Starting phenix.real_space_refine on Fri Feb 16 04:55:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vum_21390/02_2024/6vum_21390_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vum_21390/02_2024/6vum_21390.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vum_21390/02_2024/6vum_21390_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vum_21390/02_2024/6vum_21390_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vum_21390/02_2024/6vum_21390_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vum_21390/02_2024/6vum_21390.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vum_21390/02_2024/6vum_21390.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vum_21390/02_2024/6vum_21390_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vum_21390/02_2024/6vum_21390_updated.pdb" } resolution = 3.67 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 72 5.16 5 C 9868 2.51 5 N 2188 2.21 5 O 2248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 170": "OE1" <-> "OE2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A ARG 314": "NH1" <-> "NH2" Residue "A ARG 350": "NH1" <-> "NH2" Residue "A GLU 394": "OE1" <-> "OE2" Residue "B GLU 164": "OE1" <-> "OE2" Residue "B GLU 273": "OE1" <-> "OE2" Residue "B GLU 284": "OE1" <-> "OE2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "B ARG 350": "NH1" <-> "NH2" Residue "B GLU 394": "OE1" <-> "OE2" Residue "B ARG 397": "NH1" <-> "NH2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C GLU 259": "OE1" <-> "OE2" Residue "C GLU 273": "OE1" <-> "OE2" Residue "C GLU 284": "OE1" <-> "OE2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "C ARG 350": "NH1" <-> "NH2" Residue "C GLU 394": "OE1" <-> "OE2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D GLU 273": "OE1" <-> "OE2" Residue "D GLU 284": "OE1" <-> "OE2" Residue "D ARG 314": "NH1" <-> "NH2" Residue "D ARG 350": "NH1" <-> "NH2" Residue "D GLU 394": "OE1" <-> "OE2" Residue "D ARG 397": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14388 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3423 Classifications: {'peptide': 409} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 17, 'TRANS': 391} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3423 Classifications: {'peptide': 409} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 17, 'TRANS': 391} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3423 Classifications: {'peptide': 409} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 17, 'TRANS': 391} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3423 Classifications: {'peptide': 409} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 17, 'TRANS': 391} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 183 Unusual residues: {'CLR': 3, 'COA': 1, 'OLA': 1, 'ROV': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 165 Unusual residues: {'3VV': 1, 'CLR': 2, 'OLA': 1, 'ROV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'3VV:plan-5': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 183 Unusual residues: {'CLR': 3, 'COA': 1, 'OLA': 1, 'ROV': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 165 Unusual residues: {'3VV': 1, 'CLR': 2, 'OLA': 1, 'ROV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'3VV:plan-5': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 8.06, per 1000 atoms: 0.56 Number of scatterers: 14388 At special positions: 0 Unit cell: (109.956, 205.751, 78.302, 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 72 16.00 P 12 15.00 O 2248 8.00 N 2188 7.00 C 9868 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: 5.38 Conformation dependent library (CDL) restraints added in 2.3 seconds 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3152 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 0 sheets defined 67.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'A' and resid 128 through 134 removed outlier: 4.353A pdb=" N GLU A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 163 Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 182 through 206 removed outlier: 3.727A pdb=" N THR A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE A 190 " --> pdb=" O TRP A 186 " (cutoff:3.500A) Proline residue: A 199 - end of helix removed outlier: 4.097A pdb=" N TRP A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 212 No H-bonds generated for 'chain 'A' and resid 209 through 212' Processing helix chain 'A' and resid 219 through 233 Processing helix chain 'A' and resid 238 through 245 Processing helix chain 'A' and resid 253 through 283 Proline residue: A 276 - end of helix Processing helix chain 'A' and resid 295 through 302 removed outlier: 5.796A pdb=" N PHE A 300 " --> pdb=" O GLN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 343 removed outlier: 3.631A pdb=" N GLU A 342 " --> pdb=" O TYR A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 361 through 384 removed outlier: 4.342A pdb=" N LEU A 371 " --> pdb=" O PHE A 367 " (cutoff:3.500A) Proline residue: A 372 - end of helix removed outlier: 3.886A pdb=" N LEU A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 384 " --> pdb=" O THR A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 416 through 420 Processing helix chain 'A' and resid 422 through 431 Processing helix chain 'A' and resid 433 through 439 Processing helix chain 'A' and resid 447 through 467 removed outlier: 3.993A pdb=" N CYS A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 488 removed outlier: 3.548A pdb=" N PHE A 482 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 485 " --> pdb=" O PHE A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 524 removed outlier: 3.525A pdb=" N VAL A 501 " --> pdb=" O PRO A 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 134 removed outlier: 4.408A pdb=" N GLU B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 163 Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 181 through 207 Proline residue: B 199 - end of helix removed outlier: 3.941A pdb=" N TRP B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA B 207 " --> pdb=" O PHE B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 235 Processing helix chain 'B' and resid 238 through 245 Processing helix chain 'B' and resid 250 through 281 removed outlier: 3.737A pdb=" N PHE B 254 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE B 256 " --> pdb=" O SER B 252 " (cutoff:3.500A) Proline residue: B 276 - end of helix Processing helix chain 'B' and resid 294 through 302 removed outlier: 3.561A pdb=" N PHE B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 343 Processing helix chain 'B' and resid 361 through 384 removed outlier: 4.442A pdb=" N LEU B 371 " --> pdb=" O PHE B 367 " (cutoff:3.500A) Proline residue: B 372 - end of helix removed outlier: 3.679A pdb=" N LEU B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE B 384 " --> pdb=" O THR B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 395 Processing helix chain 'B' and resid 416 through 419 No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 431 Processing helix chain 'B' and resid 433 through 439 Processing helix chain 'B' and resid 447 through 468 removed outlier: 3.753A pdb=" N CYS B 467 " --> pdb=" O ALA B 463 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 488 removed outlier: 3.741A pdb=" N PHE B 482 " --> pdb=" O LEU B 478 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN B 487 " --> pdb=" O GLY B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 525 removed outlier: 3.799A pdb=" N THR B 505 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU B 507 " --> pdb=" O TRP B 504 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 509 " --> pdb=" O SER B 506 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 510 " --> pdb=" O LEU B 507 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN B 511 " --> pdb=" O PHE B 508 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 513 " --> pdb=" O GLY B 510 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B 515 " --> pdb=" O GLY B 512 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS B 516 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR B 518 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 519 " --> pdb=" O CYS B 516 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN B 520 " --> pdb=" O PHE B 517 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TRP B 522 " --> pdb=" O SER B 519 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR B 523 " --> pdb=" O GLN B 520 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 524 " --> pdb=" O GLU B 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 134 removed outlier: 4.353A pdb=" N GLU C 134 " --> pdb=" O ASP C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 163 Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 182 through 206 removed outlier: 3.727A pdb=" N THR C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE C 190 " --> pdb=" O TRP C 186 " (cutoff:3.500A) Proline residue: C 199 - end of helix removed outlier: 4.096A pdb=" N TRP C 206 " --> pdb=" O LEU C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 212 No H-bonds generated for 'chain 'C' and resid 209 through 212' Processing helix chain 'C' and resid 219 through 233 Processing helix chain 'C' and resid 238 through 245 Processing helix chain 'C' and resid 253 through 283 Proline residue: C 276 - end of helix Processing helix chain 'C' and resid 295 through 302 removed outlier: 5.797A pdb=" N PHE C 300 " --> pdb=" O GLN C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 343 removed outlier: 3.631A pdb=" N GLU C 342 " --> pdb=" O TYR C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 361 through 384 removed outlier: 4.343A pdb=" N LEU C 371 " --> pdb=" O PHE C 367 " (cutoff:3.500A) Proline residue: C 372 - end of helix removed outlier: 3.887A pdb=" N LEU C 375 " --> pdb=" O LEU C 371 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE C 384 " --> pdb=" O THR C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 395 Processing helix chain 'C' and resid 416 through 420 Processing helix chain 'C' and resid 422 through 431 Processing helix chain 'C' and resid 433 through 439 Processing helix chain 'C' and resid 447 through 467 removed outlier: 3.993A pdb=" N CYS C 467 " --> pdb=" O ALA C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 488 removed outlier: 3.547A pdb=" N PHE C 482 " --> pdb=" O LEU C 478 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C 485 " --> pdb=" O PHE C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 524 removed outlier: 3.525A pdb=" N VAL C 501 " --> pdb=" O PRO C 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 134 removed outlier: 4.408A pdb=" N GLU D 134 " --> pdb=" O ASP D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 163 Processing helix chain 'D' and resid 173 through 177 Processing helix chain 'D' and resid 181 through 207 Proline residue: D 199 - end of helix removed outlier: 3.941A pdb=" N TRP D 206 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA D 207 " --> pdb=" O PHE D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 235 Processing helix chain 'D' and resid 238 through 245 Processing helix chain 'D' and resid 250 through 281 removed outlier: 3.738A pdb=" N PHE D 254 " --> pdb=" O PRO D 250 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE D 256 " --> pdb=" O SER D 252 " (cutoff:3.500A) Proline residue: D 276 - end of helix Processing helix chain 'D' and resid 294 through 302 removed outlier: 3.560A pdb=" N PHE D 302 " --> pdb=" O LEU D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 343 Processing helix chain 'D' and resid 361 through 384 removed outlier: 4.443A pdb=" N LEU D 371 " --> pdb=" O PHE D 367 " (cutoff:3.500A) Proline residue: D 372 - end of helix removed outlier: 3.679A pdb=" N LEU D 375 " --> pdb=" O LEU D 371 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE D 384 " --> pdb=" O THR D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 395 Processing helix chain 'D' and resid 416 through 419 No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 431 Processing helix chain 'D' and resid 433 through 439 Processing helix chain 'D' and resid 447 through 468 removed outlier: 3.752A pdb=" N CYS D 467 " --> pdb=" O ALA D 463 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU D 468 " --> pdb=" O LEU D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 488 removed outlier: 3.741A pdb=" N PHE D 482 " --> pdb=" O LEU D 478 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN D 487 " --> pdb=" O GLY D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 525 removed outlier: 3.798A pdb=" N THR D 505 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU D 507 " --> pdb=" O TRP D 504 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 509 " --> pdb=" O SER D 506 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY D 510 " --> pdb=" O LEU D 507 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN D 511 " --> pdb=" O PHE D 508 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL D 513 " --> pdb=" O GLY D 510 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU D 515 " --> pdb=" O GLY D 512 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS D 516 " --> pdb=" O VAL D 513 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR D 518 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER D 519 " --> pdb=" O CYS D 516 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN D 520 " --> pdb=" O PHE D 517 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TRP D 522 " --> pdb=" O SER D 519 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR D 523 " --> pdb=" O GLN D 520 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA D 524 " --> pdb=" O GLU D 521 " (cutoff:3.500A) 694 hydrogen bonds defined for protein. 