 84.64 % 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: 0.92 (0.21), residues: 1856 helix: 1.74 (0.16), residues: 1122 sheet: 0.67 (0.61), residues: 64 loop : -1.41 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 60 HIS 0.003 0.001 HIS A 294 PHE 0.015 0.001 PHE A 452 TYR 0.012 0.001 TYR D 210 ARG 0.003 0.000 ARG B 448 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 1.808 Fit side-chains REVERT: A 485 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.6608 (mpp) REVERT: D 382 PHE cc_start: 0.8407 (t80) cc_final: 0.8149 (t80) outliers start: 13 outliers final: 10 residues processed: 112 average time/residue: 0.2345 time to fit residues: 41.9333 Evaluate side-chains 114 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain C residue 60 TRP Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 45 optimal weight: 0.0040 chunk 136 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 147 optimal weight: 0.0170 chunk 61 optimal weight: 5.9990 chunk 151 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.7232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.092771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.069523 restraints weight = 38849.097| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.59 r_work: 0.2950 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15400 Z= 0.143 Angle : 0.494 8.299 20902 Z= 0.250 Chirality : 0.037 0.130 2380 Planarity : 0.004 0.063 2612 Dihedral : 5.167 48.924 2188 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.82 % Allowed : 14.72 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.21), residues: 1856 helix: 1.74 (0.16), residues: 1126 sheet: 0.58 (0.61), residues: 64 loop : -1.47 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 60 HIS 0.002 0.001 HIS A 294 PHE 0.021 0.001 PHE C 452 TYR 0.012 0.001 TYR B 210 ARG 0.003 0.000 ARG C 300 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2708.48 seconds wall clock time: 49 minutes 58.00 seconds (2998.00 seconds total)