2010 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: 3.96 Time building geometry restraints manager: 5.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.79: 14837 1.79 - 2.40: 105 2.40 - 3.02: 0 3.02 - 3.63: 0 3.63 - 4.24: 4 Bond restraints: 14946 Sorted by residual: bond pdb=" AO6 COA C 706 " pdb=" AP2 COA C 706 " ideal model delta sigma weight residual 1.610 4.244 -2.634 2.00e-02 2.50e+03 1.73e+04 bond pdb=" AO6 COA A 706 " pdb=" AP2 COA A 706 " ideal model delta sigma weight residual 1.610 4.244 -2.634 2.00e-02 2.50e+03 1.73e+04 bond pdb=" AP1 COA A 706 " pdb="AO5* COA A 706 " ideal model delta sigma weight residual 1.610 4.201 -2.591 2.00e-02 2.50e+03 1.68e+04 bond pdb=" AP1 COA C 706 " pdb="AO5* COA C 706 " ideal model delta sigma weight residual 1.610 4.201 -2.591 2.00e-02 2.50e+03 1.68e+04 bond pdb=" PC9 COA A 706 " pdb=" PO9 COA A 706 " ideal model delta sigma weight residual 1.410 1.186 0.224 2.00e-02 2.50e+03 1.25e+02 ... (remaining 14941 not shown) Histogram of bond angle deviations from ideal: 15.18 - 39.22: 4 39.22 - 63.25: 0 63.25 - 87.29: 0 87.29 - 111.33: 5281 111.33 - 135.37: 15141 Bond angle restraints: 20426 Sorted by residual: angle pdb=" AO3 COA A 706 " pdb=" AP1 COA A 706 " pdb="AO5* COA A 706 " ideal model delta sigma weight residual 102.60 15.18 87.42 3.00e+00 1.11e-01 8.49e+02 angle pdb=" AO3 COA C 706 " pdb=" AP1 COA C 706 " pdb="AO5* COA C 706 " ideal model delta sigma weight residual 102.60 15.20 87.40 3.00e+00 1.11e-01 8.49e+02 angle pdb=" AO3 COA A 706 " pdb=" AP2 COA A 706 " pdb=" AO6 COA A 706 " ideal model delta sigma weight residual 102.60 16.44 86.16 3.00e+00 1.11e-01 8.25e+02 angle pdb=" AO3 COA C 706 " pdb=" AP2 COA C 706 " pdb=" AO6 COA C 706 " ideal model delta sigma weight residual 102.60 16.46 86.14 3.00e+00 1.11e-01 8.24e+02 angle pdb=" N63 3VV D 702 " pdb=" C62 3VV D 702 " pdb=" N64 3VV D 702 " ideal model delta sigma weight residual 103.64 121.39 -17.75 3.00e+00 1.11e-01 3.50e+01 ... (remaining 20421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.39: 8523 31.39 - 62.78: 299 62.78 - 94.18: 14 94.18 - 125.57: 2 125.57 - 156.96: 4 Dihedral angle restraints: 8842 sinusoidal: 3950 harmonic: 4892 Sorted by residual: dihedral pdb=" AO3 COA A 706 " pdb=" AP1 COA A 706 " pdb="AO5* COA A 706 " pdb="AC5* COA A 706 " ideal model delta sinusoidal sigma weight residual 291.94 134.98 156.96 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" AO3 COA C 706 " pdb=" AP1 COA C 706 " pdb="AO5* COA C 706 " pdb="AC5* COA C 706 " ideal model delta sinusoidal sigma weight residual 291.94 135.18 156.77 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" AC4 COA A 706 " pdb=" AN9 COA A 706 " pdb="AC1* COA A 706 " pdb="AC2* COA A 706 " ideal model delta sinusoidal sigma weight residual 175.22 -81.04 -103.74 1 2.00e+01 2.50e-03 2.97e+01 ... (remaining 8839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1467 0.056 - 0.113: 537 0.113 - 0.169: 113 0.169 - 0.225: 40 0.225 - 0.282: 13 Chirality restraints: 2170 Sorted by residual: chirality pdb=" CA TRP C 320 " pdb=" N TRP C 320 " pdb=" C TRP C 320 " pdb=" CB TRP C 320 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA TRP A 320 " pdb=" N TRP A 320 " pdb=" C TRP A 320 " pdb=" CB TRP A 320 " 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 TRP D 320 " pdb=" N TRP D 320 " pdb=" C TRP D 320 " pdb=" CB TRP D 320 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 2167 not shown) Planarity restraints: 2386 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 275 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO D 276 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 276 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 276 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 275 " -0.032 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO B 276 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 276 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 276 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 275 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO A 276 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 276 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 276 " 0.027 5.00e-02 4.00e+02 ... (remaining 2383 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 4 2.31 - 2.96: 5856 2.96 - 3.60: 21123 3.60 - 4.25: 30741 4.25 - 4.90: 54853 Nonbonded interactions: 112577 Sorted by model distance: nonbonded pdb=" AO6 COA A 706 " pdb=" AP1 COA A 706 " model vdw 1.659 2.720 nonbonded pdb=" AO6 COA C 706 " pdb=" AP1 COA C 706 " model vdw 1.659 2.720 nonbonded pdb=" AP2 COA C 706 " pdb="AO5* COA C 706 " model vdw 1.679 2.720 nonbonded pdb=" AP2 COA A 706 " pdb="AO5* COA A 706 " model vdw 1.679 2.720 nonbonded pdb=" N ASN C 409 " pdb=" OD1 ASN C 409 " model vdw 2.381 2.520 ... (remaining 112572 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 118 through 526 or resid 701 or resid 703 through 705)) selection = (chain 'B' and (resid 118 through 526 or resid 701 or resid 703 through 705)) selection = (chain 'C' and (resid 118 through 526 or resid 701 or resid 703 through 705)) selection = (chain 'D' and (resid 118 through 526 or resid 701 or resid 703 through 705)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 7.800 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 39.870 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.080 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 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 : 0.044 2.634 14946 Z= 2.761 Angle : 1.770 87.421 20426 Z= 0.880 Chirality : 0.065 0.282 2170 Planarity : 0.005 0.050 2386 Dihedral : 15.601 156.958 5690 Min Nonbonded Distance : 1.659 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 1.12 % Allowed : 3.43 % Favored : 95.45 % 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: -3.29 (0.17), residues: 1628 helix: -1.52 (0.13), residues: 1104 sheet: None (None), residues: 0 loop : -3.46 (0.22), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 186 HIS 0.005 0.001 HIS D 386 PHE 0.019 0.002 PHE D 384 TYR 0.015 0.002 TYR C 308 ARG 0.012 0.001 ARG B 262 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 332 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 316 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ASP cc_start: 0.8037 (t0) cc_final: 0.7791 (t0) REVERT: A 208 THR cc_start: 0.8073 (OUTLIER) cc_final: 0.7827 (t) REVERT: A 307 ILE cc_start: 0.7507 (mm) cc_final: 0.7282 (mm) REVERT: A 430 TYR cc_start: 0.8427 (m-80) cc_final: 0.8164 (m-10) REVERT: A 436 PHE cc_start: 0.7322 (t80) cc_final: 0.6304 (m-10) REVERT: A 492 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.7017 (m-30) REVERT: B 136 ASP cc_start: 0.7753 (t70) cc_final: 0.7508 (t70) REVERT: B 215 HIS cc_start: 0.8129 (t-170) cc_final: 0.7927 (t-90) REVERT: B 307 ILE cc_start: 0.7014 (mm) cc_final: 0.6606 (mm) REVERT: B 436 PHE cc_start: 0.7164 (t80) cc_final: 0.6591 (t80) REVERT: B 480 MET cc_start: 0.5776 (tpt) cc_final: 0.5391 (ttp) REVERT: C 136 ASP cc_start: 0.8179 (t0) cc_final: 0.7911 (t0) REVERT: C 204 GLN cc_start: 0.8213 (tm-30) cc_final: 0.7994 (tm-30) REVERT: C 208 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7915 (t) REVERT: C 405 LYS cc_start: 0.8136 (mttt) cc_final: 0.7665 (mtpp) REVERT: C 430 TYR cc_start: 0.8431 (m-80) cc_final: 0.8177 (m-10) REVERT: C 436 PHE cc_start: 0.7333 (t80) cc_final: 0.6240 (m-10) REVERT: C 492 ASP cc_start: 0.7266 (OUTLIER) cc_final: 0.7032 (m-30) REVERT: D 121 ILE cc_start: 0.8905 (tp) cc_final: 0.8665 (pt) REVERT: D 136 ASP cc_start: 0.7589 (t70) cc_final: 0.6996 (t0) REVERT: D 325 MET cc_start: 0.7691 (tpt) cc_final: 0.7379 (tpt) REVERT: D 436 PHE cc_start: 0.6937 (t80) cc_final: 0.6578 (t80) REVERT: D 480 MET cc_start: 0.5764 (tpt) cc_final: 0.5513 (ttp) REVERT: D 503 MET cc_start: 0.7693 (tmm) cc_final: 0.7393 (ttt) outliers start: 16 outliers final: 2 residues processed: 327 average time/residue: 0.2575 time to fit residues: 124.2827 Evaluate side-chains 234 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 228 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 409 ASN Chi-restraints excluded: chain C residue 492 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.3980 chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 GLN A 390 ASN B 204 GLN B 280 ASN B 386 HIS B 500 ASN C 231 GLN C 295 ASN C 296 GLN C 329 GLN C 390 ASN C 500 ASN D 368 ASN D 386 HIS D 500 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14946 Z= 0.223 Angle : 0.733 9.735 20426 Z= 0.355 Chirality : 0.045 0.232 2170 Planarity : 0.005 0.047 2386 Dihedral : 12.828 161.132 2732 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 2.24 % Allowed : 10.57 % Favored : 87.18 % 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: -1.54 (0.19), residues: 1628 helix: 0.05 (0.15), residues: 1112 sheet: None (None), residues: 0 loop : -3.44 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 186 HIS 0.004 0.001 HIS C 386 PHE 0.024 0.002 PHE A 476 TYR 0.017 0.002 TYR C 241 ARG 0.003 0.000 ARG B 494 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 269 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 237 time to evaluate : 1.403 Fit side-chains revert: symmetry clash REVERT: A 208 THR cc_start: 0.8291 (OUTLIER) cc_final: 0.8084 (t) REVERT: A 334 PHE cc_start: 0.7914 (t80) cc_final: 0.7681 (t80) REVERT: A 436 PHE cc_start: 0.7129 (t80) cc_final: 0.5966 (m-10) REVERT: A 520 GLN cc_start: 0.6860 (mm-40) cc_final: 0.6646 (mt0) REVERT: B 136 ASP cc_start: 0.7896 (t70) cc_final: 0.7266 (t0) REVERT: B 215 HIS cc_start: 0.8229 (t-170) cc_final: 0.7904 (t-90) REVERT: B 307 ILE cc_start: 0.7093 (mm) cc_final: 0.6644 (mm) REVERT: B 417 TYR cc_start: 0.7868 (m-80) cc_final: 0.7513 (m-80) REVERT: B 436 PHE cc_start: 0.7194 (t80) cc_final: 0.6663 (t80) REVERT: B 480 MET cc_start: 0.5677 (tpt) cc_final: 0.5174 (ttp) REVERT: C 128 LEU cc_start: 0.7923 (tt) cc_final: 0.7696 (tt) REVERT: C 204 GLN cc_start: 0.8189 (tm-30) cc_final: 0.7928 (tm-30) REVERT: C 334 PHE cc_start: 0.7907 (t80) cc_final: 0.7655 (t80) REVERT: C 368 ASN cc_start: 0.8589 (m-40) cc_final: 0.8092 (m110) REVERT: C 394 GLU cc_start: 0.8105 (tp30) cc_final: 0.7729 (tp30) REVERT: C 405 LYS cc_start: 0.8080 (mttt) cc_final: 0.7837 (mmmm) REVERT: C 436 PHE cc_start: 0.7254 (t80) cc_final: 0.5971 (m-10) REVERT: C 520 GLN cc_start: 0.6902 (mm-40) cc_final: 0.6675 (mt0) REVERT: D 121 ILE cc_start: 0.8868 (tp) cc_final: 0.8663 (pt) REVERT: D 136 ASP cc_start: 0.7836 (t70) cc_final: 0.7171 (t0) REVERT: D 215 HIS cc_start: 0.8284 (t-90) cc_final: 0.7918 (t-90) REVERT: D 218 ILE cc_start: 0.8049 (mt) cc_final: 0.7800 (mt) REVERT: D 325 MET cc_start: 0.7824 (tpt) cc_final: 0.7499 (tpt) REVERT: D 480 MET cc_start: 0.5382 (tpt) cc_final: 0.5182 (ttp) REVERT: D 503 MET cc_start: 0.7649 (tmm) cc_final: 0.7226 (ttt) outliers start: 32 outliers final: 18 residues processed: 258 average time/residue: 0.1934 time to fit residues: 79.6676 Evaluate side-chains 242 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 223 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 526 GLN Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 409 ASN Chi-restraints excluded: chain C residue 526 GLN Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 466 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 129 optimal weight: 0.1980 chunk 144 optimal weight: 0.9980 chunk 49 optimal weight: 0.0570 chunk 116 optimal weight: 5.9990 overall best weight: 1.2502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 GLN A 390 ASN A 500 ASN C 231 GLN C 295 ASN C 390 ASN D 204 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14946 Z= 0.268 Angle : 0.670 7.131 20426 Z= 0.328 Chirality : 0.043 0.158 2170 Planarity : 0.004 0.039 2386 Dihedral : 12.461 165.737 2727 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 2.59 % Allowed : 13.17 % Favored : 84.24 % 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: -1.09 (0.20), residues: 1628 helix: 0.43 (0.15), residues: 1116 sheet: None (None), residues: 0 loop : -3.41 (0.23), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 186 HIS 0.006 0.001 HIS A 425 PHE 0.017 0.001 PHE A 331 TYR 0.023 0.002 TYR C 241 ARG 0.002 0.000 ARG C 343 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 265 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 228 time to evaluate : 1.668 Fit side-chains REVERT: A 208 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8167 (t) REVERT: A 436 PHE cc_start: 0.7046 (t80) cc_final: 0.5882 (m-10) REVERT: A 473 PRO cc_start: 0.8126 (Cg_endo) cc_final: 0.7466 (Cg_exo) REVERT: A 486 PHE cc_start: 0.7421 (m-80) cc_final: 0.7193 (m-80) REVERT: B 136 ASP cc_start: 0.7965 (t70) cc_final: 0.7240 (t0) REVERT: B 215 HIS cc_start: 0.8094 (t-170) cc_final: 0.7799 (t-170) REVERT: B 417 TYR cc_start: 0.8083 (m-80) cc_final: 0.7746 (m-80) REVERT: B 436 PHE cc_start: 0.7334 (t80) cc_final: 0.6943 (t80) REVERT: B 449 MET cc_start: 0.7609 (ttm) cc_final: 0.7405 (mtt) REVERT: C 128 LEU cc_start: 0.8127 (tt) cc_final: 0.7849 (tp) REVERT: C 131 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7962 (pt0) REVERT: C 204 GLN cc_start: 0.8198 (tm-30) cc_final: 0.7937 (tm-30) REVERT: C 254 PHE cc_start: 0.7887 (t80) cc_final: 0.7668 (t80) REVERT: C 334 PHE cc_start: 0.7905 (t80) cc_final: 0.7630 (t80) REVERT: C 380 THR cc_start: 0.8879 (t) cc_final: 0.8635 (p) REVERT: C 394 GLU cc_start: 0.8243 (tp30) cc_final: 0.7622 (tp30) REVERT: C 405 LYS cc_start: 0.8037 (mttt) cc_final: 0.7630 (mmmm) REVERT: C 436 PHE cc_start: 0.7222 (t80) cc_final: 0.6904 (t80) REVERT: C 473 PRO cc_start: 0.8159 (Cg_endo) cc_final: 0.7532 (Cg_exo) REVERT: C 486 PHE cc_start: 0.7532 (m-80) cc_final: 0.7164 (m-80) REVERT: D 121 ILE cc_start: 0.8873 (tp) cc_final: 0.8657 (pt) REVERT: D 136 ASP cc_start: 0.8039 (t70) cc_final: 0.7266 (t0) REVERT: D 215 HIS cc_start: 0.8278 (t-90) cc_final: 0.7887 (t-90) REVERT: D 218 ILE cc_start: 0.8164 (mt) cc_final: 0.7880 (mt) REVERT: D 417 TYR cc_start: 0.8067 (m-80) cc_final: 0.7624 (m-80) REVERT: D 503 MET cc_start: 0.7684 (tmm) cc_final: 0.7202 (ttt) outliers start: 37 outliers final: 25 residues processed: 252 average time/residue: 0.2117 time to fit residues: 84.3197 Evaluate side-chains 230 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 203 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 526 GLN Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 526 GLN Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 449 MET Chi-restraints excluded: chain D residue 466 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 138 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 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 231 GLN A 295 ASN A 390 ASN ** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 GLN B 511 ASN C 231 GLN C 368 ASN C 390 ASN ** D 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14946 Z= 0.303 Angle : 0.679 9.582 20426 Z= 0.331 Chirality : 0.044 0.178 2170 Planarity : 0.004 0.037 2386 Dihedral : 12.356 170.863 2723 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 2.94 % Allowed : 16.11 % Favored : 80.95 % 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: -1.03 (0.20), residues: 1628 helix: 0.45 (0.15), residues: 1128 sheet: None (None), residues: 0 loop : -3.41 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 186 HIS 0.007 0.001 HIS C 425 PHE 0.027 0.002 PHE B 196 TYR 0.017 0.002 TYR A 142 ARG 0.003 0.000 ARG C 262 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 266 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 224 time to evaluate : 1.488 Fit side-chains revert: symmetry clash REVERT: A 131 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8038 (pt0) REVERT: A 205 HIS cc_start: 0.7128 (t-90) cc_final: 0.6909 (t-170) REVERT: A 208 THR cc_start: 0.8499 (OUTLIER) cc_final: 0.8245 (t) REVERT: A 254 PHE cc_start: 0.7936 (t80) cc_final: 0.7693 (t80) REVERT: A 436 PHE cc_start: 0.7078 (t80) cc_final: 0.5870 (m-10) REVERT: A 473 PRO cc_start: 0.8363 (Cg_endo) cc_final: 0.7886 (Cg_exo) REVERT: B 136 ASP cc_start: 0.8113 (t70) cc_final: 0.7315 (t0) REVERT: B 215 HIS cc_start: 0.8130 (t-170) cc_final: 0.7851 (t-170) REVERT: B 307 ILE cc_start: 0.7252 (mm) cc_final: 0.6785 (mm) REVERT: B 417 TYR cc_start: 0.8323 (m-80) cc_final: 0.8106 (m-80) REVERT: B 436 PHE cc_start: 0.7363 (t80) cc_final: 0.7047 (t80) REVERT: B 449 MET cc_start: 0.7586 (ttm) cc_final: 0.7345 (mtt) REVERT: B 488 PHE cc_start: 0.7704 (m-10) cc_final: 0.7296 (m-10) REVERT: C 128 LEU cc_start: 0.8248 (tt) cc_final: 0.7949 (tt) REVERT: C 131 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7926 (pt0) REVERT: C 204 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7982 (tm-30) REVERT: C 254 PHE cc_start: 0.7924 (t80) cc_final: 0.7703 (t80) REVERT: C 334 PHE cc_start: 0.7917 (t80) cc_final: 0.7647 (t80) REVERT: C 394 GLU cc_start: 0.8318 (tp30) cc_final: 0.7220 (tp30) REVERT: C 436 PHE cc_start: 0.7146 (t80) cc_final: 0.6848 (t80) REVERT: C 473 PRO cc_start: 0.8344 (Cg_endo) cc_final: 0.7806 (Cg_exo) REVERT: C 486 PHE cc_start: 0.7642 (m-80) cc_final: 0.7382 (m-80) REVERT: D 136 ASP cc_start: 0.8155 (t0) cc_final: 0.7324 (t0) REVERT: D 197 SER cc_start: 0.8687 (t) cc_final: 0.8407 (m) REVERT: D 215 HIS cc_start: 0.8317 (t-90) cc_final: 0.7964 (t-90) REVERT: D 218 ILE cc_start: 0.8217 (mt) cc_final: 0.7904 (mt) REVERT: D 397 ARG cc_start: 0.7072 (mtt90) cc_final: 0.6611 (mtp85) REVERT: D 417 TYR cc_start: 0.8234 (m-80) cc_final: 0.7855 (m-80) REVERT: D 436 PHE cc_start: 0.7346 (t80) cc_final: 0.7130 (t80) REVERT: D 488 PHE cc_start: 0.7595 (m-10) cc_final: 0.7343 (m-10) REVERT: D 503 MET cc_start: 0.7677 (tmm) cc_final: 0.7262 (ttt) outliers start: 42 outliers final: 29 residues processed: 250 average time/residue: 0.2067 time to fit residues: 81.9849 Evaluate side-chains 240 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 208 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 526 GLN Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 526 GLN Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 466 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 0.0970 chunk 131 optimal weight: 5.9990 chunk 106 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN A 329 GLN ** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 ASN C 231 GLN ** D 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14946 Z= 0.171 Angle : 0.606 7.904 20426 Z= 0.296 Chirality : 0.040 0.182 2170 Planarity : 0.004 0.039 2386 Dihedral : 12.063 171.481 2723 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 2.24 % Allowed : 18.07 % Favored : 79.69 % 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: -0.79 (0.21), residues: 1628 helix: 0.64 (0.15), residues: 1124 sheet: None (None), residues: 0 loop : -3.28 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 186 HIS 0.004 0.001 HIS C 425 PHE 0.024 0.001 PHE B 196 TYR 0.014 0.001 TYR A 431 ARG 0.002 0.000 ARG C 343 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 256 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 224 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7988 (pt0) REVERT: A 208 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.8177 (t) REVERT: A 334 PHE cc_start: 0.8081 (t80) cc_final: 0.7823 (t80) REVERT: A 436 PHE cc_start: 0.7037 (t80) cc_final: 0.5863 (m-10) REVERT: A 473 PRO cc_start: 0.8302 (Cg_endo) cc_final: 0.7925 (Cg_exo) REVERT: B 136 ASP cc_start: 0.7990 (t70) cc_final: 0.7140 (t0) REVERT: B 197 SER cc_start: 0.8646 (t) cc_final: 0.8366 (m) REVERT: B 215 HIS cc_start: 0.8121 (t-170) cc_final: 0.7842 (t-170) REVERT: B 436 PHE cc_start: 0.7392 (t80) cc_final: 0.7087 (t80) REVERT: B 449 MET cc_start: 0.7549 (ttm) cc_final: 0.7315 (mtt) REVERT: B 484 MET cc_start: 0.8003 (mmm) cc_final: 0.7693 (mmm) REVERT: B 488 PHE cc_start: 0.7451 (m-10) cc_final: 0.7030 (m-10) REVERT: C 128 LEU cc_start: 0.8212 (tt) cc_final: 0.7942 (tp) REVERT: C 131 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7833 (pt0) REVERT: C 204 GLN cc_start: 0.8211 (tm-30) cc_final: 0.7936 (tm-30) REVERT: C 334 PHE cc_start: 0.7882 (t80) cc_final: 0.7635 (t80) REVERT: C 394 GLU cc_start: 0.8222 (tp30) cc_final: 0.7862 (tp30) REVERT: C 436 PHE cc_start: 0.7152 (t80) cc_final: 0.6852 (t80) REVERT: C 461 GLU cc_start: 0.8480 (tp30) cc_final: 0.8154 (tp30) REVERT: C 473 PRO cc_start: 0.8291 (Cg_endo) cc_final: 0.7966 (Cg_exo) REVERT: C 486 PHE cc_start: 0.7602 (m-80) cc_final: 0.7343 (m-80) REVERT: D 136 ASP cc_start: 0.8128 (t0) cc_final: 0.7301 (t0) REVERT: D 197 SER cc_start: 0.8678 (t) cc_final: 0.8414 (m) REVERT: D 215 HIS cc_start: 0.8329 (t-90) cc_final: 0.8017 (t-90) REVERT: D 218 ILE cc_start: 0.8248 (mt) cc_final: 0.7930 (mt) REVERT: D 417 TYR cc_start: 0.8235 (m-80) cc_final: 0.7959 (m-80) REVERT: D 436 PHE cc_start: 0.7356 (t80) cc_final: 0.7044 (t80) REVERT: D 484 MET cc_start: 0.7906 (mmp) cc_final: 0.7697 (mmp) REVERT: D 488 PHE cc_start: 0.7317 (m-10) cc_final: 0.7084 (m-10) REVERT: D 503 MET cc_start: 0.7648 (tmm) cc_final: 0.7281 (ttt) outliers start: 32 outliers final: 18 residues processed: 243 average time/residue: 0.2044 time to fit residues: 79.5297 Evaluate side-chains 230 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 209 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 449 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.3980 chunk 139 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 12 optimal weight: 0.0170 chunk 51 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.8622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN A 329 GLN A 390 ASN B 511 ASN C 295 ASN C 390 ASN D 137 HIS ** D 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 511 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14946 Z= 0.358 Angle : 0.701 11.454 20426 Z= 0.342 Chirality : 0.045 0.171 2170 Planarity : 0.004 0.038 2386 Dihedral : 12.270 176.007 2723 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.32 % Favored : 89.68 % Rotamer: Outliers : 3.22 % Allowed : 17.65 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.21), residues: 1628 helix: 0.54 (0.15), residues: 1128 sheet: None (None), residues: 0 loop : -3.27 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 186 HIS 0.007 0.001 HIS B 425 PHE 0.030 0.002 PHE B 196 TYR 0.023 0.002 TYR A 431 ARG 0.005 0.001 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 264 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 218 time to evaluate : 1.586 Fit side-chains revert: symmetry clash REVERT: A 131 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8066 (pt0) REVERT: A 136 ASP cc_start: 0.8459 (t0) cc_final: 0.8245 (t0) REVERT: A 205 HIS cc_start: 0.7188 (t-90) cc_final: 0.6974 (t-170) REVERT: A 208 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.8286 (t) REVERT: A 254 PHE cc_start: 0.7964 (t80) cc_final: 0.7714 (t80) REVERT: A 342 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7823 (mm-30) REVERT: A 368 ASN cc_start: 0.8697 (m-40) cc_final: 0.8424 (m-40) REVERT: A 436 PHE cc_start: 0.7109 (t80) cc_final: 0.6806 (t80) REVERT: A 473 PRO cc_start: 0.8325 (Cg_endo) cc_final: 0.7934 (Cg_exo) REVERT: B 136 ASP cc_start: 0.8108 (t70) cc_final: 0.7287 (t0) REVERT: B 215 HIS cc_start: 0.8110 (t-170) cc_final: 0.7841 (t-170) REVERT: B 319 ARG cc_start: 0.7602 (mtt90) cc_final: 0.7364 (mtm180) REVERT: B 397 ARG cc_start: 0.7383 (mtt90) cc_final: 0.6948 (mtp85) REVERT: B 436 PHE cc_start: 0.7488 (t80) cc_final: 0.7254 (t80) REVERT: B 449 MET cc_start: 0.7531 (ttm) cc_final: 0.7327 (mtt) REVERT: B 484 MET cc_start: 0.7944 (mmm) cc_final: 0.7543 (mmm) REVERT: B 488 PHE cc_start: 0.7489 (m-10) cc_final: 0.7066 (m-10) REVERT: C 204 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7967 (tm-30) REVERT: C 254 PHE cc_start: 0.8002 (t80) cc_final: 0.7774 (t80) REVERT: C 334 PHE cc_start: 0.7994 (t80) cc_final: 0.7793 (t80) REVERT: C 394 GLU cc_start: 0.8367 (tp30) cc_final: 0.7582 (tp30) REVERT: C 436 PHE cc_start: 0.7206 (t80) cc_final: 0.6921 (t80) REVERT: C 461 GLU cc_start: 0.8583 (tp30) cc_final: 0.8210 (tp30) REVERT: C 473 PRO cc_start: 0.8315 (Cg_endo) cc_final: 0.7988 (Cg_exo) REVERT: C 486 PHE cc_start: 0.7671 (m-80) cc_final: 0.7365 (m-80) REVERT: D 136 ASP cc_start: 0.8147 (t0) cc_final: 0.7324 (t0) REVERT: D 197 SER cc_start: 0.8684 (t) cc_final: 0.8385 (m) REVERT: D 215 HIS cc_start: 0.8316 (t-90) cc_final: 0.7900 (t-170) REVERT: D 218 ILE cc_start: 0.8326 (mt) cc_final: 0.8052 (mt) REVERT: D 364 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6611 (mp) REVERT: D 397 ARG cc_start: 0.7284 (mtt90) cc_final: 0.6891 (mtp85) REVERT: D 436 PHE cc_start: 0.7413 (t80) cc_final: 0.7143 (t80) REVERT: D 484 MET cc_start: 0.7954 (mmp) cc_final: 0.7748 (mmp) REVERT: D 488 PHE cc_start: 0.7370 (m-10) cc_final: 0.7130 (m-10) REVERT: D 503 MET cc_start: 0.7697 (tmm) cc_final: 0.7285 (ttt) outliers start: 46 outliers final: 33 residues processed: 249 average time/residue: 0.2316 time to fit residues: 91.6072 Evaluate side-chains 241 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 205 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 526 GLN Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 526 GLN Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 395 MET Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 449 MET Chi-restraints excluded: chain D residue 466 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.8980 chunk 17 optimal weight: 0.0060 chunk 88 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 130 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN A 329 GLN B 511 ASN B 520 GLN C 231 GLN ** D 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 511 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14946 Z= 0.174 Angle : 0.619 9.050 20426 Z= 0.301 Chirality : 0.040 0.187 2170 Planarity : 0.004 0.039 2386 Dihedral : 11.851 177.605 2723 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.97 % Favored : 90.91 % Rotamer: Outliers : 3.01 % Allowed : 19.33 % Favored : 77.66 % 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 (0.21), residues: 1628 helix: 0.67 (0.16), residues: 1132 sheet: None (None), residues: 0 loop : -3.21 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 186 HIS 0.004 0.001 HIS C 425 PHE 0.041 0.001 PHE A 486 TYR 0.015 0.001 TYR C 241 ARG 0.003 0.000 ARG C 343 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 250 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 207 time to evaluate : 1.508 Fit side-chains revert: symmetry clash REVERT: A 131 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7997 (pt0) REVERT: A 136 ASP cc_start: 0.8448 (t0) cc_final: 0.8241 (t0) REVERT: A 208 THR cc_start: 0.8459 (OUTLIER) cc_final: 0.8201 (t) REVERT: A 217 LEU cc_start: 0.8801 (tp) cc_final: 0.8290 (mt) REVERT: A 342 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7746 (mm-30) REVERT: A 368 ASN cc_start: 0.8664 (m-40) cc_final: 0.8384 (m-40) REVERT: A 436 PHE cc_start: 0.7111 (t80) cc_final: 0.6803 (t80) REVERT: A 473 PRO cc_start: 0.8238 (Cg_endo) cc_final: 0.7935 (Cg_exo) REVERT: A 486 PHE cc_start: 0.7771 (m-80) cc_final: 0.7519 (m-80) REVERT: B 136 ASP cc_start: 0.8037 (t70) cc_final: 0.7209 (t0) REVERT: B 215 HIS cc_start: 0.8201 (t-170) cc_final: 0.7908 (t-170) REVERT: B 397 ARG cc_start: 0.7259 (mtt90) cc_final: 0.6895 (mtp85) REVERT: B 436 PHE cc_start: 0.7497 (t80) cc_final: 0.7268 (t80) REVERT: B 484 MET cc_start: 0.7905 (mmm) cc_final: 0.7338 (mmm) REVERT: B 488 PHE cc_start: 0.7464 (m-10) cc_final: 0.6981 (m-10) REVERT: C 204 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7946 (tm-30) REVERT: C 254 PHE cc_start: 0.7958 (t80) cc_final: 0.7729 (t80) REVERT: C 334 PHE cc_start: 0.7931 (t80) cc_final: 0.7725 (t80) REVERT: C 342 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7217 (mt-10) REVERT: C 394 GLU cc_start: 0.8249 (tp30) cc_final: 0.7853 (tp30) REVERT: C 436 PHE cc_start: 0.7141 (t80) cc_final: 0.6845 (t80) REVERT: C 461 GLU cc_start: 0.8518 (tp30) cc_final: 0.8213 (tp30) REVERT: C 473 PRO cc_start: 0.8243 (Cg_endo) cc_final: 0.7984 (Cg_exo) REVERT: C 486 PHE cc_start: 0.7581 (m-80) cc_final: 0.7336 (m-80) REVERT: D 136 ASP cc_start: 0.8077 (t0) cc_final: 0.7257 (t0) REVERT: D 197 SER cc_start: 0.8671 (t) cc_final: 0.8396 (m) REVERT: D 215 HIS cc_start: 0.8315 (t-90) cc_final: 0.7919 (t-170) REVERT: D 218 ILE cc_start: 0.8291 (mt) cc_final: 0.8020 (mt) REVERT: D 397 ARG cc_start: 0.7198 (mtt90) cc_final: 0.6737 (mtp85) REVERT: D 436 PHE cc_start: 0.7447 (t80) cc_final: 0.7163 (t80) REVERT: D 488 PHE cc_start: 0.7278 (m-10) cc_final: 0.7035 (m-10) REVERT: D 503 MET cc_start: 0.7621 (tmm) cc_final: 0.7301 (ttt) outliers start: 43 outliers final: 28 residues processed: 233 average time/residue: 0.2047 time to fit residues: 76.0713 Evaluate side-chains 230 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 200 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 395 MET Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 449 MET Chi-restraints excluded: chain D residue 466 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 92 optimal weight: 0.3980 chunk 46 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN B 223 HIS ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14946 Z= 0.174 Angle : 0.610 10.927 20426 Z= 0.295 Chirality : 0.040 0.183 2170 Planarity : 0.004 0.039 2386 Dihedral : 11.497 178.232 2723 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.01 % Favored : 89.86 % Rotamer: Outliers : 2.31 % Allowed : 20.03 % Favored : 77.66 % 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: -0.54 (0.21), residues: 1628 helix: 0.78 (0.16), residues: 1124 sheet: None (None), residues: 0 loop : -3.07 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 186 HIS 0.004 0.001 HIS C 425 PHE 0.034 0.001 PHE A 486 TYR 0.013 0.001 TYR C 200 ARG 0.004 0.000 ARG B 166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 252 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 219 time to evaluate : 1.638 Fit side-chains REVERT: A 131 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7950 (pt0) REVERT: A 136 ASP cc_start: 0.8534 (t0) cc_final: 0.8302 (t0) REVERT: A 208 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8111 (t) REVERT: A 342 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7715 (mm-30) REVERT: A 368 ASN cc_start: 0.8667 (m-40) cc_final: 0.8398 (m-40) REVERT: A 436 PHE cc_start: 0.7124 (t80) cc_final: 0.6816 (t80) REVERT: A 473 PRO cc_start: 0.8325 (Cg_endo) cc_final: 0.8034 (Cg_exo) REVERT: A 486 PHE cc_start: 0.7801 (m-80) cc_final: 0.7545 (m-80) REVERT: B 136 ASP cc_start: 0.7996 (t70) cc_final: 0.7173 (t0) REVERT: B 197 SER cc_start: 0.8588 (t) cc_final: 0.8314 (m) REVERT: B 215 HIS cc_start: 0.8122 (t-170) cc_final: 0.7861 (t-90) REVERT: B 394 GLU cc_start: 0.8446 (tp30) cc_final: 0.7917 (tp30) REVERT: B 397 ARG cc_start: 0.7286 (mtt90) cc_final: 0.6890 (mtp85) REVERT: B 436 PHE cc_start: 0.7498 (t80) cc_final: 0.7275 (t80) REVERT: B 484 MET cc_start: 0.7972 (mmm) cc_final: 0.7264 (mmm) REVERT: B 488 PHE cc_start: 0.7232 (m-10) cc_final: 0.6790 (m-10) REVERT: C 204 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7899 (tm-30) REVERT: C 334 PHE cc_start: 0.7923 (t80) cc_final: 0.7715 (t80) REVERT: C 342 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7159 (mt-10) REVERT: C 380 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8752 (t) REVERT: C 394 GLU cc_start: 0.8311 (tp30) cc_final: 0.7946 (tp30) REVERT: C 436 PHE cc_start: 0.7133 (t80) cc_final: 0.6845 (t80) REVERT: C 461 GLU cc_start: 0.8549 (tp30) cc_final: 0.8238 (tp30) REVERT: C 473 PRO cc_start: 0.8300 (Cg_endo) cc_final: 0.8081 (Cg_exo) REVERT: C 486 PHE cc_start: 0.7612 (m-80) cc_final: 0.7341 (m-80) REVERT: D 136 ASP cc_start: 0.8017 (t0) cc_final: 0.7202 (t0) REVERT: D 197 SER cc_start: 0.8661 (t) cc_final: 0.8380 (m) REVERT: D 215 HIS cc_start: 0.8306 (t-90) cc_final: 0.7813 (t-170) REVERT: D 218 ILE cc_start: 0.8279 (mt) cc_final: 0.7831 (mt) REVERT: D 397 ARG cc_start: 0.7238 (mtt90) cc_final: 0.6852 (mtp85) REVERT: D 436 PHE cc_start: 0.7443 (t80) cc_final: 0.7139 (t80) REVERT: D 518 TYR cc_start: 0.8536 (m-80) cc_final: 0.8277 (m-80) outliers start: 33 outliers final: 28 residues processed: 238 average time/residue: 0.2074 time to fit residues: 78.7804 Evaluate side-chains 239 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 208 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 395 MET Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 449 MET Chi-restraints excluded: chain D residue 466 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 134 optimal weight: 0.3980 chunk 143 optimal weight: 0.0060 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 129 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN D 223 HIS ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14946 Z= 0.175 Angle : 0.610 9.738 20426 Z= 0.296 Chirality : 0.040 0.184 2170 Planarity : 0.004 0.039 2386 Dihedral : 11.298 174.182 2723 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.15 % Favored : 90.72 % Rotamer: Outliers : 2.52 % Allowed : 20.31 % Favored : 77.17 % 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: -0.50 (0.21), residues: 1628 helix: 0.81 (0.16), residues: 1124 sheet: None (None), residues: 0 loop : -3.06 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 186 HIS 0.004 0.001 HIS C 425 PHE 0.034 0.001 PHE A 486 TYR 0.017 0.001 TYR C 241 ARG 0.003 0.000 ARG A 494 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 252 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 216 time to evaluate : 1.499 Fit side-chains revert: symmetry clash REVERT: A 136 ASP cc_start: 0.8526 (t0) cc_final: 0.8298 (t0) REVERT: A 208 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.8120 (t) REVERT: A 217 LEU cc_start: 0.8760 (tp) cc_final: 0.8253 (mt) REVERT: A 342 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7651 (mm-30) REVERT: A 436 PHE cc_start: 0.7140 (t80) cc_final: 0.6835 (t80) REVERT: A 473 PRO cc_start: 0.8312 (Cg_endo) cc_final: 0.8056 (Cg_exo) REVERT: A 486 PHE cc_start: 0.7864 (m-80) cc_final: 0.7590 (m-80) REVERT: B 136 ASP cc_start: 0.7987 (t70) cc_final: 0.7157 (t0) REVERT: B 197 SER cc_start: 0.8586 (t) cc_final: 0.8311 (m) REVERT: B 215 HIS cc_start: 0.8129 (t-170) cc_final: 0.7899 (t-90) REVERT: B 394 GLU cc_start: 0.8434 (tp30) cc_final: 0.8053 (tp30) REVERT: B 397 ARG cc_start: 0.7295 (mtt90) cc_final: 0.6887 (mtp85) REVERT: B 436 PHE cc_start: 0.7490 (t80) cc_final: 0.7271 (t80) REVERT: B 488 PHE cc_start: 0.7231 (m-10) cc_final: 0.6912 (m-10) REVERT: C 131 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7984 (pt0) REVERT: C 204 GLN cc_start: 0.8165 (tm-30) cc_final: 0.7887 (tm-30) REVERT: C 334 PHE cc_start: 0.7952 (t80) cc_final: 0.7738 (t80) REVERT: C 394 GLU cc_start: 0.8291 (tp30) cc_final: 0.7908 (tp30) REVERT: C 436 PHE cc_start: 0.7119 (t80) cc_final: 0.6826 (t80) REVERT: C 461 GLU cc_start: 0.8556 (tp30) cc_final: 0.8266 (tp30) REVERT: C 486 PHE cc_start: 0.7627 (m-80) cc_final: 0.7326 (m-80) REVERT: D 136 ASP cc_start: 0.7989 (t0) cc_final: 0.7169 (t0) REVERT: D 197 SER cc_start: 0.8642 (t) cc_final: 0.8376 (m) REVERT: D 215 HIS cc_start: 0.8318 (t-90) cc_final: 0.7855 (t-170) REVERT: D 273 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7076 (tp30) REVERT: D 397 ARG cc_start: 0.7249 (mtt90) cc_final: 0.6788 (mtp85) REVERT: D 436 PHE cc_start: 0.7449 (t80) cc_final: 0.7151 (t80) REVERT: D 518 TYR cc_start: 0.8538 (m-80) cc_final: 0.8278 (m-80) outliers start: 36 outliers final: 30 residues processed: 237 average time/residue: 0.2095 time to fit residues: 79.3496 Evaluate side-chains 244 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 212 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 395 MET Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 449 MET Chi-restraints excluded: chain D residue 466 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 13 optimal weight: 0.0770 chunk 98 optimal weight: 0.1980 chunk 77 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN B 215 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14946 Z= 0.231 Angle : 0.646 10.526 20426 Z= 0.311 Chirality : 0.042 0.187 2170 Planarity : 0.004 0.051 2386 Dihedral : 11.308 170.497 2723 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.20 % Favored : 89.68 % Rotamer: Outliers : 2.52 % Allowed : 20.59 % Favored : 76.89 % 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: -0.54 (0.21), residues: 1628 helix: 0.79 (0.16), residues: 1124 sheet: None (None), residues: 0 loop : -3.10 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 186 HIS 0.005 0.001 HIS C 425 PHE 0.034 0.001 PHE B 196 TYR 0.013 0.001 TYR C 200 ARG 0.003 0.000 ARG A 494 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 254 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 218 time to evaluate : 1.527 Fit side-chains revert: symmetry clash REVERT: A 136 ASP cc_start: 0.8545 (t0) cc_final: 0.8290 (t0) REVERT: A 208 THR cc_start: 0.8432 (OUTLIER) cc_final: 0.8153 (t) REVERT: A 254 PHE cc_start: 0.7948 (t80) cc_final: 0.7711 (t80) REVERT: A 342 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7618 (mm-30) REVERT: A 368 ASN cc_start: 0.8687 (m-40) cc_final: 0.8423 (m-40) REVERT: A 436 PHE cc_start: 0.7167 (t80) cc_final: 0.6862 (t80) REVERT: A 473 PRO cc_start: 0.8364 (Cg_endo) cc_final: 0.8051 (Cg_exo) REVERT: A 486 PHE cc_start: 0.7890 (m-80) cc_final: 0.7633 (m-80) REVERT: B 136 ASP cc_start: 0.7989 (t70) cc_final: 0.7170 (t0) REVERT: B 215 HIS cc_start: 0.8275 (t-90) cc_final: 0.7969 (t-90) REVERT: B 394 GLU cc_start: 0.8471 (tp30) cc_final: 0.8065 (tp30) REVERT: B 397 ARG cc_start: 0.7354 (mtt90) cc_final: 0.6931 (mtp85) REVERT: B 436 PHE cc_start: 0.7428 (t80) cc_final: 0.7204 (t80) REVERT: B 488 PHE cc_start: 0.7229 (m-10) cc_final: 0.6845 (m-10) REVERT: C 131 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7923 (pt0) REVERT: C 204 GLN cc_start: 0.8168 (tm-30) cc_final: 0.7894 (tm-30) REVERT: C 254 PHE cc_start: 0.7983 (t80) cc_final: 0.7752 (t80) REVERT: C 334 PHE cc_start: 0.7957 (t80) cc_final: 0.7697 (t80) REVERT: C 342 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7285 (mt-10) REVERT: C 380 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8740 (t) REVERT: C 394 GLU cc_start: 0.8339 (tp30) cc_final: 0.7947 (tp30) REVERT: C 436 PHE cc_start: 0.7061 (t80) cc_final: 0.6759 (t80) REVERT: C 486 PHE cc_start: 0.7653 (m-80) cc_final: 0.7347 (m-80) REVERT: D 136 ASP cc_start: 0.8000 (t0) cc_final: 0.7171 (t0) REVERT: D 197 SER cc_start: 0.8660 (t) cc_final: 0.8375 (m) REVERT: D 215 HIS cc_start: 0.8391 (t-90) cc_final: 0.8076 (t-170) REVERT: D 273 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7173 (tp30) REVERT: D 397 ARG cc_start: 0.7315 (mtt90) cc_final: 0.6937 (mtp85) REVERT: D 436 PHE cc_start: 0.7512 (t80) cc_final: 0.7219 (t80) REVERT: D 518 TYR cc_start: 0.8532 (m-80) cc_final: 0.8264 (m-80) outliers start: 36 outliers final: 31 residues processed: 239 average time/residue: 0.2282 time to fit residues: 87.7682 Evaluate side-chains 247 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 213 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 526 GLN Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 395 MET Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 449 MET Chi-restraints excluded: chain D residue 466 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 117 optimal weight: 0.0470 chunk 18 optimal weight: 0.2980 chunk 35 optimal weight: 0.6980 chunk 127 optimal weight: 0.8980 chunk 53 optimal weight: 0.0980 chunk 130 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 overall best weight: 0.3478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.135687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.111173 restraints weight = 20057.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.113980 restraints weight = 11396.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.115827 restraints weight = 8156.198| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14946 Z= 0.162 Angle : 0.620 10.536 20426 Z= 0.299 Chirality : 0.039 0.196 2170 Planarity : 0.004 0.050 2386 Dihedral : 11.027 163.913 2723 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.03 % Favored : 90.85 % Rotamer: Outliers : 1.96 % Allowed : 21.29 % Favored : 76.75 % 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: -0.35 (0.21), residues: 1628 helix: 0.98 (0.16), residues: 1100 sheet: None (None), residues: 0 loop : -2.95 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 186 HIS 0.004 0.001 HIS C 425 PHE 0.032 0.001 PHE B 196 TYR 0.019 0.001 TYR C 241 ARG 0.003 0.000 ARG A 494 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2675.50 seconds wall clock time: 49 minutes 48.08 seconds (2988.08 seconds total)